PLoS Computational Biology, Volume 17

Volume 17, Number 1, January 2021

Editorial

• 
  Korryn Bodner, Chris Brimacombe, Emily S. Chenery, Ariel Greiner, Anne M. McLeod, Stephanie R. Penk, Juan S. Vargas Soto:
  Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students.

Topic Page

• 
  Mehmet Aziz Yirik, Christoph Steinbeck:
  Chemical graph generators.

Research Articles

• 
  Graham Casey Gibson, Kelly R. Moran, Nicholas G. Reich, Dave Osthus:
  Improving probabilistic infectious disease forecasting through coherence.
• 
  Antonino Casile, Rose T. Faghih, Emery N. Brown:
  Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains.
• 
  Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A. Barrett, John R. King, Dong-Hyun Kim:
  Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.
• 
  Tristan Ursell:
  Structured environments foster competitor coexistence by manipulating interspecies interfaces.
• 
  Pedro Manuel Martínez García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado-Sainz, Francisco Gómez-Vela, Felipe Cortés-Ledesma:
  Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility.
• 
  Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone:
  Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers.
• 
  Muneki Ikeda, Hirotaka Matsumoto, Eduardo J. Izquierdo:
  Persistent thermal input controls steering behavior in Caenorhabditis elegans.
• 
  Samhita P. Banavar, Michael Trogdon, Brian Drawert, Tau-Mu Yi, Linda R. Petzold, Otger Campàs:
  Coordinating cell polarization and morphogenesis through mechanical feedback.
• 
  James Giammona, Otger Campàs:
  Physical constraints on early blastomere packings.
• 
  Daria Stepanova, Helen M. Byrne, Philip K. Maini, Tomás Alarcón:
  A multiscale model of complex endothelial cell dynamics in early angiogenesis.
• 
  Evanthia Koukouli, Dennis Wang, Frank Dondelinger, Juhyun Park:
  A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response.
• 
  Sára Sáray, Christian A. Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen Alina Lupascu, Luca Leonardo Bologna, Werner Van Geit, Armando Romani, Andrew P. Davison, Eilif Müller, Tamás F. Freund, Szabolcs Káli:
  HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data.
• 
  Satyajit D. Rao, Oleg A. Igoshin:
  Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system.
• 
  Hamed Khakzad, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran Van Nhieu, Johan Malmström, Lars Malmström:
  Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.
• 
  Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson:
  MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.
• 
  Yohsuke Murase, Seung Ki Baek:
  Friendly-rivalry solution to the iterated n-person public-goods game.
• 
  Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt:
  Causal network inference from gene transcriptional time-series response to glucocorticoids.
• 
  Jan Rombouts, Lendert Gelens:
  Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions.
• 
  Adil Alsiyabi, Ariadna Gonzalez Solis, Edgar B. Cahoon, Rajib Saha:
  Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants.
• 
  Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks:
  Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome.
• 
  Vinícius R. Carvalho, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo Mazoni Andrade Marçal Mendes:
  Active probing to highlight approaching transitions to ictal states in coupled neural mass models.
• 
  Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris:
  Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine.
• 
  Rachael L. Sumner, Meg J. Spriggs, Alexander D. Shaw:
  Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex.
• 
  David W. Eyre, Mirjam Laager, A. Sarah Walker, Ben S. Cooper, Daniel J. Wilson:
  Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.
• 
  Viacheslav N. Kachalov, Huyen Nguyen, Suraj Balakrishna, Luisa Salazar-Vizcaya, Rami Sommerstein, Stefan P. Kuster, Anthony Hauser, Pia Abel zur Wiesch, Eili Y. Klein, Roger D. Kouyos:
  Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level.
• 
  Bruce Y. Lee, Sarah M. Bartsch, Marie C. Ferguson, Patrick T. Wedlock, Kelly J. O'Shea, Sheryl S. Siegmund, Sarah N. Cox, James A. McKinnell:
  The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.
• 
  N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg:
  Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2.
• 
  Miri Gordin, Hagit Philip, Alona Zilberberg, Moriah Gidoni, Raanan Margalit, Christopher Clouser, Kristofor Adams, Francois Vigneault, Irun R. Cohen, Gur Yaari, Sol Efroni:
  Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans.
• 
  Preecha Patumcharoenpol, Massalin Nakphaichit, Gianni Panagiotou, Anchalee Senavonge, Narissara Suratannon, Wanwipa Vongsangnak:
  MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.
• 
  Maral Budak, Karl Grosh, Aritra Sasmal, Gabriel Corfas, Michal Zochowski, Victoria Booth:
  Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects.
• 
  Oleksandr Sorochynskyi, Stéphane Deny, Olivier Marre, Ulisse Ferrari:
  Predicting synchronous firing of large neural populations from sequential recordings.
• 
  Marzia Antonella Scelsi, Valerio Napolioni, Michael D. Greicius, André Altmann, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's Disease Sequencing Project:
  Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities.
• 
  Bor Kavcic, Gasper Tkacik, Tobias Bollenbach:
  Minimal biophysical model of combined antibiotic action.
• 
  Ronald E. Crump, Ching-I Huang, Edward S. Knock, Simon E. F. Spencer, Paul E. Brown, Erick Mwamba Miaka, Chansy Shampa, Matt J. Keeling, Kat S. Rock:
  Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo.
• 
  Guillaume Lingas, Kyle Rosenke, David Safronetz, Jérémie Guedj:
  Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin.
• 
  Jun Li, Juliane Manitz, Enrico Bertuzzo, Eric D. Kolaczyk:
  Sensor-based localization of epidemic sources on human mobility networks.
• 
  Beatriz Seoane, Alessandra Carbone:
  The complexity of protein interactions unravelled from structural disorder.
• 
  Albertas Janulevicius, G. Sander van Doorn:
  Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance.
• 
  Lillian R. Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic:
  CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models.
• 
  Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramon Crehuet, Kresten Lindorff-Larsen:
  DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.
• 
  Rani Moran, Mehdi Keramati, Raymond J. Dolan:
  Model based planners reflect on their model-free propensities.
• 
  Vikki Neville, Peter Dayan, Iain D. Gilchrist, Elizabeth S. Paul, Michael Mendl:
  Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach.
• 
  Zhongling Jiang, Bin Zhang:
  On the role of transcription in positioning nucleosomes.
• 
  Hungyo Kharerin, Lu Bai:
  Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.
• 
  Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stéphane Guindon, Nicola De Maio:
  Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.
• 
  Katharine Best, Dan H. Barouch, Jérémie Guedj, Ruy M. Ribeiro, Alan S. Perelson:
  Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference.
• 
  Johannes Friedrich, Andrea Giovannucci, Eftychios A. Pnevmatikakis:
  Online analysis of microendoscopic 1-photon calcium imaging data streams.
• 
  Michael C. Tackenberg, Jacob J. Hughey:
  The risks of using the chi-square periodogram to estimate the period of biological rhythms.
• 
  Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler:
  Rosetta design with co-evolutionary information retains protein function.
• 
  Andreas Tjärnberg, Omar Mahmood, Christopher A. Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel A. Christiaen, Richard A. Bonneau:
  Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.
• 
  Muir Morrison, Manuel Razo-Mejia, Rob Phillips:
  Reconciling kinetic and thermodynamic models of bacterial transcription.
• 
  Aniello Lombardi, Peter Jedlicka, Heiko J. Luhmann, Werner Kilb:
  Coincident glutamatergic depolarizations enhance GABAA receptor-dependent Cl- influx in mature and suppress Cl- efflux in immature neurons.
• 
  Grant Hartung, Shoale Badr, Mohammad Moeini, Frédéric Lesage, David Kleinfeld, Ali Alaraj, Andreas A. Linninger:
  Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex.
• 
  Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler:
  Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.
• 
  Son Hoang Nguyen, Minh Duc Cao, Lachlan J. M. Coin:
  Real-time resolution of short-read assembly graph using ONT long reads.
• 
  Filipe Tostevin, Manon Wigbers, Lotte Søgaard-Andersen, Ulrich Gerland:
  Four different mechanisms for switching cell polarity.
• 
  Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson:
  Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.
• 
  Bansho Masutani, Shin-ichi Arimura, Shinichi Morishita:
  Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing.
• 
  Samuel Planton, Timo van Kerkoerle, Leïla Abbih, Maxime Maheu, Florent Meyniel, Mariano Sigman, Liping Wang, Santiago Figueira, Sergio Romano, Stanislas Dehaene:
  A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans.
• 
  Yushuf Sharker, Eben Kenah:
  Estimating and interpreting secondary attack risk: Binomial considered biased.
• 
  Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski, Michael T. Woodside:
  Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers.
• 
  Michelangelo Bin, Peter Y. K. Cheung, Emanuele Crisostomi, Pietro Ferraro, Hugo Lhachemi, Roderick Murray-Smith, Connor Myant, Thomas Parisini, Robert Shorten, Sebastian Stein, Lewi Stone:
  Post-lockdown abatement of COVID-19 by fast periodic switching.
• 
  Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford:
  Machine learning based CRISPR gRNA design for therapeutic exon skipping.
• 
  Oren Avram, Aya Kigel, Anna Vaisman-Mentesh, Sharon Kligsberg, Shai Rosenstein, Yael Dror, Tal Pupko, Yariv Wine:
  PASA: Proteomic analysis of serum antibodies web server.
• 
  Burcu Tepekule, Anthony Hauser, Viacheslav N. Kachalov, Sara Andresen, Thomas Scheier, Peter W. Schreiber, Huldrych F. Günthard, Roger D. Kouyos:
  Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19.
• 
  Leonardo Miele, Silvia De Monte:
  Aggregative cycles evolve as a solution to conflicts in social investment.
• 
  Matt J. Keeling, Edward M. Hill, Erin E. Gorsich, Bridget S. Penman, Glen Guyver-Fletcher, Alex Holmes, Trystan Leng, Hector McKimm, Massimiliano Tamborrino, Louise Dyson, Michael J. Tildesley:
  Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies.
• 
  Seth Talyansky, Braden A. W. Brinkman:
  Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex.
• 
  Vikas Pandey, Lai-Hua Xie, Zhilin Qu, Zhen Song:
  Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model.
• 
  Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso:
  mbkmeans: Fast clustering for single cell data using mini-batch k-means.
• 
  Kathryn L. Schaber, T. Alex Perkins, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Valerie A. Paz-Soldan, John P. Elder, Alan L. Rothman, David J. Civitello, William H. Elson, Amy C. Morrison, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec:
  Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics.
• 
  Victor Boutin, Angelo Franciosini, Frédéric Chavane, Franck Ruffier, Laurent Perrinet:
  Sparse deep predictive coding captures contour integration capabilities of the early visual system.
• 
  Martina Conte, Sergio Casas-Tintò, Juan Soler:
  Modeling invasion patterns in the glioblastoma battlefield.
• 
  Dániel Vörös, Balázs Könnyü, Tamás Czárán:
  Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism.
• 
  Steven Phillips:
  A reconstruction theory of relational schema induction.
• 
  Helen M. Kurkjian, M. Javad Akbari, Babak Momeni:
  The impact of interactions on invasion and colonization resistance in microbial communities.
• 
  Daniel A. Burbano L., Maurizio Porfiri:
  Modeling multi-sensory feedback control of zebrafish in a flow.
• 
  Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl:
  PEtab - Interoperable specification of parameter estimation problems in systems biology.
• 
  Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, Torsten Schwede:
  ProMod3 - A versatile homology modelling toolbox.
• 
  Alessandro Toso, Arash Fassihi, Luciano Paz, Francesca Pulecchi, Mathew E. Diamond:
  A sensory integration account for time perception.
• 
  Carlos Valiente-Mullor, Beatriz Beamud, Iván Ansari, Carlos Francés-Cuesta, Neris García-González, Lorena Mejía, Paula Ruiz-Hueso, Fernando González-Candelas:
  One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
• 
  Shinsuke Koyama, Taiki Horie, Shigeru Shinomoto:
  Estimating the time-varying reproduction number of COVID-19 with a state-space method.

Volume 17, Number 2, February 2021

Editorials

• 
  Avni Malik, Paranjay Patel, Lubaina Ehsan, Shan Guleria, Thomas Hartka, Sodiq Adewole, Sana Syed:
  Ten simple rules for engaging with artificial intelligence in biomedicine.
• 
  Sabrina Islam, Christine A. Wells:
  Ten simple rules for navigating the computational aspect of an interdisciplinary PhD.
• 
  Johannes Werner, Debora Jeske:
  Ten simple rules for running and managing virtual internships.
• 
  Micaela S. Parker, Arlyn E. Burgess, Philip E. Bourne:
  Ten simple rules for starting (and sustaining) an academic data science initiative.
• 
  Parice A. Brandies, Carolyn J. Hogg:
  Ten simple rules for getting started with command-line bioinformatics.
• 
  Jennifer H. Kong, Latishya J. Steele, Crystal M. Botham:
  Ten simple rules for writing compelling recommendation letters.
• 
  Matthias C. Rillig, Karine Bonneval, Christian de Lutz, Johannes Lehmann, India Mansour, Regine Rapp, Sasa Spacal, Vera Meyer:
  Ten simple rules for hosting artists in a scientific lab.
• 
  Mathieu Boudreau, Jean-Baptiste Poline, Pierre Bellec, Nikola Stikov:
  On the open-source landscape of PLOS Computational Biology.

Education Articles

• 
  Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace:
  Using prototyping to choose a bioinformatics workflow management system.
• 
  Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola J. Mulder:
  Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
• 
  Kimberly A. Dill-McFarland, Stephan G. König, Florent Mazel, David C. Oliver, Lisa M. McEwen, Kris Y. Hong, Steven J. Hallam:
  An integrated, modular approach to data science education in microbiology.

Perspective

• 
  Johannes Bracher, Evan L. Ray, Tilmann Gneiting, Nicholas G. Reich:
  Evaluating epidemic forecasts in an interval format.

Research Articles

• 
  Lowell T. Edgar, Claudio A. Franco, Holger Gerhardt, Miguel O. Bernabeu:
  On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling.
• 
  Hana Susak, Laura Serra-Saurina, German Demidov, Raquel Rabionet, Laura Domènech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Geòrgia Escaramís, Stephan Ossowski:
  Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation.
• 
  Mathew Titus, George Hagstrom, James R. Watson:
  Unsupervised manifold learning of collective behavior.
• 
  Davide Bernardi, Guy Doron, Michael Brecht, Benjamin Lindner:
  A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation.
• 
  Marc A. Dämgen, Philip C. Biggin:
  State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane.
• 
  Helmut Schmidt, Gerald Hahn, Gustavo Deco, Thomas R. Knösche:
  Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays.
• 
  George G. Vega Yon, Duncan C. Thomas, John Morrison, Huaiyu Mi, Paul D. Thomas, Paul Marjoram:
  Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.
• 
  Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar:
  REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.
• 
  Sam Gijsen, Miro Grundei, Robert T. Lange, Dirk Ostwald, Felix Blankenburg:
  Neural surprise in somatosensory Bayesian learning.
• 
  Karoline Horgmo Jæger, Samuel Wall, Aslak Tveito:
  Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes.
• 
  Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith:
  Quantitative profiling of protease specificity.
• 
  Guillaume P. Dehaene, Ruben Coen Cagli, Alexandre Pouget:
  Investigating the representation of uncertainty in neuronal circuits.
• 
  Satyabrata Parida, Hari M. Bharadwaj, Michael G. Heinz:
  Spectrally specific temporal analyses of spike-train responses to complex sounds: A unifying framework.
• 
  Junho Lee, Donggu Lee, Sean Lawler, Yangjin Kim:
  Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural insights from a computational model.
• 
  Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Anton Popov, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel Fernández Calvo, Víctor M. Pérez-García:
  A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors.
• 
  Wei Lu, Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J. de Pablo, Peter G. Wolynes:
  OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations.
• 
  Filip Stefaniak, Janusz M. Bujnicki:
  AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.
• 
  Jordan Douglas, Rong Zhang, Remco R. Bouckaert:
  Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model.
• 
  Philipp Mitteroecker, Ekaterina Stansfield:
  A model of developmental canalization, applied to human cranial form.
• 
  Bethany L. Dearlove, Sodsai Tovanabutra, Christopher L. Owen, Eric Lewitus, Yifan Li, Eric Sanders-Buell, Meera Bose, Anne-Marie O'Sullivan, Gustavo Kijak, Shana Miller, Kultida Poltavee, Jenica Lee, Lydia Bonar, Elizabeth Harbolick, Bahar Ahani, Phuc Pham, Hannah Kibuuka, Lucas Maganga, Sorachai Nitayaphan, Fred K. Sawe, Jerome H. Kim, Leigh Anne Eller, Sandhya Vasan, Robert Gramzinski, Nelson L. Michael, Merlin L. Robb, Morgane Rolland, RV217 Study Team:
  Factors influencing estimates of HIV-1 infection timing using BEAST.
• 
  Mari Ganesh Kumar, Ming Hu, Aadhirai Ramanujan, Mriganka Sur, Hema A. Murthy:
  Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas.
• 
  Samuel J. Gershman, Marc Guitart-Masip, James F. Cavanagh:
  Neural signatures of arbitration between Pavlovian and instrumental action selection.
• 
  Katja Seeliger, Luca Ambrogioni, Yagmur Güçlütürk, L. M. van den Bulk, Umut Güçlü, Marcel A. J. van Gerven:
  End-to-end neural system identification with neural information flow.
• 
  Itai Dattner, Yair Goldberg, Guy Katriel, Rami Yaari, Nurit Gal, Yoav Miron, Arnona Ziv, Rivka Sheffer, Yoram Hamo, Amit Huppert:
  The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children.
• 
  Daniel J. A. Derrick, Kathryn Wolton, Richard A. Currie, Marcus John Tindall:
  A mathematical model of the role of aggregation in sonic hedgehog signalling.
• 
  Alexandre Pitti, Mathias Quoy, Sofiane Boucenna, Catherine Lavandier:
  Brain-inspired model for early vocal learning and correspondence matching using free-energy optimization.
• 
  Pascal F. Hagolani, Roland Zimm, Renske Vroomans, Isaac Salazar-Ciudad:
  On the evolution and development of morphological complexity: A view from gene regulatory networks.
• 
  Constanze Ciavarella, Neil M. Ferguson:
  Deriving fine-scale models of human mobility from aggregated origin-destination flow data.
• 
  Hannan Tahir, Luis Eduardo López-Cortés, Axel Kola, Dafna Yahav, André Karch, Hanjue Xia, Johannes Horn, Konrad Sakowski, Monika J. Piotrowska, Leonard Leibovici, Rafael T. Mikolajczyk, Mirjam E. Kretzschmar:
  Relevance of intra-hospital patient movements for the spread of healthcare-associated infections within hospitals - a mathematical modeling study.
• 
  Rustom Antia, Hasan Ahmed, James J. Bull:
  Directed attenuation to enhance vaccine immunity.
• 
  Blake J. M. Williams, Guillaume St-Onge, Laurent Hébert-Dufresne:
  Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network.
• 
  Shay Ben-Elazar, Miriam Ragle Aure, Kristin Jonsdottir, Suvi-Katri Leivonen, Vessela N. Kristensen, Emiel A. M. Janssen, Kristine Kleivi Sahlberg, Ole Christian Lingjærde, Zohar Yakhini:
  miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer.
• 
  Barbara Feulner, Claudia Clopath:
  Neural manifold under plasticity in a goal driven learning behaviour.
• 
  Philipp Mergenthaler, Santosh Hariharan, James M. Pemberton, Corey Lourenco, Linda Z. Penn, David W. Andrews:
  Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning.
• 
  Lichy Han, Zahra N. Sayyid, Russ B. Altman:
  Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease.
• 
  Gerrit Ansmann, Tobias Bollenbach:
  Building clone-consistent ecosystem models.
• 
  Thomas Notermans, Petri Tanska, Rami K. Korhonen, Hanifeh Khayyeri, Hanna Isaksson:
  A numerical framework for mechano-regulated tendon healing - Simulation of early regeneration of the Achilles tendon.
• 
  Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, Yuval B. Simons, Shweta Ramdas, Alejandro A. Schäffer, Rachel L. Kember, Maja Bucan, Sara Mathieson:
  Ancestral haplotype reconstruction in endogamous populations using identity-by-descent.
• 
  Ronan F. Arthur, James H. Jones, Matthew H. Bonds, Yoav Ram, Marcus W. Feldman:
  Adaptive social contact rates induce complex dynamics during epidemics.
• 
  Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol S. Kavvas, Bernhard O. Palsson:
  Independent component analysis recovers consistent regulatory signals from disparate datasets.
• 
  Arash Moshkforoush, Lakshmini Balachandar, Carolina Moncion, Karla A. Montejo, Jorge J. Riera:
  Unraveling ChR2-driven stochastic Ca2+ dynamics in astrocytes: A call for new interventional paradigms.
• 
  Qiao Liu, Lei Xie:
  TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations.
• 
  Aidan I. Brown, Elena F. Koslover:
  Design principles for the glycoprotein quality control pathway.
• 
  Yusuke Himeoka, Namiko Mitarai:
  When to wake up? The optimal waking-up strategies for starvation-induced persistence.
• 
  Raymond A. Haggerty, Jeremy E. Purvis:
  Inferring the structures of signaling motifs from paired dynamic traces of single cells.
• 
  Isaac J. Stopard, Thomas S. Churcher, Ben Lambert:
  Estimating the extrinsic incubation period of malaria using a mechanistic model of sporogony.
• 
  Günter Schneckenreither, Philipp Tschandl, Claire Rippinger, Christoph Sinz, Dominik Brunmeir, Nikolas Popper, Harald Kittler:
  Reproduction of patterns in melanocytic proliferations by agent-based simulation and geometric modeling.
• 
  Yuanhong Tang, Lingling An, Ye Yuan, Qingqi Pei, Quan Wang, Jian K. Liu:
  Modulation of the dynamics of cerebellar Purkinje cells through the interaction of excitatory and inhibitory feedforward pathways.
• 
  Yiran Huang, Yusi Xie, Cheng Zhong, Fengfeng Zhou:
  Finding branched pathways in metabolic network via atom group tracking.
• 
  Chen Ming, Stephanie Haro, Andrea Megela Simmons, James A. Simmons:
  A comprehensive computational model of animal biosonar signal processing.
• 
  Linda Martini, Sophie Brameyer, Elisabeth Hoyer, Kirsten Jung, Ulrich Gerland:
  Dynamics of chromosomal target search by a membrane-integrated one-component receptor.
• 
  Bingjie Xue, Benjamin Jordan, Saqib Rizvi, Kristen M. Naegle:
  KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.
• 
  Stewart Heitmann, Anton Shpak, Jamie I. Vandenberg, Adam P. Hill:
  Arrhythmogenic effects of ultra-long and bistable cardiac action potentials.
• 
  Anjalika Nande, Ben Adlam, Justin Sheen, Michael Z. Levy, Alison L. Hill:
  Dynamics of COVID-19 under social distancing measures are driven by transmission network structure.
• 
  Agatha Treveil, Balázs Bohár, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Marton Olbei, Martina Poletti, Matthew Madgwick, Tahila Andrighetti, Isabelle Hautefort, Dezsö Módos, Tamás Korcsmáros:
  ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.
• 
  Giulia Fiscon, Federica Conte, Lorenzo Farina, Paola Paci:
  SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19.
• 
  Viktor Sip, Meysam Hashemi, Anirudh Nihalani Vattikonda, Michael Marmaduke Woodman, Huifang E. Wang, Julia Scholly, Samuel Medina Villalon, Maxime Guye, Fabrice Bartolomei, Viktor K. Jirsa:
  Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography.
• 
  Benjamin Allen, Christine Sample, Patricia Steinhagen, Julia Shapiro, Matthew King, Timothy Hedspeth, Megan Goncalves:
  Fixation probabilities in graph-structured populations under weak selection.
• 
  Liang Yu, Meng Wang, Yang Yang, Fengdan Xu, Xu Zhang, Fei Xie, Lin Gao, Xiangzhi Li:
  Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways.
• 
  Benjamin Gallois, Raphaël Candelier:
  FastTrack: An open-source software for tracking varying numbers of deformable objects.
• 
  Tzu-Hao Lin, Tomonari Akamatsu, Yu Tsao:
  Sensing ecosystem dynamics via audio source separation: A case study of marine soundscapes off northeastern Taiwan.
• 
  Huat Chye Lim, John D. Gordan:
  Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma.
• 
  Yoshiki Ito, Taro Toyoizumi:
  Learning poly-synaptic paths with traveling waves.
• 
  Hwai-Ray Tung, Rick Durrett:
  Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective.
• 
  Michael Raatz, Saumil Shah, Guranda Chitadze, Monika Brüggemann, Arne Traulsen:
  The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics.
• 
  Mohammad Salahshour:
  Freedom to choose between public resources promotes cooperation.
• 
  Rocky Diegmiller, Lun Zhang, Marcio Gameiro, Justinn Barr, Jasmin Imran Alsous, Paul Schedl, Stanislav Y. Shvartsman, Konstantin Mischaikow:
  Mapping parameter spaces of biological switches.
• 
  Joshua Havumaki, Ted Cohen, Chengwei Zhai, Joel C. Miller, Seth D. Guikema, Marisa C. Eisenberg, Jon Zelner:
  Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns.
• 
  Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam-Rudloff, Christian Brandt:
  Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).
• 
  John P. Lloyd, Matthew B. Soellner, Sofía D. Merajver, Jun Z. Li:
  Impact of between-tissue differences on pan-cancer predictions of drug sensitivity.
• 
  Angus Leung, Dror Cohen, Bruno van Swinderen, Naotsugu Tsuchiya:
  Integrated information structure collapses with anesthetic loss of conscious arousal in Drosophila melanogaster.
• 
  Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J. J. van der Hooft:
  Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships.
• 
  Markus J. Sommer, Steven L. Salzberg:
  Balrog: A universal protein model for prokaryotic gene prediction.
• 
  Judith A. Bouman, Julien Riou, Sebastian Bonhoeffer, Roland R. Regoes:
  Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches.
• 
  Qixin He, Mercedes Pascual:
  An antigenic diversification threshold for falciparum malaria transmission at high endemicity.
• 
  Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan:
  DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks.
• 
  Viktor Sip, Julia Scholly, Maxime Guye, Fabrice Bartolomei, Viktor K. Jirsa:
  Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings.
• 
  Yaron Goldberg, Jonathan Friedman:
  Positive interactions within and between populations decrease the likelihood of evolutionary rescue.
• 
  Gil Jorge Barros Henriques, Koichi Ito, Christoph Hauert, Michael Doebeli:
  On the importance of evolving phenotype distributions on evolutionary diversification.
• 
  Richard P. Mann:
  Evolution of heterogeneous perceptual limits and indifference in competitive foraging.
• 
  Ann-Kristin Becker, Marcus Dörr, Stephan B. Felix, Fabian Frost, Hans Jörgen Grabe, Markus M. Lerch, Matthias Nauck, Uwe Völker, Henry Völzke, Lars Kaderali:
  From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach.
• 
  Alex Hawkins-Hooker, Florence Depardieu, Sebastien Baur, Guillaume Couairon, Arthur Chen, David Bikard:
  Generating functional protein variants with variational autoencoders.
• 
  Carlos Coronel-Oliveros, Rodrigo Cofré, Patricio Orio:
  Cholinergic neuromodulation of inhibitory interneurons facilitates functional integration in whole-brain models.
• 
  Kentaro Katahira, Asako Toyama:
  Revisiting the importance of model fitting for model-based fMRI: It does matter in computational psychiatry.
• 
  Johannes Asplund-Samuelsson, Elton P. Hudson:
  Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes.
• 
  Sitong Wang, Ting Ye, Guansheng Li, Xuejiao Zhang, Huixin Shi:
  Margination and adhesion dynamics of tumor cells in a real microvascular network.
• 
  Martín Garrido-Rodriguez, Daniel López-López, Francisco M. Ortuño, María Peña-Chilet, Eduardo Muñoz, Marco A. Calzado, Joaquín Dopazo:
  A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
• 
  Jordane Preto, Isabelle Krimm:
  The intrinsically disordered N-terminus of the voltage-dependent anion channel.
• 
  Rahmatullah Roche, Sutanu Bhattacharya, Debswapna Bhattacharya:
  Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins.
• 
  Inês G. Gonçalves, José Manuel García-Aznar:
  Extracellular matrix density regulates the formation of tumour spheroids through cell migration.
• 
  Zutan Li, Hangjin Jiang, Lingpeng Kong, Yuanyuan Chen, Kun Lang, Xiaodan Fan, Liangyun Zhang, Cong Pian:
  Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species.
• 
  Christof Fehrman, Tyler D. Robbins, C. Daniel Meliza:
  Nonlinear effects of intrinsic dynamics on temporal encoding in a model of avian auditory cortex.
• 
  Mark R. Winter, Miri Morgulis, Tsvia Gildor, Andrew R. Cohen, Smadar Ben-Tabou de-Leon:
  Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization.
• 
  Michael A. Henson:
  Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection.

Corrections

• 
  Caglar Cakan, Klaus Obermayer:
  Correction: Biophysically grounded mean-field models of neural populations under electrical stimulation.
• 
  PLOS Computational Biology Staff:
  Correction: Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities.
• 
  Rasmus S. Petersen, Andrea Colins Rodriguez, Mathew H. Evans, Dario Campagner, Michaela S. E. Loft:
  Correction: A system for tracking whisker kinematics and whisker shape in three dimensions.

Volume 17, Number 3, March 2021

Editorials

• 
  Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve:
  Ten simple rules for quick and dirty scientific programming.
• 
  Whitney Rachel Morgan, Erik Scott Wright:
  Ten simple rules for hitting a home run with your elevator pitch.
• 
  Lauren Cadwallader, Jason A. Papin, Feilim Mac Gabhann, Rebecca Kirk:
  Collaborating with our community to increase code sharing.

Education Articles

• 
  Danielle Smalls, Greg Wilson:
  Ten quick tips for staying safe online.
• 
  Janez Demsar, Blaz Zupan:
  Hands-on training about overfitting.
• 
  Christina R. Hall, Philippa C. Griffin, Andrew Lonie, Jeffrey H. Christiansen:
  Application of a bioinformatics training delivery method for reaching dispersed and distant trainees.
• 
  Sara Stoudt, Valeri N. Vasquez, Ciera C. Martinez:
  Principles for data analysis workflows.

Research Articles

• 
  Jilt Sebastian, Mriganka Sur, Hema A. Murthy, Mathew Magimai-Doss:
  Signal-to-signal neural networks for improved spike estimation from calcium imaging data.
• 
  Yanbo Lian, Ali Almasi, David B. Grayden, Tatiana Kameneva, Anthony N. Burkitt, Hamish Meffin:
  Learning receptive field properties of complex cells in V1.
• 
  Julian Rossbroich, Daniel Trotter, John Beninger, Katalin Toth, Richard Naud:
  Linear-nonlinear cascades capture synaptic dynamics.
• 
  Brian Coventry, David Baker:
  Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds.
• 
  Yangxiaolu Cao, John Neu, Andrew E. Blanchard, Ting Lu, Lingchong You:
  Repulsive expansion dynamics in colony growth and gene expression.
• 
  Yacong Li, Kuanquan Wang, Qince Li, Jules C. Hancox, Henggui Zhang:
  Reciprocal interaction between IK1 and If in biological pacemakers: A simulation study.
• 
  Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk:
  Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.
• 
  Joseph H. R. Hetmanski, Matthew C. Jones, Fatima Chunara, Jean-Marc Schwartz, Patrick T. Caswell:
  Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration.
• 
  Shuonan Chen, Jackson Loper, Xiaoyin Chen, Alex Vaughan, Anthony M. Zador, Liam Paninski:
  BARcode DEmixing through Non-negative Spatial Regression (BarDensr).
• 
  Jichao Pan, Yan Cai, Liang Wang, Akiko Maehara, Gary S. Mintz, Dalin Tang, Zhiyong Li:
  A prediction tool for plaque progression based on patient-specific multi-physical modeling.
• 
  Javier Rasero, Amy Isabella Sentis, Fang-Cheng Yeh, Timothy D. Verstynen:
  Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability.
• 
  Ilya Belevich, Eija Jokitalo:
  DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation.
• 
  Xiaoqiang Sun, Ji Zhang, Qing Nie:
  Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.
• 
  Akseli Niemelä, Artturi Koivuniemi:
  Positive allosteric modulators of lecithin: Cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile.
• 
  Simon Rogers, Virgilio L. Lew:
  PIEZO1 and the mechanism of the long circulatory longevity of human red blood cells.
• 
  Christophe Guyeux, Christophe Sola, Camille Noûs, Guislaine Refregier:
  CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
• 
  Stéphanie M. C. Abo, Anita T. Layton:
  Modeling the circadian regulation of the immune system: Sexually dimorphic effects of shift work.
• 
  Wahbi K. El-Bouri, Andrew MacGowan, Tamás I. Józsa, Matthew J. Gounis, Stephen J. Payne:
  Modelling the impact of clot fragmentation on the microcirculation after thrombectomy.
• 
  Alberto Pérez-Cervera, Jaroslav Hlinka:
  Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators.
• 
  Mark J. Panaggio, Daniel M. Abrams, Fan Yang, Tanvi Banerjee, Nirmish Shah:
  Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease.
• 
  Zixuan Cang, Yangyang Wang, Qixuan Wang, Ken W. Y. Cho, William R. Holmes, Qing Nie:
  A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.
• 
  A. J. Harris, Aaron David Goldman:
  The very early evolution of protein translocation across membranes.
• 
  Simone Sturniolo, William Waites, Tim Colbourn, David Manheim, Jasmina Panovska-Griffiths:
  Testing, tracing and isolation in compartmental models.
• 
  Casey M. Zipfel, Vittoria Colizza, Shweta Bansal:
  Health inequities in influenza transmission and surveillance.
• 
  John G. Mikhael, Lucy Lai, Samuel J. Gershman:
  Rational inattention and tonic dopamine.
• 
  Jailos Lubinda, Yaxin Bi, Busiku Hamainza, Ubydul Haque, Adrian J. Moore:
  Modelling of malaria risk, rates, and trends: A spatiotemporal approach for identifying and targeting sub-national areas of high and low burden.
• 
  Wen-Ting Chu, Jin Wang:
  Thermodynamic and sequential characteristics of phase separation and droplet formation for an intrinsically disordered region/protein ensemble.
• 
  Brandon Lieberthal, Allison M. Gardner:
  Connectivity, reproduction number, and mobility interact to determine communities' epidemiological superspreader potential in a metapopulation network.
• 
  Pieter J. K. Libin, Lander Willem, Timothy Verstraeten, Andrea Torneri, Joris Vanderlocht, Niel Hens:
  Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics.
• 
  David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard C. Laubenbacher, Clarissa J. Nobile, Réka Albert:
  Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies.
• 
  Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia R. Rodrigues, Oscar Dias:
  A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli.
• 
  Simon Rogers, Virgilio L. Lew:
  Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits.
• 
  Akira Nagamori, Christopher M. Laine, Gerald E. Loeb, Francisco J. Valero Cuevas:
  Force variability is mostly not motor noise: Theoretical implications for motor control.
• 
  Su Datt Lam, M. Madan Babu, Jonathan G. Lees, Christine A. Orengo:
  Biological impact of mutually exclusive exon switching.
• 
  Kasper Vinken, Hans P. Op de Beeck:
  Using deep neural networks to evaluate object vision tasks in rats.
• 
  Qi Huang, Monika Tokmina-Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, Simone Raugei:
  Mechanical coupling in the nitrogenase complex.
• 
  Vincent Brault, Bastien Mallein, Jean-François Rupprecht:
  Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance.
• 
  Catalina Rivera, David Hofmann, Ilya Nemenman:
  Inferring phenomenological models of first passage processes.
• 
  Ya-Wei Eileen Lin, Tal Shnitzer, Ronen Talmon, Franz Villarroel-Espindola, Shruti Desai, Kurt A. Schalper, Yuval Kluger:
  Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.
• 
  Vedant Sachdeva, Thierry Mora, Aleksandra M. Walczak, Stephanie E. Palmer:
  Optimal prediction with resource constraints using the information bottleneck.
• 
  Ingo R. Titze, Anil Palaparthi, Karin Cox, Amanda Stark, Lynn Maxfield, Brian Manternach:
  Vocalization with semi-occluded airways is favorable for optimizing sound production.
• 
  Kseniia Cheloshkina, Maria Poptsova:
  Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements.
• 
  Steven Schulz, Sebastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire:
  Parameters and determinants of responses to selection in antibody libraries.
• 
  Peter Czuppon, Florence Débarre, António Gonçalves, Olivier Tenaillon, Alan S. Perelson, Jérémie Guedj, François Blanquart:
  Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action.
• 
  Timothy J. Hackmann, Bo Zhang:
  Using neural networks to mine text and predict metabolic traits for thousands of microbes.
• 
  Francesco Di Lauro, István Z. Kiss, Joel C. Miller:
  Optimal timing of one-shot interventions for epidemic control.
• 
  Song He, Xinyu Song, Xiaoxi Yang, Jijun Yu, Yuqi Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo:
  COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data.
• 
  Min Wu, Lyudmyla Dorosh, Gerold Schmitt-Ulms, Holger Wille, Maria Stepanova:
  Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations.
• 
  Anton J. M. Larsson, Christoph Ziegenhain, Michael Hagemann-Jensen, Björn Reinius, Tina Jacob, Tim Dalessandri, Gert-Jan Hendriks, Maria Kasper, Rickard Sandberg:
  Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance.
• 
  Annika Hagemann, Jens Wilting, Bita Samimizad, Florian Mormann, Viola Priesemann:
  Assessing criticality in pre-seizure single-neuron activity of human epileptic cortex.
• 
  Koichiro Uriu, Hajime Tei:
  Complementary phase responses via functional differentiation of dual negative feedback loops.
• 
  Haider Al-Tahan, Yalda Mohsenzadeh:
  Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder.
• 
  Quentin Richard, Samuel Alizon, Marc Choisy, Mircea-Traian Sofonea, Ramsès Djidjou-Demasse:
  Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic.
• 
  Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz:
  Assessing the contribution of tumor mutational phenotypes to cancer progression risk.
• 
  Jared Brown, Chris Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Michael P. Schwartz, Amy Van Aartsen, John W. Steill, Scott Swanson, Ron M. Stewart, James A. Thomson, Christina Kendziorski:
  Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells.
• 
  Brian Maniscalco, Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Michele A. Basso, Hakwan Lau, Megan A. K. Peters:
  Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior.
• 
  Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane:
  Public Baseline and shared response structures support the theory of antibody repertoire functional commonality.
• 
  António Gonçalves, Pauline Maisonnasse, Flora Donati, Mélanie Albert, Sylvie Behillil, Vanessa Contreras, Thibaut Naninck, Romain Marlin, Caroline Solas, Andres Pizzorno, Julien Lemaitre, Nidhal Kahlaoui, Olivier Terrier, Raphael Ho Tsong Fang, Vincent Enouf, Nathalie Dereuddre-Bosquet, Angela Brisebarre, Franck Touret, Catherine Chapon, Bruno Hoen, Bruno Lina, Manuel Rosa Calatrava, Xavier de Lamballerie, France Mentré, Roger Le Grand, Sylvie van der Werf, Jérémie Guedj:
  SARS-CoV-2 viral dynamics in non-human primates.
• 
  Laurens F. M. Verscheijden, Carlijn H. C. Litjens, Jan B. Koenderink, Ron H. J. Mathijssen, Marcel M. Verbeek, Saskia N. de Wildt, Frans G. M. Russel:
  Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children.
• 
  Alejandro Tabas, Katharina von Kriegstein:
  Neural modelling of the encoding of fast frequency modulation.
• 
  Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W. Shen, May Sabry, Ive Logister, Richard I. Sherwood, David K. Gifford:
  Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
• 
  Warren Woodrich Pettine, Kenway Louie, John D. Murray, Xiao-Jing Wang:
  Excitatory-inhibitory tone shapes decision strategies in a hierarchical neural network model of multi-attribute choice.
• 
  Bruno Merlin, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, Mônica Silva de Oliveira, Larissa Maranhão Dias, Gislenne da Silva Moia, Victória Cardoso dos Santos, Adonney Allan de Oliveira Veras:
  CODON - Software to manual curation of prokaryotic genomes.
• 
  Konstantin Shestopaloff, Mei Dong, Fan Gao, Wei Xu:
  DCMD: Distance-based classification using mixture distributions on microbiome data.
• 
  Hong Seo Lim, Peng Qiu:
  JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters.
• 
  David Holcomb, Aikaterini Alexaki, Nancy Hernandez, Ryan Hunt, Kyle Laurie, Jacob Kames, Nobuko Hamasaki-Katagiri, Anton A. Komar, Michael DiCuccio, Chava Kimchi-Sarfaty:
  Gene variants of coagulation related proteins that interact with SARS-CoV-2.
• 
  Jun Ding, David Earl Hostallero, Mohamed Reda El Khili, Gregory Joseph Fonseca, Simon Milette, Nuzha Noorah, Myriam Guay-Belzile, Jonathan Spicer, Noriko Daneshtalab, Martin Sirois, Karine Tremblay, Amin Emad, Simon Rousseau:
  A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19.
• 
  Andrew J. Basinski, Elisabeth Fichet-Calvet, Anna R. Sjodin, Tanner J. Varrelman, Christopher H. Remien, Nathan C. Layman, Brian H. Bird, David J. Wolking, Corina Monagin, Bruno M. Ghersi, Peter A. Barry, Michael A. Jarvis, Paul E. Gessler, Scott L. Nuismer:
  Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa.
• 
  Talia M. Quandelacy, Jessica M. Healy, Bradford Greening, Dania M. Rodriguez, Koo-Whang Chung, Matthew J. Kuehnert, Brad J. Biggerstaff, Emilio Dirlikov, Luis Mier-y-Teran-Romero, Tyler M. Sharp, Stephen Waterman, Michael A. Johansson:
  Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016.
• 
  Moritz F. P. Becker, Christian Tetzlaff:
  The biophysical basis underlying the maintenance of early phase long-term potentiation.
• 
  Emmi Jokinen, Jani Huuhtanen, Satu Mustjoki, Markus Heinonen, Harri Lähdesmäki:
  Predicting recognition between T cell receptors and epitopes with TCRGP.
• 
  Phillip Andrew Richmond, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, Wyeth W. Wasserman:
  Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.
• 
  Olga A. Nev, Richard J. Lindsay, Alys Jepson, Lisa Butt, Robert E. Beardmore, Ivana Gudelj:
  Predicting microbial growth dynamics in response to nutrient availability.
• 
  Alican Gulsevin, Jens Meiler:
  Prediction of amphipathic helix - membrane interactions with Rosetta.
• 
  Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, GENESIS study group, Dominique Stoppa-Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott:
  Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer.
• 
  Mukuo Wang, Shujing Hou, Yu Wei, Dongmei Li, Jianping Lin:
  Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking.
• 
  Ayuna Barlukova, Igor M. Rouzine:
  The evolutionary origin of the universal distribution of mutation fitness effect.
• 
  Yevhen Tupikov, Dezhe Z. Jin:
  Addition of new neurons and the emergence of a local neural circuit for precise timing.
• 
  Zhaoqian Su, Kalyani Dhusia, Yinghao Wu:
  A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells.
• 
  Nobuhiko Wagatsuma, Brian Hu, Rüdiger von der Heydt, Ernst Niebur:
  Analysis of spiking synchrony in visual cortex reveals distinct types of top-down modulation signals for spatial and object-based attention.
• 
  Denis A. Shah, Erick D. De Wolf, Pierce A. Paul, Laurence V. Madden:
  Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models.
• 
  Pascal P. Klamser, Pawel Romanczuk:
  Collective predator evasion: Putting the criticality hypothesis to the test.
• 
  Cosmin Stamate, Joan Saez-Pons, David Weston, George Roussos:
  PDKit: A data science toolkit for the digital assessment of Parkinson's Disease.
• 
  Ji Hyun Bak, Min Hyeok Kim, Lei Liu, Changbong Hyeon:
  A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C.
• 
  Gregory L. Watson, Di Xiong, Lu Zhang, Joseph A. Zoller, John Shamshoian, Phillip Sundin, Teresa Bufford, Anne W. Rimoin, Marc A. Suchard, Christina M. Ramirez:
  Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model.
• 
  Ruping Sun, Athanasios N. Nikolakopoulos:
  Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors.
• 
  Lukasz Mioduszewski, Marek Cieplak:
  Viscoelastic properties of wheat gluten in a molecular dynamics study.
• 
  Yekaterina S. Pavlova, David Páez-Espino, Andrew Yu. Morozov, Ilya S. Belalov:
  Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.
• 
  Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao, Jianyang Zeng:
  Full-length ribosome density prediction by a multi-input and multi-output model.
• 
  Chang Xu, Yuxiang Wang, Gregory J. Gerling:
  An elasticity-curvature illusion decouples cutaneous and proprioceptive cues in active exploration of soft objects.
• 
  Amber Kunkel, Michael White, Patrice Piola:
  Novel anti-malarial drug strategies to prevent artemisinin partner drug resistance: A model-based analysis.
• 
  Balázs Erdos, Bart van Sloun, Michiel E. Adriaens, Shauna D. O'Donovan, Dominique Langin, Arne Astrup, Ellen E. Blaak, Ilja C. W. Arts, Natal A. W. van Riel:
  Personalized computational model quantifies heterogeneity in postprandial responses to oral glucose challenge.
• 
  Pratiti Bhadra, Lalitha Yadhanapudi, Karin Römisch, Volkhard Helms:
  How does Sec63 affect the conformation of Sec61 in yeast?
• 
  Josh L. Espinoza, Chris L. Dupont, Aubrie O'Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J. Meyer, Agnes P. Chan, Yongwook Choi, William C. Nierman, Kim Lewis, Karen E. Nelson:
  Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
• 
  Frederick Callaway, Antonio Rangel, Thomas L. Griffiths:
  Fixation patterns in simple choice reflect optimal information sampling.
• 
  Daniel R. Ripoll, Sidhartha Chaudhury, Anders Wallqvist:
  Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.
• 
  Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang:
  Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.
• 
  Amadeus Maes, Mauricio Barahona, Claudia Clopath:
  Learning compositional sequences with multiple time scales through a hierarchical network of spiking neurons.
• 
  Irina Veith, Arianna Mencattini, Valentin Picant, Marco Serra, Marine Leclerc, Maria Colomba Comes, Fathia Mami-Chouaib, Jacques Camonis, Stéphanie Descroix, Hamasseh Shirvani, Fatima Mechta-Grigoriou, Gérard Zalcman, Maria Carla Parrini, Eugenio Martinelli:
  Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death.
• 
  Yannick Marcon, Tom Bishop, Demetris Avraam, Xavier Escriba-Montagut, Patricia Ryser-Welch, Stuart Wheater, Paul R. Burton, Juan R. González:
  Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
• 
  Andrea Torneri, Pieter Libin, Gianpaolo Scalia Tomba, Christel Faes, James G. Wood, Niel Hens:
  On realized serial and generation intervals given control measures: The COVID-19 pandemic case.

Correction

• 
  PLOS Computational Biology Staff:
  Correction: Up-down biphasic volume response of human red blood cells to PIEZO1 activation during capillary transits.

Volume 17, Number 4, April 2021

Research Articles

• 
  Yifu Luo, Chris S. Bresee, John W. Rudnicki, Mitra J. Z. Hartmann:
  Constraints on the deformation of the vibrissa within the follicle.
• 
  Alejandro Lerer, Hans Supèr, Matthias S. Keil:
  Dynamic decorrelation as a unifying principle for explaining a broad range of brightness phenomena.
• 
  David Peter Shorten, Richard E. Spinney, Joseph T. Lizier:
  Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data.
• 
  Lisette Meerstein-Kessel, Jeron Venhuizen, Daniel Garza, Nicolas Pröllochs, Emma J. Vos, Joshua M. Obiero, Philip L. Felgner, Robert W. Sauerwein, Marynthe Peters, Annie S. P. Yang, Martijn A. Huynen:
  Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies.
• 
  Aref Pariz, Ingo Fischer, Alireza Valizadeh, Claudio R. Mirasso:
  Transmission delays and frequency detuning can regulate information flow between brain regions.
• 
  Zhuliu Li, Tianci Song, Jeongsik Yong, Rui Kuang:
  Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion.
• 
  Rositsa Raikova, Vessela Tz. Krasteva, Piotr Krutki, Hanna Drzymala-Celichowska, Katarzyna Krysciak, Jan Celichowski:
  Effect of synchronization of firings of different motor unit types on the force variability in a model of the rat medial gastrocnemius muscle.
• 
  Andrey A. Mironov, Stepan Denisov, Alexander Greß, Olga V. Kalinina, Dmitri D. Pervouchine:
  An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.
• 
  Tsuyoshi Ikegami, Gowrishankar Ganesh, Tricia L. Gibo, Toshinori Yoshioka, Rieko Osu, Mitsuo Kawato:
  Hierarchical motor adaptations negotiate failures during force field learning.
• 
  Maria Kleshnina, Sabrina S. Streipert, Jerzy A. Filar, Krishnendu Chatterjee:
  Mistakes can stabilise the dynamics of rock-paper-scissors games.
• 
  Diego Vidaurre:
  A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation.
• 
  Fleur Zeldenrust, Boris S. Gutkin, Sophie Denève:
  Efficient and robust coding in heterogeneous recurrent networks.
• 
  Benjamin R. Pittman-Polletta, Yangyang Wang, David A. Stanley, Charles E. Schroeder, Miles A. Whittington, Nancy J. Kopell:
  Differential contributions of synaptic and intrinsic inhibitory currents to speech segmentation via flexible phase-locking in neural oscillators.
• 
  Mateusz Sikora, Sören von Bülow, Florian E. C. Blanc, Michael Gecht, Roberto Covino, Gerhard Hummer:
  Computational epitope map of SARS-CoV-2 spike protein.
• 
  Lifan Liang, Kunju Zhu, Junyan Tao, Songjian Lu:
  ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network.
• 
  Claudio Bassot, Arne Elofsson:
  Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families.
• 
  Changjia Cai, Johannes Friedrich, Amrita Singh, M. Hossein Eybposh, Eftychios A. Pnevmatikakis, Kaspar Podgorski, Andrea Giovannucci:
  VolPy: Automated and scalable analysis pipelines for voltage imaging datasets.
• 
  Avishek Paul, Helen McLendon, Veronica Rally, Jon T. Sakata, Sarah C. Woolley:
  Behavioral discrimination and time-series phenotyping of birdsong performance.
• 
  Steffen Lange, Benjamin M. Friedrich:
  Sperm chemotaxis in marine species is optimal at physiological flow rates according theory of filament surfing.
• 
  H. Juliette T. Unwin, Isobel Routledge, Seth R. Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin Cohen, Daniel J. Weiss, Swapnil Mishra, Samir Bhatt:
  Using Hawkes Processes to model imported and local malaria cases in near-elimination settings.
• 
  Peter J. Bishop, Krijn B. Michel, Antoine Falisse, Andrew R. Cuff, Vivian R. Allen, Friedl De Groote, John R. Hutchinson:
  Computational modelling of muscle fibre operating ranges in the hindlimb of a small ground bird (Eudromia elegans), with implications for modelling locomotion in extinct species.
• 
  Motoki Kajiwara, Ritsuki Nomura, Felix Goetze, Masanori Kawabata, Yoshikazu Isomura, Tatsuya Akutsu, Masanori Shimono:
  Inhibitory neurons exhibit high controlling ability in the cortical microconnectome.
• 
  Michael Foley, Rory Smead, Patrick Forber, Christoph Riedl:
  Avoiding the bullies: The resilience of cooperation among unequals.
• 
  Cristóbal Rodero, Marina Strocchi, Maciej Marciniak, Stefano Longobardi, John Whitaker, Mark D. O'Neill, Karli Gillette, Christoph M. Augustin, Gernot Plank, Edward J. Vigmond, Pablo Lamata, Steven A. Niederer:
  Linking statistical shape models and simulated function in the healthy adult human heart.
• 
  Christopher Wills, Bin Wang, Shuai Fang, Yunquan Wang, Yi Jin, James A. Lutz, Jill Thompson, Kyle E. Harms, Sandeep Pulla, Bonifacio Pasion, Sara Germain, Heming Liu, Joseph Smokey, Sheng-Hsin Su, Nathalie Butt, Chengjin Chu, George Chuyong, Chia-Hao Chang-Yang, H. S. Dattaraja, Stuart Davies, Sisira Ediriweera, Shameema Esufali, Christine Dawn Fletcher, Nimal Gunatilleke, Savi Gunatilleke, Chang-Fu Hsieh, Fangliang He, Stephen Hubbell, Zhanqing Hao, Akira Itoh, David Kenfack, Buhang Li, Xiankun Li, Keping Ma, Michael Morecroft, Xiangcheng Mi, Yadvinder Malhi, Perry Ong, Lillian Jennifer Rodriguez, H. S. Suresh, I Fang Sun, Raman Sukumar, Sylvester Tan, Duncan Thomas, María Uriarte, Xihua Wang, Xugao Wang, T. L. Yao, Jess Zimmermann:
  Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories.
• 
  Claude Gérard, Laurane De Mot, Sabine Cordi, Jonathan van Eyll, Frédéric Lemaigre:
  Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy.
• 
  Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz, Alexis Joly:
  Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment.
• 
  Piyush Nanda, Amit Ghosh:
  Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection.
• 
  Jean-Charles Walter, Thibaut Lepage, Jérôme Dorignac, Frédéric Geniet, Andrea Parmeggiani, John Palmeri, Jean-Yves Bouet, Ivan Junier:
  Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex.
• 
  Mel W. Khaw, Luminita Stevens, Michael Woodford:
  Individual differences in the perception of probability.
• 
  Vladislav Uzunangelov, Christopher K. Wong, Joshua M. Stuart:
  Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.
• 
  Alex Baranski, Idan Milo, Shirley Greenbaum, John-Paul Oliveria, Dunja Mrdjen, Michael Angelo, Leeat Keren:
  MAUI (MBI Analysis User Interface) - An image processing pipeline for Multiplexed Mass Based Imaging.
• 
  Spencer J. Mitchell, Deeptak Verma, Karl E. Griswold, Chris Bailey-Kellogg:
  Building blocks and blueprints for bacterial autolysins.
• 
  Valeria Velásquez-Zapata, J. Mitch Elmore, Sagnik Banerjee, Karin S. Dorman, Roger P. Wise:
  Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor.
• 
  Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic:
  A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism.
• 
  Pablo Martínez-Cañada, Torbjørn V. Ness, Gaute T. Einevoll, Tommaso Fellin, Stefano Panzeri:
  Computation of the electroencephalogram (EEG) from network models of point neurons.
• 
  Kai Röth, Shuai Shao, Julijana Gjorgjieva:
  Efficient population coding depends on stimulus convergence and source of noise.
• 
  Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens Nielsen, Jonathan L. Robinson:
  Machine learning-based investigation of the cancer protein secretory pathway.
• 
  Christophe Menichelli, Vincent Guitard, Rafael Miyazawa Martins, Sophie Lèbre, Jose-Juan Lopez-Rubio, Charles-Henri Lecellier, Laurent Bréhélin:
  Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.
• 
  Laetitia Hebert, Tosif Ahamed, Antonio C. Costa, Liam O'Shaughnessy, Greg J. Stephens:
  WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans.
• 
  Yao Li, Lai-Sang Young:
  Unraveling the mechanisms of surround suppression in early visual processing.
• 
  Kaiwen Shi, Tao Liu, Hanjiang Fu, Wuju Li, Xiaofei Zheng:
  Genome-wide analysis of lncRNA stability in human.
• 
  Lorenzo Betti, Gianmarco De Francisci Morales, Laetitia Gauvin, Kyriaki Kalimeri, Yelena Mejova, Daniela Paolotti, Michele Starnini:
  Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum.
• 
  Rohan N. Shah, Alexander J. Ruthenburg:
  Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads.
• 
  Takumi Sase, Keiichi Kitajo:
  The metastable brain associated with autistic-like traits of typically developing individuals.
• 
  Eric A. Chadwick, Takaya Suzuki, Michael G. George, David A. Romero, Cristina H. Amon, Thomas K. Waddell, Golnaz Karoubi, Aimy Bazylak:
  Vessel network extraction and analysis of mouse pulmonary vasculature via X-ray micro-computed tomographic imaging.
• 
  Jan Stenum, Cristina Rossi, Ryan T. Roemmich:
  Two-dimensional video-based analysis of human gait using pose estimation.
• 
  James H. Joly, Brandon T. L. Chew, Nicholas A. Graham:
  The landscape of metabolic pathway dependencies in cancer cell lines.
• 
  Yao Jiang, Hui-Fang Liu, Rong Liu:
  Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions.

Corrections

• 
  Georges Hattab, Theresa-Marie Rhyne, Dominik Heider:
  Correction: Ten simple rules to colorize biological data visualization.
• 
  Maral Budak, Karl Grosh, Aritra Sasmal, Gabriel Corfas, Michal Zochowski, Victoria Booth:
  Correction: Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects.
• 
  PLOS Computational Biology Staff:
  Correction: An antigenic diversification threshold for falciparum malaria transmission at high endemicity.

Volume 17, Number 5, May 2021

Editorials

• 
  Faryad Sahneh, Meghan A. Balk, Marina Kisley, Chi-Kwan Chan, Mercury Fox, Brian Nord, Eric Lyons, Tyson Lee Swetnam, Daniela Huppenkothen, Will Sutherland, Ramona L. Walls, Daven P. Quinn, Tonantzin Tarin, David S. LeBauer, David Ribes, Dunbar P. Birnie III, Carol Lushbough, Eric Carr, Grey Nearing, Jeremy Fischer, Kevin Tyle, Luis Carrasco, Meagan Lang, Peter W. Rose, Richard R. Rushforth, Samapriya Roy, Thomas Matheson, Tina Lee, C. Titus Brown, Tracy K. Teal, Monica Papes, Stephen G. Kobourov, Nirav C. Merchant:
  Ten simple rules to cultivate transdisciplinary collaboration in data science.
• 
  Friederike Ehrhart, Chris T. A. Evelo:
  Ten simple rules to make your publication look better.
• 
  Nigel Golden, Kadambari Devarajan, Cathleen Balantic, Joseph Drake, Michael T. Hallworth, Toni Lyn Morelli:
  Ten simple rules for productive lab meetings.

Education Articles

• 
  Jasia King, Kerbaï Saïd Eroumé, Roman Truckenmüller, Stefan Giselbrecht, Ann E. Cowan, Leslie M. Loew, Aurélie Carlier:
  Ten steps to investigate a cellular system with mathematical modeling.
• 
  Cristóbal Gallardo-Alba, Björn A. Grüning, Beatriz Serrano-Solano:
  A constructivist-based proposal for bioinformatics teaching practices during lockdown.
• 
  Beatriz Serrano-Solano, Melanie Christine Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia D. Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A. Grüning:
  Fostering accessible online education using Galaxy as an e-learning platform.
• 
  Paul Medvedev, Mihai Pop:
  What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Research Articles

• 
  Leonard Campanello, Maria K. Traver, Hari Shroff, Brian C. Schaefer, Wolfgang Losert:
  Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10.
• 
  Derek Reiman, Godhev Kumar Manakkat Vijay, Heping Xu, Andrew Sonin, Dianyu Chen, Nathan Salomonis, Harinder Singh, Aly A. Khan:
  Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination.
• 
  Marco António Dias Louro, Mónica Bettencourt-Dias, Jorge Carneiro:
  A first-takes-all model of centriole copy number control based on cartwheel elongation.
• 
  Susana Andrea Contreras, Jan-Hendrik Schleimer, Allan T. Gulledge, Susanne Schreiber:
  Activity-mediated accumulation of potassium induces a switch in firing pattern and neuronal excitability type.
• 
  Christian Schulz, Tjasa Kumelj, Emil Karlsen, Eivind Almaas:
  Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition.
• 
  Ian D. Estabrook, Hawa Racine Thiam, Matthieu Piel, Rhoda J. Hawkins:
  Calculation of the force field required for nucleus deformation during cell migration through constrictions.
• 
  Shalmali Kharche, Manali Joshi, Amitabha Chattopadhyay, Durba Sengupta:
  Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1.
• 
  Andrea Di Russo, Dimitar Stanev, Stéphane Armand, Auke Jan Ijspeert:
  Sensory modulation of gait characteristics in human locomotion: A neuromusculoskeletal modeling study.
• 
  Chaitanya Chintaluri, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, Kacper Kondrakiewicz, Ewa Kublik, Daniel K. Wójcik:
  What we can and what we cannot see with extracellular multielectrodes.
• 
  Marco António Dias Louro, Mónica Bettencourt-Dias, Claudia Bank:
  Patterns of selection against centrosome amplification in human cell lines.
• 
  Daniel Ch. Haspinger, Sandra Klinge, Gerhard A. Holzapfel:
  Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport.
• 
  Arthur Mensch, Julien Mairal, Bertrand Thirion, Gaël Varoquaux:
  Extracting representations of cognition across neuroimaging studies improves brain decoding.
• 
  Sam Moore, Edward M. Hill, Louise Dyson, Michael J. Tildesley, Matt J. Keeling:
  Modelling optimal vaccination strategy for SARS-CoV-2 in the UK.
• 
  Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson:
  Hierarchical semantic composition of biosimulation models using bond graphs.
• 
  Andrew D. Marquis, Filip Jezek, David J. Pinsky, Daniel A. Beard:
  Hypoxic pulmonary vasoconstriction as a regulator of alveolar-capillary oxygen flux: A computational model of ventilation-perfusion matching.
• 
  Christopher J. Arthurs, Rostislav Khlebnikov, Alex Melville, Marija Marcan, Alberto Gómez, Desmond Dillon-Murphy, Federica Cuomo, Miguel Silva Vieira, Jonas Schollenberger, Sabrina R. Lynch, Christopher Tossas-Betancourt, Kritika Iyer, Sara Hopper, Elizabeth Livingston, Pouya Youssefi, Alia Noorani, Sabrina Ben Ahmed, Foeke J. H. Nauta, Theodorus M. J. van Bakel, Yunus Ahmed, Petrus A. J. van Bakel, Jonathan P. Mynard, Paolo Di Achille, Hamid Gharahi, Kevin D. Lau, Vasilina Filonova, Miquel Aguirre, Nitesh Nama, Nan Xiao, Seungik Baek, Krishna C. Garikipati, Onkar Sahni, David Nordsletten, C. Alberto Figueroa:
  CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation.
• 
  Arunabha Majumdar, Claudia Giambartolomei, Na Cai, Tanushree Haldar, Tommer Schwarz, Michael J. Gandal, Jonathan Flint, Bogdan Pasaniuc:
  Leveraging eQTLs to identify individual-level tissue of interest for a complex trait.
• 
  Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers:
  Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.
• 
  Jeet Sukumaran, Mark T. Holder, L. Lacey Knowles:
  Incorporating the speciation process into species delimitation.
• 
  Peter K. Koo, Antonio Majdandzic, Matthew Ploenzke, Praveen Anand, Steffan B. Paul:
  Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks.
• 
  Greta Simionato, Konrad Hinkelmann, Revaz Chachanidze, Paola Bianchi, Elisa Fermo, Richard van Wijk, Marc Leonetti, Christian Wagner, Lars Kaestner, Stephan Quint:
  Red blood cell phenotyping from 3D confocal images using artificial neural networks.
• 
  Jon Kapla, Ismael Rodriguez-Espigares, Flavio Ballante, Jana Selent, Jens Carlsson:
  Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
• 
  Amanda M. Westman, Shayn M. Peirce, George J. Christ, Silvia S. Blemker:
  Agent-based model provides insight into the mechanisms behind failed regeneration following volumetric muscle loss injury.
• 
  Fan Jin, Frauke Gräter:
  How multisite phosphorylation impacts the conformations of intrinsically disordered proteins.
• 
  Hanjue Xia, Johannes Horn, Monika J. Piotrowska, Konrad Sakowski, André Karch, Hannan Tahir, Mirjam E. Kretzschmar, Rafael T. Mikolajczyk:
  Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections.
• 
  JaeAnn M. Dwulet, Jennifer K. Briggs, Richard K. P. Benninger:
  Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication.
• 
  Fandi Wu, Jinbo Xu:
  Deep template-based protein structure prediction.
• 
  Mads L. Pedersen, Maria Ironside, Ken-ichi Amemori, Callie L. McGrath, Min S. Kang, Ann M. Graybiel, Diego A. Pizzagalli, Michael J. Frank:
  Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder.
• 
  Felipe Dalvi-Garcia, Luís L. Fonseca, Ana Tereza Ribeiro de Vasconcelos, Cecilia Hedin-Pereira, Eberhard O. Voit:
  A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression.
• 
  Edwin Rodriguez Horta, Martin Weigt:
  On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins.
• 
  Alan Eric Akil, Robert Rosenbaum, Kresimir Josic:
  Balanced networks under spike-time dependent plasticity.
• 
  Jue Tao Lim, Kenwin Maung, Sok Teng Tan, Suan Ee Ong, Jane Mingjie Lim, Joel Ruihan Koo, Haoyang Sun, Minah Park, Ken Wei Tan, Joanne Yoong, Alex R. Cook, Borame Sue Dickens:
  Estimating direct and spill-over impacts of political elections on COVID-19 transmission using synthetic control methods.
• 
  Juho A. J. Kontio, Tanja Pyhäjärvi, Mikko J. Sillanpää:
  Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways.
• 
  E. Georg Luebeck, Thomas L. Vaughan, Kit Curtius, William D. Hazelton:
  Modeling historic incidence trends implies early field cancerization in esophageal squamous cell carcinoma.
• 
  Weifeng Guo, Xiangtian Yu, Qianqian Shi, Jing Liang, Shao-Wu Zhang, Tao Zeng:
  Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis.
• 
  Gloria Cecchini, Alessandro Scaglione, Anna Letizia Allegra Mascaro, Curzio Checcucci, Emilia Conti, Ihusan Adam, Duccio Fanelli, Roberto Livi, Francesco Saverio Pavone, Thomas Kreuz:
  Cortical propagation tracks functional recovery after stroke.
• 
  Siwei Wang, Idan Segev, Alexander Borst, Stephanie E. Palmer:
  Maximally efficient prediction in the early fly visual system may support evasive flight maneuvers.
• 
  Chun-Nan Hsu, Chia-Hui Chang, Thamolwan Poopradubsil, Amanda Lo, Karen A. William, Ko-Wei Lin, Anita E. Bandrowski, Ibrahim Burak Özyurt, Jeffrey S. Grethe, Maryann E. Martone:
  Antibody Watch: Text mining antibody specificity from the literature.
• 
  Kristjan Kalm, Dennis Norris:
  Sequence learning recodes cortical representations instead of strengthening initial ones.
• 
  Saskia Haupt, Alexander Zeilmann, Aysel Ahadova, Hendrik Bläker, Magnus von Knebel Doeberitz, Matthias Kloor, Vincent Heuveline:
  Mathematical modeling of multiple pathways in colorectal carcinogenesis using dynamical systems with Kronecker structure.
• 
  Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin:
  A method for achieving complete microbial genomes and improving bins from metagenomics data.
• 
  Lakshitha P. Wijesinghe, Melville Wohlgemuth, Richard Hau Yue So, Jochen Triesch, Cynthia F. Moss, Bertram E. Shi:
  Active head rolls enhance sonar-based auditory localization performance.
• 
  Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert:
  The hierarchical packing of euchromatin domains can be described as multiplicative cascades.
• 
  Akhil John, Carlos Aleluia, A. John van Opstal, Alexandre Bernardino:
  Modelling 3D saccade generation by feedforward optimal control.
• 
  Yan Guo, Hui Yu, Haocan Song, Jiapeng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott Ness, Yu Shyr, Fei Ye:
  MetaGSCA: A tool for meta-analysis of gene set differential coexpression.
• 
  Amir Bahmani, Kyle Ferriter, Vandhana Krishnan, Arash Alavi, Amir Alavi, Philip S. Tsao, Michael P. Snyder, Cuiping Pan:
  Swarm: A federated cloud framework for large-scale variant analysis.
• 
  Xinjun Li, Fan Feng, Hongxi Pu, Wai Yan Leung, Jie Liu:
  scHiCTools: A computational toolbox for analyzing single-cell Hi-C data.
• 
  Wojciech Wesolowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk:
  VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset.
• 
  Alexander Karollus, Ziga Avsec, Julien Gagneur:
  Predicting mean ribosome load for 5'UTR of any length using deep learning.
• 
  Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr, Costas D. Maranas:
  Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.
• 
  Olivia L. Calvin, A. David Redish:
  Global disruption in excitation-inhibition balance can cause localized network dysfunction and Schizophrenia-like context-integration deficits.
• 
  Martin R. Ralph, Shu-qun Shi, Carl H. Johnson, Pavel Houdek, Tenjin C. Shrestha, Priya Crosby, John S. O'Neill, Martin Sládek, Adam R. Stinchcombe, Alena Sumová:
  Targeted modification of the Per2 clock gene alters circadian function in mPer2luciferase (mPer2Luc) mice.
• 
  Nikolina Sostaric, Vera van Noort:
  Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions.
• 
  Antoine Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, Alain Denise, Jérôme Waldispühl:
  Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.
• 
  Kathleen Jacquerie, Guillaume Drion:
  Robust switches in thalamic network activity require a timescale separation between sodium and T-type calcium channel activations.
• 
  Halil Ibrahim Kuru, Mustafa Buyukozkan, Öznur Tastan:
  PRER: A patient representation with pairwise relative expression of proteins on biological networks.
• 
  Jonathan Liu, Donald Hansen, Elizabeth Eck, Yang Joon Kim, Meghan Turner, Simon Alamos, Hernan G. Garcia:
  Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage.
• 
  Marko Sterk, Lidija Krizancic Bombek, Masa Skelin Klemen, Marjan Slak Rupnik, Marko Marhl, Andraz Stozer, Marko Gosak:
  NMDA receptor inhibition increases, synchronizes, and stabilizes the collective pancreatic beta cell activity: Insights through multilayer network analysis.
• 
  Suyeon Heo, Yoondo Sung, Sang Wan Lee:
  Effects of subclinical depression on prefrontal-striatal model-based and model-free learning.
• 
  Kazuki Kuga, Kazuhide Ito, Wenhao Chen, Ping Wang, Jeff Fowles, Kazukiyo Kumagai:
  Secondary indoor air pollution and passive smoking associated with cannabis smoking using electric cigarette device-demonstrative in silico study.
• 
  Toviah Moldwin, Menachem Kalmenson, Idan Segev:
  The gradient clusteron: A model neuron that learns to solve classification tasks via dendritic nonlinearities, structural plasticity, and gradient descent.
• 
  Derek Reiman, Brian T. Layden, Yang Dai:
  MiMeNet: Exploring microbiome-metabolome relationships using neural networks.
• 
  Noele Norris, Naomi M. Levine, Vicente I. Fernandez, Roman Stocker:
  Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria.
• 
  Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo, Yanjie Wei:
  Evaluation of residue-residue contact prediction methods: From retrospective to prospective.
• 
  Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang:
  G2S3: A gene graph-based imputation method for single-cell RNA sequencing data.
• 
  Sean L. Wu, Jared B. Bennett, Héctor M. Sánchez C., Andrew J. Dolgert, Tomás M. León, John M. Marshall:
  MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics.
• 
  Claudio Daniel Tenorio de Barros, Maira Arruda Cardoso, Paulo Mascarello Bisch, Helena M. Araujo, Francisco J. P. Lopes:
  A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila.
• 
  Adam L. Tyson, Charly V. Rousseau, Christian J. Niedworok, Sepiedeh Keshavarzi, Chryssanthi Tsitoura, Lee Cossell, Molly Strom, Troy W. Margrie:
  A deep learning algorithm for 3D cell detection in whole mouse brain image datasets.

Corrections

• 
  Peter M. C. Harrison, Roberta Bianco, Maria Chait, Marcus T. Pearce:
  Correction: PPM-Decay: A computational model of auditory prediction with memory decay.
• 
  Xiangyu Yao, Shihoko Kojima, Jing Chen:
  Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.

Volume 17, Number 6, June 2021

Editorials

• 
  Sam Illingworth, Paul Wake:
  Ten simple rules for designing analogue science games.
• 
  Dalen Chan, Christina M. Fitzsimmons, Mariana D. Mandler, Pedro J. Batista:
  Ten simple rules for acing virtual interviews.

Education

• 
  Matthew R. Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W. Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R. Keefe, Jamie T. Morton, Renato R. M. Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vazquez-Baeza, Michal Ziemski, Hazuki E. Miwa, Terry A. Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D. Kaehler, Emily K. Cope, Jessica L. Metcalf, Michael S. Robeson II, Nicholas A. Bokulich, J. Gregory Caporaso:
  Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Perspective

• 
  Jitao David Zhang:
  Ten simple rules for doing a postdoc in pharma.

Review

• 
  Amy Trentham-Dietz, Oguzhan Alagöz, Christina Chapman, Xuelin Huang, Jinani Jayasekera, Nicolien T. van Ravesteyn, Sandra J. Lee, Clyde B. Schechter, Jennifer M. Yeh, Sylvia K. Plevritis, Jeanne S. Mandelblatt, Breast Working Group of the Cancer Intervention, Surveillance Modeling Network (CISNET):
  Reflecting on 20 years of breast cancer modeling in CISNET: Recommendations for future cancer systems modeling efforts.

Research Articles

• 
  Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson:
  Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.
• 
  Andreas Bauer, Magdalena Prechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry:
  pyTFM: A tool for traction force and monolayer stress microscopy.
• 
  Maarten Afschrift, Friedl De Groote, Ilse Jonkers:
  Similar sensorimotor transformations control balance during standing and walking.
• 
  Fatemeh Mirzapour-Shafiyi, Yukinori Kametani, Takao Hikita, Yosuke Hasegawa, Masanori Nakayama:
  Numerical evaluation reveals the effect of branching morphology on vessel transport properties during angiogenesis.
• 
  Tomás Alarcón, Josep Sardanyés, Antoni Guillamón, Javier A. Menéndez:
  Bivalent chromatin as a therapeutic target in cancer: An in silico predictive approach for combining epigenetic drugs.
• 
  Xize Xu, Hermann Riecke:
  Paradoxical phase response of gamma rhythms facilitates their entrainment in heterogeneous networks.
• 
  Melinda Liu Perkins:
  Implications of diffusion and time-varying morphogen gradients for the dynamic positioning and precision of bistable gene expression boundaries.
• 
  Ali-Kemal Aydin, William Davis Haselden, Julie Dang, Patrick J. Drew, Serge Charpak, Davide Boido:
  Iliski, a software for robust calculation of transfer functions.
• 
  Jing Jiao, Gonzalo P. Suárez, Nina H. Fefferman:
  How public reaction to disease information across scales and the impacts of vector control methods influence disease prevalence and control efficacy.
• 
  Nicholas Mikolajewicz, Delaney Smith, Svetlana V. Komarova, Anmar Khadra:
  High-affinity P2Y2 and low-affinity P2X7 receptor interaction modulates ATP-mediated calcium signaling in murine osteoblasts.
• 
  Lucas Rudelt, Daniel González Marx, Michael Wibral, Viola Priesemann:
  Embedding optimization reveals long-lasting history dependence in neural spiking activity.
• 
  Qian Ke, Wikum Dinalankara, Laurent Younes, Donald Geman, Luigi Marchionni:
  Efficient representations of tumor diversity with paired DNA-RNA aberrations.
• 
  Long Luu, Alan A. Stocker:
  Categorical judgments do not modify sensory representations in working memory.
• 
  Rachel Rac-Lubashevsky, Michael J. Frank:
  Analogous computations in working memory input, output and motor gating: Electrophysiological and computational modeling evidence.
• 
  Michael Hellstern, Jing Ma, Kun Yue, Ali Shojaie:
  netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis.
• 
  Yaniv Morgenstern, Frieder Hartmann, Filipp Schmidt, Henning Tiedemann, Eugen Prokott, Guido Maiello, Roland W. Fleming:
  An image-computable model of human visual shape similarity.
• 
  Fred S. Lu, André T. Nguyen, Nicholas B. Link, Mathieu Molina, Jessica T. Davis, Matteo Chinazzi, Xinyue Xiong, Alessandro Vespignani, Marc Lipsitch, Mauricio Santillana:
  Estimating the cumulative incidence of COVID-19 in the United States using influenza surveillance, virologic testing, and mortality data: Four complementary approaches.
• 
  Ankur Sinha, Christoph Metzner, Neil Davey, Rod Adams, Michael Schmuker, Volker Steuber:
  Growth rules for the repair of Asynchronous Irregular neuronal networks after peripheral lesions.
• 
  Bronner P. Gonçalves, Simon R. Procter, Sam Clifford, Artemis Koukounari, Proma Paul, Alexandra M. Lewin, Mark Jit, Joy Lawn:
  Estimation of country-level incidence of early-onset invasive Group B Streptococcus disease in infants using Bayesian methods.
• 
  Anthony O'Hare, Daniel Balaz, David M. Wright, Carl McCormick, Stanley McDowell, Hannah Trewby, Robin A. Skuce, Rowland R. Kao:
  A new phylodynamic model of Mycobacterium bovis transmission in a multi-host system uncovers the role of the unobserved reservoir.
• 
  Jan Huertas, Hans Robert Schöler, Vlad Cojocaru:
  Histone tails cooperate to control the breathing of genomic nucleosomes.
• 
  Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn A. Grüning, Jeremy Goecks:
  Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine.
• 
  Grace Wan Yu Ang, Clara S. Tang, Y. Audrey Hay, Sara Zannone, Ole Paulsen, Claudia Clopath:
  The functional role of sequentially neuromodulated synaptic plasticity in behavioural learning.
• 
  Manu Kalia, Hil G. E. Meijer, Stephan A. van Gils, Michel J. A. M. van Putten, Christine R. Rose:
  Ion dynamics at the energy-deprived tripartite synapse.
• 
  Diana Széliová, Jerneja Stor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha:
  Inclusion of maintenance energy improves the intracellular flux predictions of CHO.
• 
  Jonathan Cannon:
  Expectancy-based rhythmic entrainment as continuous Bayesian inference.
• 
  Max F. Burg, Santiago A. Cadena, George H. Denfield, Edgar Y. Walker, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker:
  Learning divisive normalization in primary visual cortex.
• 
  Chad R. Wells, Youfang Cao, David P. Durham, Siddappa N. Byrareddy, Aftab A. Ansari, Nancy H. Ruddle, Jeffrey P. Townsend, Alison P. Galvani, Alan S. Perelson:
  Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy.
• 
  Elena Camacho-Aguilar, Aryeh Warmflash, David A. Rand:
  Quantifying cell transitions in C. elegans with data-fitted landscape models.
• 
  Martina Prugger, Lukas Einkemmer, Samantha P. Beik, Perry T. Wasdin, Leonard A. Harris, Carlos F. Lopez:
  Unsupervised logic-based mechanism inference for network-driven biological processes.
• 
  Simon J. D. Cox, Alejandra N. González-Beltrán, Barbara Magagna, Maria-Cristina V. Marinescu:
  Ten simple rules for making a vocabulary FAIR.
• 
  Misaki Sakashita, Shintaro Yamasaki, Kentaro Yaji, Atsushi Kawamoto, Shigeru Kondo:
  Three-dimensional topology optimization model to simulate the external shapes of bone.
• 
  Wenwen Min, Tsung-Hui Chang, Shihua Zhang, Xiang Wan:
  TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers.
• 
  Bruno Golosio, Chiara De Luca, Cristiano Capone, Elena Pastorelli, Giovanni Stegel, Gianmarco Tiddia, Giulia De Bonis, Pier Stanislao Paolucci:
  Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep.
• 
  Alexander Y. Zhigalov, Katharina Duecker, Ole Jensen:
  The visual cortex produces gamma band echo in response to broadband visual flicker.
• 
  Bastien Berret, Adrien Conessa, Nicolas Schweighofer, Etienne Burdet:
  Stochastic optimal feedforward-feedback control determines timing and variability of arm movements with or without vision.
• 
  Zhong Li, Kaiyancheng Jiang, Shengwei Qin, Yijun Zhong, Arne Elofsson:
  GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction.
• 
  Gonca Erdemci-Tandogan, M. Lisa Manning:
  Effect of cellular rearrangement time delays on the rheology of vertex models for confluent tissues.
• 
  Haokun Yuan, Sarah C. Kramer, Eric H. Y. Lau, Benjamin J. Cowling, Wan Yang:
  Modeling influenza seasonality in the tropics and subtropics.
• 
  Adarsh Chitradurga Achutha, Herbert Peremans, Uwe Firzlaff, Dieter Vanderelst:
  Efficient encoding of spectrotemporal information for bat echolocation.
• 
  Mitchell E. Gronowitz, Adam Liu, Qiang Qiu, C. Ron Yu, Thomas A. Cleland:
  A physicochemical model of odor sampling.
• 
  Edward M. Hill, Benjamin D. Atkins, Matt J. Keeling, Louise Dyson, Michael J. Tildesley:
  A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2.
• 
  Pengcheng Zeng, Zhixiang Lin:
  coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data.
• 
  Andreas Deutsch, Josué Manik Nava-Sedeño, Simon Syga, Haralampos Hatzikirou:
  BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration.
• 
  Simran K. Sandhu, Christopher D. Bayliss, Andrew Morozov:
  How does feedback from phage infections influence the evolution of phase variation in Campylobacter?
• 
  Takeru Kameda, Katsura Asano, Yuichi Togashi:
  Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex.
• 
  Salvatore Alaimo, Rosaria Valentina Rapicavoli, Gioacchino P. Marceca, Alessandro La Ferlita, Oksana B. Serebrennikova, Philip N. Tsichlis, Bud Mishra, Alfredo Pulvirenti, Alfredo Ferro:
  PHENSIM: Phenotype Simulator.
• 
  He A. Xu, Alireza Modirshanechi, Marco P. Lehmann, Wulfram Gerstner, Michael H. Herzog:
  Novelty is not surprise: Human exploratory and adaptive behavior in sequential decision-making.
• 
  Ross J. Burton, Raya Ahmed, Simone M. Cuff, Sarah Baker, Andreas Artemiou, Matthias Eberl:
  CytoPy: An autonomous cytometry analysis framework.
• 
  Catherine M. Byrne, Christine Johnston, Jackson Orem, Fred Okuku, Meei-Li Huang, Habibur Rahman, Anna Wald, Lawrence Corey, Joshua T. Schiffer, Corey Casper, Daniel Coombs, Soren Gantt:
  Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads.
• 
  Anamika Agrawal, Elena F. Koslover:
  Optimizing mitochondrial maintenance in extended neuronal projections.
• 
  Yuchi Qiu, Lianna Fung, Thomas F. Schilling, Qing Nie:
  Multiple morphogens and rapid elongation promote segmental patterning during development.
• 
  Jingwen Ren, Mark J. P. Chaisson:
  lra: A long read aligner for sequences and contigs.
• 
  Julian Hartmann, Martin Zacharias:
  Mechanism of collagen folding propagation studied by Molecular Dynamics simulations.
• 
  Felix Barber, Jiseon Min, Andrew W. Murray, Ariel Amir:
  Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells.
• 
  Sahar Jafari Nivlouei, Madjid Soltani, João Carvalho, Rui Travasso, Mohammad Reza Salimpour, Ebrahim Shirani:
  Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy.
• 
  H. Robert Frost:
  Analyzing cancer gene expression data through the lens of normal tissue-specificity.
• 
  Andreas Kopf, Vincent Fortuin, Vignesh Ram Somnath, Manfred Claassen:
  Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data.
• 
  Vincent Prost, Stéphane Gazut, Thomas Brüls:
  A zero inflated log-normal model for inference of sparse microbial association networks.
• 
  Sonja Langthaler, Theresa Rienmüller, Susanne Scheruebel, Brigitte Pelzmann, Niroj Shrestha, Klaus Zorn-Pauly, Wolfgang Schreibmayer, Andrew Koff, Christian Baumgartner:
  A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma.
• 
  Pavlos Stephanos Bekiaris, Steffen Klamt:
  Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
• 
  John T. Nardini, Bernadette J. Stolz, Kevin B. Flores, Heather A. Harrington, Helen M. Byrne:
  Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis.
• 
  Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann:
  Identifying the combinatorial control of signal-dependent transcription factors.
• 
  Rachael Miller Neilan, Gabrielle Majetic, Mauricio Gil-Silva, Anisha P. Adke, Yarimar Carrasquillo, Benedict J. Kolber:
  Agent-based modeling of the central amygdala and pain using cell-type specific physiological parameters.
• 
  Diego del Alamo, Kevin L. Jagessar, Jens Meiler, Hassane S. Mchaourab:
  Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.
• 
  Necati Esener, Alexandre Maciel-Guerra, Katharina Giebel, Daniel Lea, Martin J. Green, Andrew J. Bradley, Tania Dottorini:
  Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis.
• 
  Natalie Ness, Simon R. Schultz:
  A computational grid-to-place-cell transformation model indicates a synaptic driver of place cell impairment in early-stage Alzheimer's Disease.
• 
  Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin:
  SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data.
• 
  Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti:
  De novo mutational signature discovery in tumor genomes using SparseSignatures.
• 
  Massimo Cavallaro, Haseeb Moiz, Matt J. Keeling, Noel D. McCarthy:
  Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values.
• 
  Billy J. Gardner, A. Marm Kilpatrick:
  Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics.
• 
  Cemal Erdem, Adrian V. Lee, D. Lansing Taylor, Timothy R. Lezon:
  Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.
• 
  Adam C. Richie-Halford, Jason D. Yeatman, Noah Simon, Ariel Rokem:
  Multidimensional analysis and detection of informative features in human brain white matter.
• 
  Namit Gaur, Xiao-Yan Qi, David Benoist, Olivier Bernus, Ruben Coronel, Stanley Nattel, Edward J. Vigmond:
  A computational model of pig ventricular cardiomyocyte electrophysiology and calcium handling: Translation from pig to human electrophysiology.
• 
  Satoshi Nishida, Antoine Blanc, Naoya Maeda, Masataka Kado, Shinji Nishimoto:
  Behavioral correlates of cortical semantic representations modeled by word vectors.
• 
  Jumpei F. Yamagishi, Nen Saito, Kunihiko Kaneko:
  Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem.
• 
  Steffen S. Docken, Colleen E. Clancy, Timothy J. Lewis:
  Rate-dependent effects of lidocaine on cardiac dynamics: Development and analysis of a low-dimensional drug-channel interaction model.
• 
  Yuanhong Tang, Lingling An, Quan Wang, Jian K. Liu:
  Regulating synchronous oscillations of cerebellar granule cells by different types of inhibition.
• 
  Jonathan P. Alberding, Timothy W. Secomb:
  Simulation of angiogenesis in three dimensions: Application to cerebral cortex.
• 
  Silvia Ambrós, Neus Gómez-Muñoz, Silvia Giménez-Santamarina, Javier Sánchez-Vicente, Josep Navarro-López, Fernando Martínez, José-Antonio Daròs, Guillermo Rodrigo:
  Molecular signatures of silencing suppression degeneracy from a complex RNA virus.

Correction

• 
  PLOS Computational Biology Staff:
  Correction: A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation.

Volume 17, Number 7, July 2021

Editorials

• 
  Michael John Bartlett, Feyza Nur Arslan, Adriana Bankston, Sarvenaz Sarabipour:
  Ten simple rules to improve academic work-life balance.
• 
  Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna M. Ritz:
  Ten simple rules for attending your first conference.
• 
  Maya L. Gosztyla, Lydia Kwong, Naomi A. Murray, Claire E. Williams, Nicholas Behnke, Porsia Curry, Kevin D. Corbett, Karen N. DSouza, Julia Gala de Pablo, Joanina Gicobi, Monica Javidnia, Navina Lotay, Sidney Madison Prescott, James P. Quinn, Zeena M. G. Rivera, Markia A. Smith, Karen T. Y. Tang, Aarya Venkat, Megan A. Yamoah:
  Responses to 10 common criticisms of anti-racism action in STEMM.

Research Articles

• 
  Jennifer Crodelle, David W. McLaughlin:
  Modeling the role of gap junctions between excitatory neurons in the developing visual cortex.
• 
  Marte J. Sætra, Gaute T. Einevoll, Geir Halnes:
  An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain.
• 
  Fillipe Georgiou, Jérôme Buhl, J. Edward F. Green, Bishnu P. Lamichhane, Ngamta Thamwattana:
  Modelling locust foraging: How and why food affects group formation.
• 
  Liyu Xia, Sarah L. Master, Maria K. Eckstein, Beth Baribault, Ronald E. Dahl, Linda Wilbrecht, Anne Gabrielle Eva Collins:
  Modeling changes in probabilistic reinforcement learning during adolescence.
• 
  Samuel A. Ramirez, Michael Pablo, Sean Burk, Daniel J. Lew, Timothy C. Elston:
  A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement.
• 
  Alexander O. B. Whitlock, Jonathan J. Juliano, Nicole Mideo:
  Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread.
• 
  Ilan N. Rubin, Iaroslav Ispolatov, Michael Doebeli:
  Evolution to alternative levels of stable diversity leaves areas of niche space unexplored.
• 
  Felipe A. Torres, Patricio Orio, María-José Escobar:
  Selection of stimulus parameters for enhancing slow wave sleep events with a neural-field theory thalamocortical model.
• 
  Christophe Noroy, Damien F. Meyer:
  The super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis.
• 
  Debojyoti Biswas, Peter N. Devreotes, Pablo A. Iglesias:
  Three-dimensional stochastic simulation of chemoattractant-mediated excitability in cells.
• 
  Mikael Ljungholm, Dan-E. Nilsson:
  Modelling the visual world of a velvet worm.
• 
  Dori M. Grijseels, Kira Shaw, Caswell Barry, Catherine N. Hall:
  Choice of method of place cell classification determines the population of cells identified.
• 
  Mandhri Abeysooriya, Megan Soria, Mary Sravya Kasu, Mark Ziemann:
  Gene name errors: Lessons not learned.
• 
  Arghya Datta, Noah R. Flynn, Dustyn A. Barnette, Keith F. Woeltje, Grover P. Miller, S. Joshua Swamidass:
  Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort.
• 
  Ioanna Miliou, Xinyue Xiong, Salvatore Rinzivillo, Qian Zhang, Giulio Rossetti, Fosca Giannotti, Dino Pedreschi, Alessandro Vespignani:
  Predicting seasonal influenza using supermarket retail records.
• 
  Andrés Flores Valle, Pedro J. Gonçalves, Johannes D. Seelig:
  Integration of sleep homeostasis and navigation in Drosophila.
• 
  Andrea Parisi, Samuel P. C. Brand, Joe Hilton, Rabia Aziza, Matt J. Keeling, D. James Nokes:
  Spatially resolved simulations of the spread of COVID-19 in three European countries.
• 
  Nicholas Menghi, Kemal Kacar, Will D. Penny:
  Multitask learning over shared subspaces.
• 
  Gustav Markkula, Zeynep Uludag, Richard McGilchrist Wilkie, Jac Billington:
  Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection.
• 
  Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Alex R. Cook, Mark Jit:
  Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.
• 
  Sandya Subramanian, Patrick L. Purdon, Riccardo Barbieri, Emery N. Brown:
  Elementary integrate-and-fire process underlies pulse amplitudes in Electrodermal activity.
• 
  Asaminew H. Aytenfisu, Daniel Deredge, Erik H. Klontz, Jonathan Du, Eric J. Sundberg, Alexander D. MacKerell Jr.:
  Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.
• 
  Jorin Diemer, Jens Hahn, Björn Goldenbogen, Karin Müller, Edda Klipp:
  Sperm migration in the genital tract - In silico experiments identify key factors for reproductive success.
• 
  Justin D. Silverman, Rachael J. Bloom, Sharon Jiang, Heather K. Durand, Eric Dallow, Sayan Mukherjee, Lawrence A. David:
  Measuring and mitigating PCR bias in microbiota datasets.
• 
  Michael R. Lindstrom, Manuel B. Chavez, Elijah A. Gross-Sable, Eric Y. Hayden, David B. Teplow:
  From reaction kinetics to dementia: A simple dimer model of Alzheimer's disease etiology.
• 
  Benoit Duchet, Filippo Ghezzi, Gihan Weerasinghe, Gerd Tinkhauser, Andrea A. Kühn, Peter Brown, Christian Bick, Rafal Bogacz:
  Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson's disease.
• 
  Paul F. Tupper, Caroline Colijn:
  COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission.
• 
  Philip Cherian, Sandeep Krishna, Gautam I. Menon:
  Optimizing testing for COVID-19 in India.
• 
  Nono S. C. Merleau, Sophie Penisson, Philip J. Gerrish, Santiago F. Elena, Matteo Smerlak:
  Why are viral genomes so fragile? The bottleneck hypothesis.
• 
  Meysam Hashemi, Anirudh Nihalani Vattikonda, Viktor Sip, Sandra Diaz-Pier, Alexander Peyser, Huifang E. Wang, Maxime Guye, Fabrice Bartolomei, Michael Marmaduke Woodman, Viktor K. Jirsa:
  On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread.
• 
  Go Ashida, Daniel J. Tollin, Jutta Kretzberg:
  Robustness of neuronal tuning to binaural sound localization cues against age-related loss of inhibitory synaptic inputs.
• 
  Maciej Migdal, Dan Fu Ruan, William F. Forrest, Amir Horowitz, Christian Hammer:
  MiDAS - Meaningful Immunogenetic Data at Scale.
• 
  Alexis M. Thornton, Lishan Fang, April Lo, Maria McSharry, David Haan, Casey O'Brien, Alice H. Berger, Marios Giannakis, Angela N. Brooks:
  eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants.
• 
  Federico Mancinelli, Jonathan P. Roiser, Peter Dayan:
  Internality and the internalisation of failure: Evidence from a novel task.
• 
  Adrian J. Green, Martin J. Mohlenkamp, Jhuma Das, Meenal Chaudhari, Lisa Truong, Robyn L. Tanguay, David M. Reif:
  Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology.
• 
  Yonatan Sanz Perl, Carla Pallavicini, Ignacio Perez Ipiña, Athena Demertzi, Vincent Bonhomme, Charlotte Martial, Rajanikant Panda, Jitka Annen, Agustín Ibáñez, Morten L. Kringelbach, Gustavo Deco, Helmut Laufs, Jacobo D. Sitt, Steven Laureys, Enzo Tagliazucchi:
  Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness.
• 
  Liliana Angeles-Martinez, Vassily Hatzimanikatis:
  Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities.
• 
  Rachel Coy, Maxime Berg, James B. Phillips, Rebecca J. Shipley:
  Modelling-informed cell-seeded nerve repair construct designs for treating peripheral nerve injuries.
• 
  George Crowley, James Kim, Sophia Kwon, Rachel Lam, David J. Prezant, Mengling Liu, Anna Nolan:
  PEDF, a pleiotropic WTC-LI biomarker: Machine learning biomarker identification and validation.
• 
  Robert Hinch, William J. M. Probert, Anel Nurtay, Michelle Kendall, Chris Wymant, Matthew Hall, Katrina A. Lythgoe, Ana Bulas Cruz, Lele Zhao, Andrea Stewart, Luca Ferretti, Daniel Montero, James Warren, Nicole Mather, Matthew Abueg, Neo Wu, Olivier Legat, Katie Bentley, Thomas Mead, Kelvin Van-Vuuren, Dylan Feldner-Busztin, Tommaso Ristori, Anthony Finkelstein, David G. Bonsall, Lucie Abeler-Dörner, Christophe Fraser:
  OpenABM-Covid19 - An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.
• 
  Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik:
  The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins.
• 
  Pol Castellano-Escuder, Raúl González-Domínguez, Francesc Carmona-Pontaque, Cristina Andres-Lacueva, Alex Sánchez-Pla:
  POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis.
• 
  Cliff C. Kerr, Robyn M. Stuart, Dina Mistry, Romesh G. Abeysuriya, Katherine Rosenfeld, Gregory R. Hart, Rafael C. Núñez, Jamie A. Cohen, Prashanth Selvaraj, Brittany Hagedorn, Lauren George, Michal Jastrzebski, Amanda S. Izzo, Greer Fowler, Anna Palmér, Dominic Delport, Nick Scott, Sherrie L. Kelly, Caroline S. Bennette, Bradley G. Wagner, Stewart T. Chang, Assaf P. Oron, Edward A. Wenger, Jasmina Panovska-Griffiths, Michael Famulare, Daniel J. Klein:
  Covasim: An agent-based model of COVID-19 dynamics and interventions.
• 
  Marianyela Sabina Petrizzelli, Dominique de Vienne, Thibault Nidelet, Camille Noûs, Christine Dillmann:
  Data integration uncovers the metabolic bases of phenotypic variation in yeast.
• 
  Liliana Angeles-Martinez, Vassily Hatzimanikatis:
  The influence of the crowding assumptions in biofilm simulations.
• 
  Hamish Gibbs, Emily Nightingale, Yang Liu, James A. Cheshire, Leon Danon, Liam Smeeth, Carl A. B. Pearson, Chris Grundy, LSHTM CMMID COVID-19 Working Group, Adam J. Kucharski, Rosalind M. Eggo:
  Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19.
• 
  Lei Li, Zhen Gao, Yu-Tian Wang, Ming-Wen Zhang, Jian-Cheng Ni, Chun-Hou Zheng, Yansen Su:
  SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization.
• 
  Pedro L. Ferreira, Francisco C. Santos, Sérgio Pequito:
  Risk sensitivity and theory of mind in human coordination.
• 
  Francesco Trozzi, Feng Wang, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao:
  Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE.
• 
  Michael C. Holcomb, Guo-Jie Jason Gao, Mahsa Servati, Dylan Schneider, Presley K. McNeely, Jeffrey H. Thomas, Jerzy Blawzdziewicz:
  Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation.
• 
  Kelly Charniga, Zulma M. Cucunubá, Marcela Mercado, Franklyn Prieto, Martha Ospina, Pierre Nouvellet, Christl A. Donnelly:
  Spatial and temporal invasion dynamics of the 2014-2017 Zika and chikungunya epidemics in Colombia.
• 
  Zhaoqiang Wang, Yichen Ding, Sandro Satta, Mehrdad Roustaei, Peng Fei, Tzung K. Hsiai:
  A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development.
• 
  Simon P. Orozco, Scott T. Albert, Reza Shadmehr:
  Adaptive control of movement deceleration during saccades.
• 
  Hankyu Jang, Philip M. Polgreen, Alberto M. Segre, Sriram V. Pemmaraju:
  COVID-19 modeling and non-pharmaceutical interventions in an outpatient dialysis unit.
• 
  Ben G. Weinstein, Sarah J. Graves, Sergio Marconi, Aditya Singh, Alina Zare, Dylan Stewart, Stephanie A. Bohlman, Ethan P. White:
  A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.
• 
  Shirlee Wohl, John R. Giles, Justin Lessler:
  Sample size calculation for phylogenetic case linkage.
• 
  Vladimir Naumov, Evgeny Putin, Stefan Pushkov, Ekaterina Kozlova, Konstantin Romantsov, Alexander A. Kalashnikov, Fedor Galkin, Nina Tihonova, Anastasia Shneyderman, Egor Galkin, Arsenii Zinkevich, Stephanie M. Cope, Ramanathan Sethuraman, Tudor I. Oprea, Alexander T. Pearson, Savas Tay, Nishant Agrawal, Alexey Dubovenko, Quentin Vanhaelen, Ivan Ozerov, Alex Aliper, Evgeny Izumchenko, Alex Zhavoronkov:
  COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity.
• 
  Omer Yuval, Yael Iosilevskii, Anna Meledin, Benjamin Podbilewicz, Tom Shemesh:
  Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans.
• 
  Alban Bornet, Adrien Doerig, Michael H. Herzog, Gregory Francis, Erik Van der Burg:
  Shrinking Bouma's window: How to model crowding in dense displays.
• 
  Zhongneng Xu, Shuichi Asakawa:
  A model explaining mRNA level fluctuations based on activity demands and RNA age.
• 
  Marcio Gameiro, Tomás Gedeon, Shane Kepley, Konstantin Mischaikow:
  Rational design of complex phenotype via network models.
• 
  Vlada S. Rozova, Ayad G. Anwer, Anna E. Guller, Hamidreza Aboulkheyr Es, Zahra Khabir, Anastasiya I. Sokolova, Maxim U. Gavrilov, Ewa M. Goldys, Majid Ebrahimi Warkiani, Jean-Paul Thiery, Andrei V. Zvyagin:
  Machine learning reveals mesenchymal breast carcinoma cell adaptation in response to matrix stiffness.
• 
  Gowthami Somepalli, Sarthak Sahoo, Arashdeep Singh, Sridhar Hannenhalli:
  Prioritizing and characterizing functionally relevant genes across human tissues.
• 
  Samantha P. Sherrill, Nicholas M. Timme, John M. Beggs, Ehren L. Newman:
  Partial information decomposition reveals that synergistic neural integration is greater downstream of recurrent information flow in organotypic cortical cultures.
• 
  Tessa Lloyd, Pia Steigler, Cheleka A. M. Mpande, Virginie Rozot, Boitumelo Mosito, Constance Schreuder, Timothy D. Reid, Mark Hatherill, Thomas J. Scriba, Francesca Little, Elisa Nemes, ACS Study Team:
  Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection.
• 
  Nadim A. A. Atiya, Quentin J. M. Huys, Raymond J. Dolan, Stephen M. Fleming:
  Explaining distortions in metacognition with an attractor network model of decision uncertainty.
• 
  Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
  ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.
• 
  Jonathan W. Cody, Amy L. Ellis-Connell, Shelby L. O'Connor, Elsje Pienaar:
  Mathematical modeling of N-803 treatment in SIV-infected non-human primates.
• 
  Jessica L. Kingsley, James R. Costello, Natarajan Raghunand, Katarzyna A. Rejniak:
  Bridging cell-scale simulations and radiologic images to explain short-time intratumoral oxygen fluctuations.
• 
  Laurens H. J. Krah, Rutger Hermsen:
  The effect of natural selection on the propagation of protein expression noise to bacterial growth.
• 
  Tenglong Li, Laura F. White:
  Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic.
• 
  Bernard Cazelles, Clara Champagne, Benjamin Nguyen-Van-Yen, Catherine Comiskey, Elisabeta Vergu, Benjamin Roche:
  A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic.
• 
  Moritz Möller, Jan Grohn, Sanjay G. Manohar, Rafal Bogacz:
  An association between prediction errors and risk-seeking: Theory and behavioral evidence.
• 
  Davin Lunz, Grégory Batt, Jakob Ruess, J. Frédéric Bonnans:
  Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.
• 
  Toru Niina, Yasuhiro Matsunaga, Shoji Takada:
  Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.
• 
  Shirit Dvorkin, Reut Levi, Yoram Louzoun:
  Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors.
• 
  Kaiyi Zhu, Lingyi Cai, Chenqian Cui, Juan R. de los Toyos, Dimitris Anastassiou:
  Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts.
• 
  Yuansheng Liu, Jinyan Li:
  Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.
• 
  James Turtle, Pete Riley, Michal Ben-Nun, Steven Riley:
  Accurate influenza forecasts using type-specific incidence data for small geographic units.
• 
  Leon Avery, Brian P. Ingalls, Catherine I. Dumur, Alexander Artyukhin:
  A Keller-Segel model for C elegans L1 aggregation.
• 
  Dheeraj Prakaash, Graham P. Cook, Oreste Acuto, Antreas C. Kalli:
  Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region.
• 
  Pedro de Atauri, Míriam Tarrado-Castellarnau, Josep Tarragó-Celada, Carles Foguet, Effrosyni Karakitsou, Josep J. Centelles, Marta Cascante:
  Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations.
• 
  Yihao Yang, Howard Gritton, Martin Sarter, Sara J. Aton, Victoria Booth, Michal Zochowski:
  Theta-gamma coupling emerges from spatially heterogeneous cholinergic neuromodulation.
• 
  Louisiane Lemaire, Mathieu Desroches, Martin Krupa, Lara Pizzamiglio, Paolo Scalmani, Massimo Mantegazza:
  Modeling NaV1.1/SCN1A sodium channel mutations in a microcircuit with realistic ion concentration dynamics suggests differential GABAergic mechanisms leading to hyperexcitability in epilepsy and hemiplegic migraine.
• 
  Maximilian Hanussek, Felix Bartusch, Jens Krüger:
  Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources.
• 
  Matthias Niemann, Nils Lachmann, Kirsten Geneugelijk, Eric Spierings:
  Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching.
• 
  Saurabh Modi, Supravat Dey, Abhyudai Singh:
  Noise suppression in stochastic genetic circuits using PID controllers.
• 
  Giovanni B. Brandani, Cheng Tan, Shoji Takada:
  The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
• 
  Justin Torok, Pedro D. Maia, Parul Verma, Christopher Mezias, Ashish Raj:
  Emergence of directional bias in tau deposition from axonal transport dynamics.
• 
  Thibault Dubois, Cristian Pasquaretta, Andrew B. Barron, Jacques Gautrais, Mathieu Lihoreau:
  A model of resource partitioning between foraging bees based on learning.
• 
  Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa:
  Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy.

Volume 17, Number 8, August 2021

Editorials

• 
  Frances Hooley, Peter J. Freeman, Angela C. Davies:
  Ten simple rules for teaching applied programming in an authentic and immersive online environment.
• 
  Benjamin L. Moore, Patricia Carvajal López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, Nicola J. Mulder:
  Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.
• 
  Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. A. Evelo, Alexander R. Pico:
  Ten simple rules for creating reusable pathway models for computational analysis and visualization.
• 
  Sarah A. Gagliano Taliun, David M. Evans:
  Ten simple rules for conducting a mendelian randomization study.
• 
  Andrea I. Luppi, Charlotte Coco Newton, Lynde Folsom, Elisa Galliano, Rafael Romero-Garcia:
  Ten simple rules for aspiring graduate students.
• 
  Danny Haelewaters, Tina A. Hofmann, Adriana L. Romero-Olivares:
  Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South.

Education

• 
  Jamie J. Alnasir:
  Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster.

Review

• 
  Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao:
  Review of machine learning methods for RNA secondary structure prediction.

Research Articles

• 
  Marc Durand:
  Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime.
• 
  Leif Zinn-Brooks, Marcus L. Roper:
  Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells.
• 
  Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes:
  PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
• 
  Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel:
  Using machine learning and big data to explore the drug resistance landscape in HIV.
• 
  Antonio de Candia, Alessandro Sarracino, Ilenia Apicella, Lucilla de Arcangelis:
  Critical behaviour of the stochastic Wilson-Cowan model.
• 
  Wesley M. Marin, Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, Jill A. Hollenbach:
  High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.
• 
  Kathryn E. Mangold, Wei Wang, Eric K. Johnson, Druv Bhagavan, Jonathan D. Moreno, Jeanne M. Nerbonne, Jonathan R. Silva:
  Identification of structures for ion channel kinetic models.
• 
  Anton V. Chizhov, Lyle J. Graham:
  A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex.
• 
  Jolan De Boeck, Jan Rombouts, Lendert Gelens:
  A modular approach for modeling the cell cycle based on functional response curves.
• 
  Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan:
  Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism.
• 
  John R. Giles, Derek A. T. Cummings, Bryan T. Grenfell, Andrew J. Tatem, Elisabeth Zu Erbach-Schoenberg, C. Jessica E. Metcalf, Amy Wesolowski:
  Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread.
• 
  Zhi-Wei Li, Wei Ji Ma:
  An uncertainty-based model of the effects of fixation on choice.
• 
  Alison I. Weber, Thomas L. Daniel, Bingni W. Brunton:
  Wing structure and neural encoding jointly determine sensing strategies in insect flight.
• 
  Alex D. Bird, Peter Jedlicka, Hermann Cuntz:
  Dendritic normalisation improves learning in sparsely connected artificial neural networks.
• 
  Linnie Jiang, Ashok Litwin-Kumar:
  Models of heterogeneous dopamine signaling in an insect learning and memory center.
• 
  Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomás Helikar:
  A multi-approach and multi-scale platform to model CD4+ T cells responding to infections.
• 
  Dean A. Pospisil, Wyeth Bair:
  The unbiased estimation of the fraction of variance explained by a model.
• 
  Yanshuai Tu, Duyan Ta, Zhonglin Lu, Yalin Wang:
  Topology-preserving smoothing of retinotopic maps.
• 
  Ran Duan, Lin Gao, Yong Gao, Yuxuan Hu, Han Xu, Mingfeng Huang, Kuo Song, Hongda Wang, Yongqiang Dong, Chaoqun Jiang, Chenxing Zhang, Songwei Jia:
  Evaluation and comparison of multi-omics data integration methods for cancer subtyping.
• 
  Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher:
  Relating simulation studies by provenance - Developing a family of Wnt signaling models.
• 
  Karoline Horgmo Jæger, Andrew G. Edwards, Wayne R. Giles, Aslak Tveito:
  A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes.
• 
  Ritabrata Dutta, Susana N. Gomes, Dante Kalise, Lorenzo Pacchiardi:
  Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic.
• 
  Daisuke Imoto, Nen Saito, Akihiko Nakajima, Gen Honda, Motohiko Ishida, Toyoko Sugita, Sayaka Ishihara, Koko Katagiri, Chika Okimura, Yoshiaki Iwadate, Satoshi Sawai:
  Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space.
• 
  Adrián Aguirre-Tamaral, Isabel Guerrero:
  Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling.
• 
  Frances L. Heredia, Abiel Roche-Lima, Elsie I. Parés-Matos:
  A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers.
• 
  Zhonghe Shao, Ting Wang, Meng Zhang, Zhou Jiang, Shuiping Huang, Ping Zeng:
  IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA.
• 
  Alex D. Reyes:
  Mathematical framework for place coding in the auditory system.
• 
  Luke Tait, Marinho A. Lopes, George Stothart, John Baker, Nina Kazanina, Jiaxiang Zhang, Marc Goodfellow:
  A large-scale brain network mechanism for increased seizure propensity in Alzheimer's disease.
• 
  Jiayuan Zhang, Hannah Roberts, David S. C. Flores, Antony J. Cutler, Andrew C. Brown, Justin P. Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C. Knight, John A. Todd, Gavin Band:
  Using de novo assembly to identify structural variation of eight complex immune system gene regions.
• 
  René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon:
  Computational identification and experimental characterization of preferred downstream positions in human core promoters.
• 
  Paul Lebel, Rebekah Dial, Venkata Naga Pranathi Vemuri, Valentina Garcia, Joseph L. DeRisi, Rafael Gómez-Sjöberg:
  Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining.
• 
  Fentaw Abegaz, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Melany Rios-Morales, Dirk-Jan Reijngoud, Ernst C. Wit, Barbara M. Bakker:
  Bistability in fatty-acid oxidation resulting from substrate inhibition.
• 
  Lukas Ramlow, Benjamin Lindner:
  Interspike interval correlations in neuron models with adaptation and correlated noise.
• 
  Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaïs Baudot:
  A multi-objective genetic algorithm to find active modules in multiplex biological networks.
• 
  Simon Mauras, Vincent Cohen-Addad, Guillaume Duboc, Max Dupré la Tour, Paolo Frasca, Claire Mathieu, Lulla Opatowski, Laurent Viennot:
  Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting.
• 
  Yangqing Deng, Wei Pan:
  Model checking via testing for direct effects in Mendelian Randomization and transcriptome-wide association studies.
• 
  Kshitij Dwivedi, Michael F. Bonner, Radoslaw Martin Cichy, Gemma Roig:
  Unveiling functions of the visual cortex using task-specific deep neural networks.
• 
  Daniel Schindler, Ted Moldenhawer, Maike Stange, Valentino Lepro, Carsten Beta, Matthias Holschneider, Wilhelm Huisinga:
  Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows.
• 
  Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gómez-Sjöberg:
  Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations.
• 
  Xiaochuan Zhao, Germán Plata, Purushottam D. Dixit:
  SiGMoiD: A super-statistical generative model for binary data.
• 
  Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson:
  The evolutionary history of topological variations in the CPA/AT transporters.
• 
  Indie C. Garwood, Sourish Chakravarty, Jacob A. Donoghue, Meredith Mahnke, Pegah Kahali, Shubham Chamadia, Oluwaseun Akeju, Earl K. Miller, Emery N. Brown:
  A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms.
• 
  Gihan Weerasinghe, Benoit Duchet, Christian Bick, Rafal Bogacz:
  Optimal closed-loop deep brain stimulation using multiple independently controlled contacts.
• 
  Jennifer Hammelman, David K. Gifford:
  Discovering differential genome sequence activity with interpretable and efficient deep learning.
• 
  Tomasz Konopka, Sandra Ng, Damian Smedley:
  Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base.
• 
  Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, Jian Peng:
  Deep geometric representations for modeling effects of mutations on protein-protein binding affinity.
• 
  Natália Teruel, Olivier Mailhot, Rafael J. Najmanovich:
  Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.
• 
  Jason A. Hendry, Dominic Kwiatkowski, Gil McVean:
  Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria.
• 
  Prerna Tewari, Eugene Kashdan, Cathal Walsh, Cara M. Martin, Andrew C. Parnell, John J. O'Leary:
  Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling.
• 
  Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks:
  miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data.
• 
  Tatsuya Haga, Tomoki Fukai:
  Multiscale representations of community structures in attractor neural networks.
• 
  Natalie Schaworonkow, Bradley Voytek:
  Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters.
• 
  Lubna Pinky, Crystal W. Burke, Charles J. Russell, Amber M. Smith:
  Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection.
• 
  Jason Liu, Daniel J. Spakowicz, Garrett I. Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M. Nally, Julien S. Baker, Lisa M. Fucito, Stuart A. Weinzimer, Andrew V. Papachristos, Mark Gerstein:
  Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions.
• 
  Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis:
  ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
• 
  Sam R. Hill, Reidun Twarock, Eric C. Dykeman:
  The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus.
• 
  Anshul Saini, James M. Gallo:
  Epigenetic instability may alter cell state transitions and anticancer drug resistance.
• 
  Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphaël Mourad:
  DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions.
• 
  Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber:
  A probabilistic model for the ultradian timing of REM sleep in mice.
• 
  Sharon Guerstein, Victoria Romeo-Aznar, Ma'ayan Dekel, Oren Miron, Nadav Davidovitch, Rami Puzis, Shai Pilosof:
  The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes.
• 
  Akshay Jagatap, Simran Purokayastha, Hritik Jain, Sridharan Devarajan:
  Neurally-constrained modeling of human gaze strategies in a change blindness task.
• 
  Simon M. Lichtinger, Adiran Garaizar, Rosana Collepardo-Guevara, Aleks Reinhardt:
  Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence.
• 
  Javier S. Utgés, Maxim I. Tsenkov, Noah J. M. Dietrich, Stuart A. MacGowan, Geoffrey J. Barton:
  Ankyrin repeats in context with human population variation.
• 
  Tyler Cassidy, Daniel Nichol, Mark Robertson-Tessi, Morgan Craig, Alexander R. A. Anderson:
  The role of memory in non-genetic inheritance and its impact on cancer treatment resistance.
• 
  Shenghao Yang, Priyabrata Senapati, Di Wang, Chris T. Bauch, Kimon Fountoulakis:
  Targeted pandemic containment through identifying local contact network bottlenecks.
• 
  Kenny F. Chou, Kamal Sen:
  AIM: A network model of attention in auditory cortex.

Corrections

• 
  PLOS Computational Biology Staff:
  Correction: Bayesian inference and comparison of stochastic transcription elongation models.
• 
  David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadoeuf, Emmanuel Jacquot, Gaël Thébaud:
  Correction: Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape.
• 
  David J. Albers, Matthew E. Levine, Bruce J. Gluckman, Henry N. Ginsberg, George Hripcsak, Lena Mamykina:
  Correction: Personalized glucose forecasting for type 2 diabetes using data assimilation.
• 
  André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabian Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher, Benjamin M. Friedrich:
  Correction: Quantification of nematic cell polarity in three-dimensional tissues.

Volume 17, Number 9, September 2021

Editorials

• 
  Suchinta Arif, Melanie Duc Bo Massey, Natalie Klinard, Julie Charbonneau, Loay Jabre, Ana Barbosa Martins, Danielle Gaitor, Rhiannon Kirton, Catalina Albury, Karma Nanglu:
  Ten simple rules for supporting historically underrepresented students in science.
• 
  Loïc Lannelongue, Jason Grealey, Alex Bateman, Michael Inouye:
  Ten simple rules to make your computing more environmentally sustainable.
• 
  Loay Jabre, Catherine Bannon, J. Scott P. McCain, Yana Eglit:
  Ten simple rules for choosing a PhD supervisor.
• 
  Michelle Leonard, Suzanne Stapleton, Perry Collins, Terry Kit Selfe, Tara Tobin Cataldo:
  Ten simple rules for avoiding predatory publishing scams.
• 
  Kevin A. Janes:
  Ten simple rules for being a faculty advocate of first-year graduate students.

Research Articles

• 
  Daril E. Brown II, Jairo I. Chavez, Derek H. Nguyen, Adam Kadwory, Bradley Voytek, Ezequiel M. Arneodo, Timothy Q. Gentner, Vikash Gilja:
  Local field potentials in a pre-motor region predict learned vocal sequences.
• 
  Susana Posada-Céspedes, Gert van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D. Kouyos, Huldrych F. Günthard, Niko Beerenwinkel:
  Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C.
• 
  Charles-Elie Rabier, Vincent Berry, Marnus Stoltz, João D. Santos, Wensheng Wang, Jean-Christophe Glaszmann, Fabio Pardi, Céline Scornavacca:
  On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.
• 
  Milad Ghomlaghi, Guang Yang, Sung-Young Shin, David E. James, Lan K. Nguyen:
  Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1.
• 
  Jiayin Hong, Julius Palme, Bo Hua, Michael Springer:
  Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation.
• 
  Kai J. Miller, Klaus-Robert Müller, Dora Hermes:
  Basis profile curve identification to understand electrical stimulation effects in human brain networks.
• 
  Andreas Haahr Larsen, Lilya Tata, Laura H. John, Mark S. P. Sansom:
  Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations.
• 
  Kwang Il Ryom, Vezha Boboeva, Oleksandra Soldatkina, Alessandro Treves:
  Latching dynamics as a basis for short-term recall.
• 
  Pablo Galaz-Davison, Ernesto A. Román, César A. Ramírez-Sarmiento:
  The N-terminal domain of RfaH plays an active role in protein fold-switching.
• 
  Nienke E. R. van Bueren, Thomas L. Reed, Vu Nguyen, James G. Sheffield, Sanne H. G. van der Ven, Michael A. Osborne, Evelyn H. Kroesbergen, Roi Cohen Kadosh:
  Personalized brain stimulation for effective neurointervention across participants.
• 
  Gil Jorge Barros Henriques, Simon van Vliet, Michael Doebeli:
  Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities.
• 
  Siyuan Ma, Boyu Ren, Himel Mallick, Yo Sup Moon, Emma H. Schwager, Sagun Maharjan, Timothy L. Tickle, Yiren Lu, Rachel N. Carmody, Eric A. Franzosa, Lucas Janson, Curtis Huttenhower:
  A statistical model for describing and simulating microbial community profiles.
• 
  Joyneel Misra, Sriniwas Govinda Surampudi, Manasij Venkatesh, Chirag Limbachia, Joseph F. JáJá, Luiz Pessoa:
  Learning brain dynamics for decoding and predicting individual differences.
• 
  Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Elodie Renvoisé, Jukka Jernvall:
  Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.
• 
  Thomas K. F. Wong, Teng Li, Louis Ranjard, Steven H. Wu, Jeet Sukumaran, Allen G. Rodrigo:
  An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.
• 
  Magali Tournus, Miguel Escobedo, Wei-Feng Xue, Marie Doumic:
  Insights into the dynamic trajectories of protein filament division revealed by numerical investigation into the mathematical model of pure fragmentation.
• 
  Spencer L. Nystrom, Daniel J. McKay:
  Memes: A motif analysis environment in R using tools from the MEME Suite.
• 
  Nikitas Angeletos Chrysaitis, Renaud Jardri, Sophie Denève, Peggy Seriès:
  No increased circular inference in adults with high levels of autistic traits or autism.
• 
  John Ksander, Donald B. Katz, Paul Miller:
  A model of naturalistic decision making in preference tests.
• 
  Jack B. Maguire, Daniele Grattarola, Vikram Khipple Mulligan, Eugene Klyshko, Hans Melo:
  XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers.
• 
  Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel P. J. Lai, Jacob G. Bundy, Fabien Jourdan, Timothy M. D. Ebbels:
  Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis.
• 
  Michelle F. Craft, Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly:
  Differences in olfactory bulb mitral cell spiking with ortho- and retronasal stimulation revealed by data-driven models.
• 
  David Meder, Finn Rabe, Tobias Morville, Kristoffer H. Madsen, Magnus T. Koudahl, Raymond J. Dolan, Hartwig R. Siebner, Oliver J. Hulme:
  Ergodicity-breaking reveals time optimal decision making in humans.
• 
  Brian Hu, Marina E. Garrett, Peter A. Groblewski, Douglas R. Ollerenshaw, Jiaqi Shang, Kate Roll, Sahar Manavi, Christof Koch, Shawn R. Olsen, Stefan Mihalas:
  Adaptation supports short-term memory in a visual change detection task.
• 
  Lara Goscé, Gerard J. Abou Jaoude, David Jacob Kedziora, Clemens Benedikt, Azfar Hussain, Sarah Jarvis, Alena Skrahina, Dzmitry Klimuk, Henadz Hurevich, Feng Zhao, Nicole Fraser-Hurt, Nejma Cheikh, Marelize Gorgens, David J. Wilson, Romesh G. Abeysuriya, Rowan Martin-Hughes, Sherrie L. Kelly, Anna Roberts, Robyn M. Stuart, Tom Palmer, Jasmina Panovska-Griffiths, Cliff C. Kerr, David P. Wilson, Hassan Haghparast-Bidgoli, Jolene Skordis, Ibrahim Abubakar:
  Optima TB: A tool to help optimally allocate tuberculosis spending.
• 
  Eric Behle, Adélaïde Raguin:
  Stochastic model of lignocellulosic material saccharification.
• 
  Eric W. Bridgeford, Shangsi Wang, Zeyi Wang, Ting Xu, R. Cameron Craddock, Jayanta Dey, Gregory Kiar, William R. Gray Roncal, Carlo Colantuoni, Christopher Douville, Stephanie Noble, Carey E. Priebe, Brian Caffo, Michael P. Milham, Xi-Nian Zuo, Joshua T. Vogelstein:
  Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics.
• 
  Eric D. Musselman, Jake E. Cariello, Warren M. Grill, Nicole A. Pelot:
  ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves.
• 
  Simon Bauer, Sebastián Contreras, Jonas Dehning, Matthias Linden, Emil Iftekhar, Sebastian B. Mohr, Alvaro Olivera-Nappa, Viola Priesemann:
  Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves.
• 
  Barbara Bravi, Vinod P. Balachandran, Benjamin D. Greenbaum, Aleksandra M. Walczak, Thierry Mora, Rémi Monasson, Simona Cocco:
  Probing T-cell response by sequence-based probabilistic modeling.
• 
  Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M. Switzer:
  MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
• 
  Michael Pickles, Anne Cori, William J. M. Probert, Rafael Sauter, Robert Hinch, Sarah Fidler, Helen Ayles, Peter Bock, Deborah Donnell, Ethan Wilson, Estelle Piwowar-Manning, Sian Floyd, Richard J. Hayes, Christophe Fraser, HPTN 071 (PopART) Study Team:
  PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial.
• 
  Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan:
  Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.
• 
  Suraj Kannan, Michael Farid, Brian L. Lin, Matthew Miyamoto, Chulan Kwon:
  Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level.
• 
  Ilario De Toma, Cesar Sierra, Mara Dierssen:
  Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome.
• 
  Marisabel Rodriguez Messan, Osman N. Yogurtçu, Joseph R. McGill, Ujwani Nukala, Zuben E. Sauna, Hong Yang:
  Mathematical model of a personalized neoantigen cancer vaccine and the human immune system.
• 
  Guojun Yu, Yingru Wu, Zhi Duan, Catherine Tang, Haipeng Xing, Matthew D. Scharff, Thomas MacCarthy:
  A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes.
• 
  Gergely Palla, Péter Pollner, Judit Börcsök, András Major, Béla Molnár, István Csabai:
  Hierarchy and control of ageing-related methylation networks.
• 
  Erik Saberski, Antonia K. Bock, Rachel Goodridge, Vitul Agarwal, Tom Lorimer, Scott A. Rifkin, George Sugihara:
  Networks of Causal Linkage Between Eigenmodes Characterize Behavioral Dynamics of Caenorhabditis elegans.
• 
  Noelia Grande Gutiérrez, Mark S. Alber, Andrew M. Kahn, Jane C. Burns, Mathew Mathew, Brian W. McCrindle, Alison L. Marsden:
  Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease.
• 
  Fredrik Allenmark, Ahu Gokce, Thomas Geyer, Artyom Zinchenko, Hermann J. Müller, Zhuanghua Shi:
  Inter-trial effects in priming of pop-out: Comparison of computational updating models.
• 
  Mathieu Le Verge-Serandour, Hervé Turlier:
  A hydro-osmotic coarsening theory of biological cavity formation.
• 
  Sheng Zhang, Joan Ponce, Zhen Zhang, Guang Lin, George E. Karniadakis:
  An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City.
• 
  Sepideh Mazrouee, Susan J. Little, Joel O. Wertheim:
  Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.
• 
  Chenhao Li, Tamar Vered Av-Shalom, Jun Wei Gerald Tan, Junmei Samantha Kwah, Kern Rei Chng, Niranjan Nagarajan:
  BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data.
• 
  Lars Keuninckx, Axel Cleeremans:
  The color phi phenomenon: Not so special, after all?
• 
  Zhengqiao Zhao, Stephen Woloszynek, Felix Agbavor, Joshua Chang Mell, Bahrad A. Sokhansanj, Gail L. Rosen:
  Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.
• 
  Nicolò Gozzi, Paolo Bajardi, Nicola Perra:
  The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout.
• 
  Kris V. Parag:
  Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves.
• 
  Michael R. Smith, Rachel Chan, Maaz Khurram, Paul M. K. Gordon:
  Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing.
• 
  Thomas Beneteau, Christian Selinger, Mircea-Traian Sofonea, Samuel Alizon:
  Episome partitioning and symmetric cell divisions: Quantifying the role of random events in the persistence of HPV infections.
• 
  Nimrod Sherf, Maoz Shamir:
  STDP and the distribution of preferred phases in the whisker system.
• 
  Federica Gugole, Luc E. Coffeng, Wouter Edeling, Benjamin Sanderse, Sake J. De Vlas, Daan Crommelin:
  Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model.
• 
  Daniel Rüdiger, Lars Pelz, Marc D. Hein, Sascha Young Kupke, Udo Reichl:
  Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture.
• 
  Nathaniel J. Zuk, Jeremy W. Murphy, Richard B. Reilly, Edmund C. Lalor:
  Envelope reconstruction of speech and music highlights stronger tracking of speech at low frequencies.
• 
  Mehrdad Shahmohammadi, Hongxing Luo, Philip Westphal, Richard N. Cornelussen, Frits W. Prinzen, Tammo Delhaas:
  Hemodynamics-driven mathematical model of first and second heart sound generation.
• 
  Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Yoshiyuki Kubota, Shin Ishii:
  The critical balance between dopamine D2 receptor and RGS for the sensitive detection of a transient decay in dopamine signal.
• 
  Torrington Callan, Stephen Woodcock, Wilhelmina May Huston:
  Ascension of Chlamydia is moderated by uterine peristalsis and the neutrophil response to infection.
• 
  Elham Ghazizadeh, ShiNung Ching:
  Slow manifolds within network dynamics encode working memory efficiently and robustly.
• 
  Maryam Aliee, Matt J. Keeling, Kat S. Rock:
  Modelling to explore the potential impact of asymptomatic human infections on transmission and dynamics of African sleeping sickness.
• 
  Mar González-Ramírez, Cecilia Ballaré, Francesca Mugianesi, Malte Beringer, Alexandra Santanach, Enrique Blanco, Luciano Di Croce:
  Differential contribution to gene expression prediction of histone modifications at enhancers or promoters.
• 
  Jaie C. Woodard, Wei Zheng, Yang Zhang:
  Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders.
• 
  Christopher J. Knowlton, Tabea Ines Ziouziou, Niklas Hammer, Jochen Roeper, Carmen C. Canavier:
  Inactivation mode of sodium channels defines the different maximal firing rates of conventional versus atypical midbrain dopamine neurons.
• 
  Gabriel A. Vignolle, Denise Schaffer, Leopold Zehetner, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl:
  FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution.
• 
  Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker:
  Genetic dissection of complex traits using hierarchical biological knowledge.
• 
  Weihsueh A. Chiu, Martial L. Ndeffo Mbah:
  Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States.
• 
  Christian Selinger, Samuel Alizon:
  Reconstructing contact network structure and cross-immunity patterns from multiple infection histories.
• 
  Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner:
  ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
• 
  Adrienn Szabó, Katalin Schlett, Attila Szücs:
  Conventional measures of intrinsic excitability are poor estimators of neuronal activity under realistic synaptic inputs.
• 
  Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce:
  Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants.
• 
  James J. Winkle, Bhargav R. Karamched, Matthew R. Bennett, William Ott, Kresimir Josic:
  Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia.
• 
  Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro:
  Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes.
• 
  Roman Goulard, Cornelia Buehlmann, Jeremy E. Niven, Paul Graham, Barbara Webb:
  A unified mechanism for innate and learned visual landmark guidance in the insect central complex.
• 
  Abhisek Dwivedy, Richard Mariadasse, Mohammed Ahmad, Sayan Chakraborty, Deepsikha Kar, Satish Tiwari, Sankar Bhattacharyya, Sudipta Sonar, Shailendra Mani, Prafullakumar Tailor, Tanmay Majumdar, Jeyaraman Jeyakanthan, Bichitra Kumar Biswal:
  Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2.
• 
  Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi:
  FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks.
• 
  Juan L. Trincado, Marina Reixachs-Solé, Judith Pérez-Granado, Tim Fugmann, Ferran Sanz, Jun Yokota, Eduardo Eyras:
  ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer.
• 
  Zhenzhen Shi, Yang Li, Majid Jaberi Douraki:
  Hybrid computational modeling demonstrates the utility of simulating complex cellular networks in type 1 diabetes.
• 
  Giulio Matteucci, Benedetta Zattera, Rosilari Bellacosa Marotti, Davide Zoccolan:
  Rats spontaneously perceive global motion direction of drifting plaids.
• 
  Eduarda Susin, Alain Destexhe:
  Integration, coincidence detection and resonance in networks of spiking neurons expressing Gamma oscillations and asynchronous states.
• 
  José Camacho Mateu, Matteo Sireci, Miguel A. Muñoz:
  Phenotypic-dependent variability and the emergence of tolerance in bacterial populations.
• 
  Teemu Kuosmanen, Johannes Cairns, Robert Noble, Niko Beerenwinkel, Tommi Mononen, Ville Mustonen:
  Drug-induced resistance evolution necessitates less aggressive treatment.
• 
  Md. Shahriar Karim, Aasakiran Madamanchi, James A. Dutko, Mary C. Mullins, David M. Umulis:
  Heterodimer-heterotetramer formation mediates enhanced sensor activity in a biophysical model for BMP signaling.
• 
  Quinton M. Skilling, Bolaji Eniwaye, Brittany C. Clawson, James Shaver, Nicolette Ognjanovski, Sara J. Aton, Michal Zochowski:
  Acetylcholine-gated current translates wake neuronal firing rate information into a spike timing-based code in Non-REM sleep, stabilizing neural network dynamics during memory consolidation.
• 
  Alison Pereira Ribeiro, Nádia Félix Felipe da Silva, Fernanda Neiva Mesquita, Priscila de Cássia Souza Araújo, Thierson Couto Rosa, José Neiva Mesquita-Neto:
  Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds.
• 
  Yuval R. Zelnik, Yair Mau, Moshe Shachak, Ehud Meron:
  High-integrity human intervention in ecosystems: Tracking self-organization modes.
• 
  Yijia Yan, Neil Burgess, Andrej Bicanski:
  A model of head direction and landmark coding in complex environments.
• 
  Siyu Chen, Jennifer A. Flegg, Lisa J. White, Ricardo Aguas:
  Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys.
• 
  Matthew R. Whiteway, Dan Biderman, Yoni Friedman, Mario Dipoppa, Estefany Kelly Buchanan, Anqi Wu, John Zhou, Niccolò Bonacchi, Nathaniel J. Miska, Jean-Paul Noel, Erica Rodriguez, Michael Schartner, Karolina Socha, Anne E. Urai, C. Daniel Salzman, International Brain Laboratory, John P. Cunningham, Liam Paninski:
  Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders.
• 
  Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello:
  GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
• 
  Elzbieta Rembeza, Martin K. M. Engqvist:
  Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.
• 
  Hyun Gyu Lee, Kyoung J. Lee:
  Neighbor-enhanced diffusivity in dense, cohesive cell populations.
• 
  Lin Wang, Vikas Upadhyay, Costas D. Maranas:
  dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
• 
  Gregory J. Tawa, John C. Braisted, David Gerhold, Gurmit Grewal, Christina Mazcko, Matthew Breen, Gurusingham Sittampalam, Amy K. LeBlanc:
  Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species.
• 
  Bruce C. Hansen, Michelle R. Greene, David J. Field:
  Dynamic Electrode-to-Image (DETI) mapping reveals the human brain's spatiotemporal code of visual information.

Corrections

• 
  PLOS Computational Biology Staff:
  Correction: Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention.
• 
  PLOS Computational Biology Staff:
  Correction: Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results.

Volume 17, Number 10, October 2021

Editorials

• 
  Valentin Guignon, Catherine Breton, Jérôme Mariette, François Sabot, Julien Fumey, Vincent Lefort, Anna-Sophie Fiston-Lavier:
  Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.
• 
  Whitney M. Woelmer, L. M. Bradley, Lisa T. Haber, David H. Klinges, Abigail S. L. Lewis, Elizabeth J. Mohr, Christa L. Torrens, Kathryn I. Wheeler, Alyssa M. Willson:
  Ten simple rules for training yourself in an emerging field.

Education Articles

• 
  Sofia B. Mohamed, Sumaya Kambal, Sabah A. E. Ibrahim, Esra Abdalwhab, Abdalla Munir, Arwa Ibrahim, Qurashi Mohamed Ali:
  Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan.
• 
  Jolene Ramsey, Brenley K. McIntosh, Daniel P. Renfro, Suzanne A. Aleksander, Sandra A. LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan M. Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu:
  Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Review

• 
  Maxwell W. Libbrecht, Rachel C. W. Chan, Michael M. Hoffman:
  Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.

Research Articles

• 
  Vince Enachescu, Paul R. Schrater, Stefan Schaal, Vassilios N. Christopoulos:
  Action planning and control under uncertainty emerge through a desirability-driven competition between parallel encoding motor plans.
• 
  Chaitanya S. Gokhale, Stefano Giaimo, Philippe Remigi:
  Memory shapes microbial populations.
• 
  Luke Y. Prince, Travis Bacon, Rachel Humphries, Krasimira Tsaneva-Atanasova, Claudia Clopath, Jack R. Mellor:
  Separable actions of acetylcholine and noradrenaline on neuronal ensemble formation in hippocampal CA3 circuits.
• 
  Sergio Sarnataro, Andrea Riba, Nacho Molina:
  Regulation of transcription reactivation dynamics exiting mitosis.
• 
  Junior Samuel López-Yépez, Juliane Martin, Oliver J. Hulme, Duda Kvitsiani:
  Choice history effects in mice and humans improve reward harvesting efficiency.
• 
  Lorenzo Ferrucci, Aldo Genovesio, Encarni Marcos:
  The importance of urgency in decision making based on dynamic information.
• 
  Bikash K. Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig van Dolleweerd, Paul P. Gardner:
  Analysis of 11, 430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.
• 
  Ramzan Umarov, Yu Li, Erik Arner:
  DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.
• 
  Vladimir Smirnov:
  Recursive MAGUS: Scalable and accurate multiple sequence alignment.
• 
  Yashika Arora, Pushpinder Walia, Mitsuhiro Hayashibe, Makii Muthalib, Shubhajit Roy Chowdhury, Stéphane Perrey, Anirban Dutta:
  Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans.
• 
  Bill Zhao, Kehan Zhang, Christopher S. Chen, Emma Lejeune:
  Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes.
• 
  Jakub Jurasz, Maciej Baginski, Jacek Czub, Milosz Wieczór:
  Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE.
• 
  Jason Bennett, Mikhail Pomaznoy, Akul Singhania, Bjoern Peters:
  A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC.
• 
  Daniel E. Mattox, Chris Bailey-Kellogg:
  Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity.
• 
  Peter Ford Dominey:
  Narrative event segmentation in the cortical reservoir.
• 
  Rosa A. Rossi-Goldthorpe, Yuan Chang Leong, Pantelis Leptourgos, Philip R. Corlett:
  Paranoia, self-deception and overconfidence.
• 
  Thibault Lagache, Alison Hanson, Jesús E. Pérez-Ortega, Adrienne Fairhall, Rafael Yuste:
  Tracking calcium dynamics from individual neurons in behaving animals.
• 
  Samuel A. Mihelic, William A. Sikora, Ahmed M. Hassan, Michael R. Williamson, Theresa A. Jones, Andrew K. Dunn:
  Segmentation-Less, Automated, Vascular Vectorization.
• 
  Antoine L. Decrulle, Antoine Frénoy, Thomas A. Meiller-Legrand, Aude Bernheim, Chantal Lotton, Arnaud Gutierrez, Ariel B. Lindner:
  Engineering gene overlaps to sustain genetic constructs in vivo.
• 
  Rupamanjari Majumder, Sayedeh Hussaini, Vladimir S. Zykov, Stefan Luther, Eberhard Bodenschatz:
  Pulsed low-energy stimulation initiates electric turbulence in cardiac tissue.
• 
  Matthew Z. DeMaere, Aaron E. Darling:
  qc3C: Reference-free quality control for Hi-C sequencing data.
• 
  Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
  Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
• 
  Zifeng Wang, Aria Masoomi, Zhonghui Xu, Adel Boueiz, Sool Lee, Tingting Zhao, Russell Bowler, Michael H. Cho, Edwin K. Silverman, Craig P. Hersh, Jennifer G. Dy, Peter J. Castaldi:
  Improved prediction of smoking status via isoform-aware RNA-seq deep learning models.
• 
  Carolin Scholl, Michael Everett Rule, Matthias H. Hennig:
  The information theory of developmental pruning: Optimizing global network architectures using local synaptic rules.
• 
  Sarah Kosta, Pierre C. Dauby:
  Frank-Starling mechanism, fluid responsiveness, and length-dependent activation: Unravelling the multiscale behaviors with an in silico analysis.
• 
  Gaia Tavoni, David E. Chen Kersen, Vijay Balasubramanian:
  Cortical feedback and gating in odor discrimination and generalization.
• 
  Daniel H. Baker, Greta Vilidaite, Alex R. Wade:
  Steady-state measures of visual suppression.
• 
  Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin:
  Modular assembly of dynamic models in systems biology.
• 
  Mattia Mazzoli, Emanuele Pepe, David Mateo, Ciro Cattuto, Laetitia Gauvin, Paolo Bajardi, Michele Tizzoni, Alberto Hernando, Sandro Meloni, José J. Ramasco:
  Interplay between mobility, multi-seeding and lockdowns shapes COVID-19 local impact.
• 
  Yi Huang, Ishanu Chattopadhyay:
  Universal risk phenotype of US counties for flu-like transmission to improve county-specific COVID-19 incidence forecasts.
• 
  Veronika Zarnitsyna, Rama S. Akondy, Hasan Ahmed, Donald J. McGuire, Vladimir G. Zarnitsyn, Mia Moore, Philip L. F. Johnson, Rafi Ahmed, Kelvin W. Li, Marc K. Hellerstein, Rustom Antia:
  Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination.
• 
  Vasilina Zayats, Agata P. Perlinska, Aleksandra I. Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I. Sulkowska:
  Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
• 
  Hua-Chun Sun, David St-Amand, Curtis L. Baker Jr., Frederick A. A. Kingdom:
  Visual perception of texture regularity: Conjoint measurements and a wavelet response-distribution model.
• 
  Alexander Bryson, Samuel F. Berkovic, Steven Petrou, David B. Grayden:
  State transitions through inhibitory interneurons in a cortical network model.
• 
  Davis T. Weaver, Kathleen I. Pishas, Drew F. K. Williamson, Jessica Scarborough, Stephen L. Lessnick, Andrew Dhawan, Jacob G. Scott:
  Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma.
• 
  Yun Min Song, Hyukpyo Hong, Jae Kyoung Kim:
  Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities.
• 
  Zachary J. Cotman, Michael J. Bowden, Barrett P. Richter, Joseph H. Phelps, Christopher J. Dibble:
  Factors affecting aerosol SARS-CoV-2 transmission via HVAC systems; a modeling study.
• 
  Daniel Cresta, Donald C. Warren, Christian Quirouette, Amanda P. Smith, Lindey C. Lane, Amber M. Smith, Catherine A. A. Beauchemin:
  Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration.
• 
  David M. Rutkowski, Dimitrios Vavylonis:
  Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes.
• 
  Snehalika Lall, Sumanta Ray, Sanghamitra Bandyopadhyay:
  RgCop-A regularized copula based method for gene selection in single-cell RNA-seq data.
• 
  Eric Ching-Pan Chu, Alexander M. Morin, Tak Hou Calvin Chang, Tue Nguyen, Yi-Cheng Tsai, Aman Sharma, Chao Chun Liu, Paul Pavlidis:
  Experiment level curation of transcriptional regulatory interactions in neurodevelopment.
• 
  Grégory Hammad, Mathilde Reyt, Nikita Beliy, Marion Baillet, Michele Deantoni, Alexia Lesoinne, Vincenzo Muto, Christina Schmidt:
  pyActigraphy: Open-source python package for actigraphy data visualization and analysis.
• 
  Qingchu Jin, Joseph L. Greenstein, Raimond L. Winslow:
  Estimating ectopic beat probability with simplified statistical models that account for experimental uncertainty.
• 
  Gal Gilad, Mark D. M. Leiserson, Roded Sharan:
  A data-driven approach for constructing mutation categories for mutational signature analysis.
• 
  Yang Xu, Hongmei Jiang, Wenxin Jiang:
  Extended graphical lasso for multiple interaction networks for high dimensional omics data.
• 
  Junho Lee, Jin Su Kim, Yangjin Kim:
  Atorvastatin-mediated rescue of cancer-related cognitive changes in combined anticancer therapies.
• 
  Folco Panizza, Alexander Vostroknutov, Giorgio Coricelli:
  How conformity can lead to polarised social behaviour.
• 
  Ryota Sugimoto, Luca Nishimura, Phuong Thanh Nguyen, Jumpei Ito, Nicholas F. Parrish, Hiroshi Mori, Ken Kurokawa, Hirofumi Nakaoka, Ituro Inoue:
  Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.
• 
  Ruth Johnson, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman:
  Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits.
• 
  Arjun Chandrasekhar, James A. R. Marshall, Cortnea Austin, Saket Navlakha, Deborah M. Gordon:
  Better tired than lost: Turtle ant trail networks favor coherence over short edges.
• 
  Charlie M. Carpenter, Weiming Zhang, Lucas A. Gillenwater, Cameron Severn, Tusharkanti Ghosh, Russell Bowler, Katerina J. Kechris, Debashis Ghosh:
  PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes.
• 
  Tariq Daouda, Maude Dumont-Lagacé, Albert Feghaly, Yahya Benslimane, Rébecca Panes, Mathieu Courcelles, Mohamed Benhammadi, Lea Harrington, Pierre Thibault, François Major, Yoshua Bengio, Etienne Gagnon, Sébastien Lemieux, Claude Perreault:
  CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation.
• 
  Josua Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker:
  Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics.
• 
  Stacy Tessler Lindau, Jennifer A. Makelarski, Chaitanya Kaligotla, Emily Abramsohn, David G. Beiser, Chiahung Chou, Nicholson T. Collier, Elbert S. Huang, Charles M. Macal, Jonathan Ozik, Elizabeth L. Tung:
  Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention.
• 
  Stefan T. Radev, Frederik Graw, Simiao Chen, Nico T. Mutters, Vanessa Eichel, Till Bärnighausen, Ullrich Köthe:
  OutbreakFlow: Model-based Bayesian inference of disease outbreak dynamics with invertible neural networks and its application to the COVID-19 pandemics in Germany.
• 
  Shian Su, Quentin Gouil, Marnie E. Blewitt, Dianne Cook, Peter F. Hickey, Matthew E. Ritchie:
  NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
• 
  Ziniu Wu, Harold Rockwell, Yimeng Zhang, Shiming Tang, Tai Sing Lee:
  Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons.
• 
  Martijn C. Sierksma, J. Gerard G. Borst:
  Using ephaptic coupling to estimate the synaptic cleft resistivity of the calyx of Held synapse.
• 
  Suraj Balakrishna, Luisa Salazar-Vizcaya, Axel J. Schmidt, Viacheslav N. Kachalov, Katharina Kusejko, Maria Christine Thurnheer, Jan A. Roth, Dunja Nicca, Matthias Cavassini, Manuel Battegay, Patrick Schmid, Enos Bernasconi, Huldrych F. Günthard, Andri Rauch, Roger D. Kouyos, The Swiss Hiv Cohort Study:
  Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study.
• 
  Antonina Kalkus, Joy Barrett, Theyjasvi Ashok, Brian R. Morton:
  Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene.
• 
  Susanne Pettersson, Martin Nilsson Jacobi:
  Spatial heterogeneity enhance robustness of large multi-species ecosystems.
• 
  Daipeng Chen, Yuyi Xue, Yanni Xiao:
  Determining travel fluxes in epidemic areas.
• 
  Mohammad Ali Dehghani, Amir Hossein Darooneh, Mohammad Kohandel:
  The network structure affects the fixation probability when it couples to the birth-death dynamics in finite population.
• 
  Joseph Aylett-Bullock, Carolina Cuesta-Lázaro, Arnau Quera-Bofarull, Anjali Katta, Katherine Hoffmann Pham, Benjamin Hoover, Hendrik Strobelt, Rebeca Moreno Jimenez, Aidan Sedgewick, Egmond Samir Evers, David Kennedy, Sandra Harlass, Allen Gidraf Kahindo Maina, Ahmad Hussien, Miguel A. Luengo-Oroz:
  Operational response simulation tool for epidemics within refugee and IDP settlements: A scenario-based case study of the Cox's Bazar settlement.
• 
  Eline De Borre, Wout Joseph, Reza Aminzadeh, Pie Müller, Matthieu N. Boone, Iván Josipovic, Sina Hashemizadeh, Niels Kuster, Sven Kühn, Arno Thielens:
  Radio-frequency exposure of the yellow fever mosquito (A. aegypti) from 2 to 240 GHz.
• 
  Emily Howerton, Matthew J. Ferrari, Ottar N. Bjørnstad, Tiffany L. Bogich, Rebecca K. Borchering, Chris P. Jewell, James D. Nichols, William J. M. Probert, Michael C. Runge, Michael J. Tildesley, Cécile Viboud, Katriona Shea:
  Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing.
• 
  Jennifer Laura Lee, Wei Ji Ma:
  Point-estimating observer models for latent cause detection.
• 
  Petar I. Penev, Claudia Alvarez-Carreño, Eric Smith, Anton S. Petrov, Loren Dean Williams:
  TwinCons: Conservation score for uncovering deep sequence similarity and divergence.

Correction

• 
  Lillian R. Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic:
  Correction: CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models.

Formal Comments

• 
  Alejandro Fernández Villaverde, Gemma Massonis:
  On testing structural identifiability by a simple scaling method: Relying on scaling symmetries can be misleading.
• 
  Mario Castro, Rob J. De Boer:
  The limitations, dangers, and benefits of simple methods for testing identifiability.

Volume 17, Number 11, November 2021

Editorial

• 
  Haley S. Hunter-Zinck, Alexandre Fioravante de Siqueira, Valeri N. Vasquez, Richard Barnes, Ciera C. Martinez:
  Ten simple rules on writing clean and reliable open-source scientific software.

Education Articles

• 
  Luíza Zuvanov, Ana Letycia Basso Garcia, Fernando Henrique Correr, Rodolfo Bizarria Jr., Ailton Pereira da Costa Filho, Alisson Hayasi da Costa, Andréa T. Thomaz, Ana Lucia Mendes Pinheiro, Diego Mauricio Riaño-Pachón, Flavia Vischi Winck, Franciele Grego Esteves, Gabriel Rodrigues Alves Margarido, Giovanna Maria Stanfoca Casagrande, Henrique Cordeiro Frajacomo, Leonardo Martins, Mariana Feitosa Cavalheiro, Nathalia Graf Grachet, Raniere Gaia Costa da Silva, Ricardo Cerri, Rommel Thiago Juca Ramos, Simone Daniela Sartorio de Medeiros, Thayana Vieira Tavares, Renato Augusto Corrêa dos Santos:
  The experience of teaching introductory programming skills to bioscientists in Brazil.
• 
  Eva Loth, Jumana Ahmad, Chris Chatham, Beatriz López, Ben Carter, Daisy Crawley, Bethany Oakley, Hannah Hayward, Jennifer Cooke, Antonia San José Cáceres, Danilo Bzdok, Emily J. H. Jones, Tony Charman, Christian F. Beckmann, Thomas Bourgeron, Roberto Toro, Jan K. Buitelaar, Declan G. M. Murphy, Guillaume Dumas:
  The meaning of significant mean group differences for biomarker discovery.

Research Articles

• 
  Dafni Giannari, Cleo Hanchen Ho, Radhakrishnan Mahadevan:
  A gap-filling algorithm for prediction of metabolic interactions in microbial communities.
• 
  Tania Mendonca, Ana A. Jones, Jose M. Pozo, Sarah Baxendale, Tanya T. Whitfield, Alejandro F. Frangi:
  Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
• 
  Shinya Ito, Yufei Si, Alan M. Litke, David A. Feldheim:
  Nonlinear visuoauditory integration in the mouse superior colliculus.
• 
  Johannes Waschke, Mario Hlawitschka, Kerim Anlas, Vikas Trivedi, Ingo Roeder, Jan Huisken, Nico Scherf:
  linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser.
• 
  He Li, Zixiang Leonardo Liu, Lu Lu, Pierre Buffet, George Em Karniadakis:
  How the spleen reshapes and retains young and old red blood cells: A computational investigation.
• 
  Alireza Poshtkohi, John J. Wade, Liam McDaid, Junxiu Liu, Mark Dallas, Angela Bithell:
  Mathematical modelling of human P2X-mediated plasma membrane electrophysiology and calcium dynamics in microglia.
• 
  Dharsan K. Soundarrajan, Francisco J. Huizar, Ramezan Paravi Torghabeh, Trent Robinett, Jeremiah J. Zartman:
  From spikes to intercellular waves: Tuning intercellular calcium signaling dynamics modulates organ size control.
• 
  Eilam Goldenberg Leleo, Idan Segev:
  Burst control: Synaptic conditions for burst generation in cortical layer 5 pyramidal neurons.
• 
  Qibin Duan, Chris Carmody, Basil Donovan, Rebecca J. Guy, Ben B. Hui, John M. Kaldor, Monica M. Lahra, Matthew G. Law, David A. Lewis, Michael Maley, Skye McGregor, Anna M. McNulty, Christine Selvey, David J. Templeton, David M. Whiley, David G. Regan, James G. Wood:
  Modelling response strategies for controlling gonorrhoea outbreaks in men who have sex with men in Australia.
• 
  Mathurin Dorel, Bertram Klinger, Tommaso Mari, Joern Toedling, Eric Blanc, Clemens Messerschmidt, Michal Nadler-Holly, Matthias Ziehm, Anja Sieber, Falk Hertwig, Dieter Beule, Angelika Eggert, Johannes H. Schulte, Matthias Selbach, Nils Blüthgen:
  Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
• 
  Erik B. Nordquist, Charles A. English, Eugenia M. Clerico, Woody Sherman, Lila M. Gierasch, Jianhan Chen:
  Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones.
• 
  Filip Vercruysse, Richard Naud, Henning Sprekeler:
  Self-organization of a doubly asynchronous irregular network state for spikes and bursts.
• 
  Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E. Adriaens, Chris T. A. Evelo, Ilja C. W. Arts:
  Comparison of metabolic states using genome-scale metabolic models.
• 
  Yi-Jie Zhao, Tianye Ma, Li Zhang, Xuemei Ran, Ru-Yuan Zhang, Yixuan Ku:
  Atypically larger variability of resource allocation accounts for visual working memory deficits in schizophrenia.
• 
  Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco:
  The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
• 
  Marzia Di Filippo, Chiara Damiani, Dario Pescini:
  GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.
• 
  Nina G. Bozhanova, Joel M. Harp, Brian Joseph Bender, Alexey S. Gavrikov, Dmitry A. Gorbachev, Mikhail S. Baranov, Christina B. Mercado, Xuan Zhang, Konstantin A. Lukyanov, Alexander S. Mishin, Jens Meiler:
  Computational redesign of a fluorogen activating protein with Rosetta.
• 
  Patrizia Zamberletti, Khadija Sabir, Thomas Opitz, Olivier Bonnefon, Edith Gabriel, Julien Papaïx:
  More pests but less pesticide applications: Ambivalent effect of landscape complexity on conservation biological control.
• 
  Yipei Guo, Mor Nitzan, Michael P. Brenner:
  Programming cell growth into different cluster shapes using diffusible signals.
• 
  Michael S. Robeson II, Devon R. O'Rourke, Benjamin D. Kaehler, Michal Ziemski, Matthew R. Dillon, Jeffrey T. Foster, Nicholas A. Bokulich:
  RESCRIPt: Reproducible sequence taxonomy reference database management.
• 
  Pablo Lechón-Alonso, Tom Clegg, Jacob Cook, Thomas P. Smith, Samraat Pawar:
  The role of competition versus cooperation in microbial community coalescence.
• 
  Naoto Nishiura, Kunihiko Kaneko:
  Evolution of phenotypic fluctuation under host-parasite interactions.
• 
  Sean M. Devlin, Axel Martin, Irina Ostrovnaya:
  Identifying prognostic pairwise relationships among bacterial species in microbiome studies.
• 
  Qunlun Shen, Shihua Zhang:
  Approximate distance correlation for selecting highly interrelated genes across datasets.
• 
  Jaejoong Kim, Sang Wan Lee, Seokho Yoon, Haeorm Park, Bumseok Jeong:
  Neurocomputational mechanism of controllability inference under a multi-agent setting.
• 
  Torfinn S. Madssen, Guro F. Giskeødegård, Age K. Smilde, Johan A. Westerhuis:
  Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data.
• 
  Javier J. How, Saket Navlakha, Sreekanth H. Chalasani:
  Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans.
• 
  Xiakun Chu, Jin Wang:
  Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics.
• 
  Mrinmoy Mukherjee, Herbert Levine:
  Cluster size distribution of cells disseminating from a primary tumor.
• 
  Sudharshan Ravi, Rudiyanto Gunawan:
  ΔFBA - Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data.
• 
  Konstantina Charmpi, Manopriya Chokkalingam, Ronja Johnen, Andreas Beyer:
  Optimizing network propagation for multi-omics data integration.
• 
  Maxim Barenboim, Michal Kovác, Baptiste Ameline, David T. W. Jones, Olaf Witt, Stefan Bielack, Stefan Burdach, Daniel Baumhoer, Michaela Nathrath:
  DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma.
• 
  Julia C. Gorman, Oliver L. Tufte, Anna V. R. Miller, William M. DeBello, José Luis Peña, Brian J. Fischer:
  Diverse processing underlying frequency integration in midbrain neurons of barn owls.
• 
  Zhisheng Jiang, Serena F. Generoso, Marta Badia, Bernhard Payer, Lucas B. Carey:
  A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences.
• 
  Júlia V. Gallinaro, Claudia Clopath:
  Memories in a network with excitatory and inhibitory plasticity are encoded in the spiking irregularity.
• 
  Larry N. Singh, Brian Ennis, Bryn Loneragan, Noah L. Tsao, M. Isabel G. Lopez Sanchez, Jianping Li, Patrick Acheampong, Oanh Tran, Ian A. Trounce, Yuankun Zhu, Prasanth Potluri, Regeneron Genetics Center, Beverly S. Emanuel, Daniel J. Rader, Zoltan Arany, Scott M. Damrauer, Adam C. Resnick, Stewart A. Anderson, Douglas C. Wallace:
  MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.
• 
  Aniello Lombardi, Heiko J. Luhmann, Werner Kilb:
  Modelling the spatial and temporal constrains of the GABAergic influence on neuronal excitability.
• 
  Udo A. Ernst, Xiao Chen, Lisa Bohnenkamp, Fingal Orlando Galashan, Detlef Wegener:
  Dynamic divisive normalization circuits explain and predict change detection in monkey area MT.
• 
  Guodong Hu, Huan-Xiang Zhou:
  Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.
• 
  Fangfang Hong, Stephanie Badde, Michael S. Landy:
  Causal inference regulates audiovisual spatial recalibration via its influence on audiovisual perception.
• 
  Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna:
  Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.
• 
  Alex McAvoy, Andrew Rao, Christoph Hauert:
  Intriguing effects of selection intensity on the evolution of prosocial behaviors.
• 
  Himel Mallick, Ali Rahnavard, Lauren J. McIver, Siyuan Ma, Yancong Zhang, Long H. Nguyen, Timothy L. Tickle, George Weingart, Boyu Ren, Emma H. Schwager, Suvo Chatterjee, Kelsey N. Thompson, Jeremy E. Wilkinson, Ayshwarya Subramanian, Yiren Lu, Levi Waldron, Joseph N. Paulson, Eric A. Franzosa, Héctor Corrada Bravo, Curtis Huttenhower:
  Multivariable association discovery in population-scale meta-omics studies.
• 
  Tigist F. Menkir, Horace Cox, Canelle Poirier, Melanie Saul, Sharon Jones-Weekes, Collette Clementson, Pablo M. De Salazar, Mauricio Santillana, Caroline O. Buckee:
  A nowcasting framework for correcting for reporting delays in malaria surveillance.
• 
  Justin Jao, Annie Vogel Ciernia:
  MGEnrichment: A web application for microglia gene list enrichment analysis.
• 
  Natalie Klein, Joshua H. Siegle, Tobias Teichert, Robert E. Kass:
  Cross-population coupling of neural activity based on Gaussian process current source densities.
• 
  Pavel I. Kos, Aleksandra A. Galitsyna, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin, Alexander V. Chertovich:
  Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
• 
  Sean B. King, Mona Singh:
  Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections.
• 
  Jason W. Hoskins, Charles C. Chung, Aidan O'Brien, Jun Zhong, Katelyn Connelly, Irene Collins, Jianxin Shi, Laufey T. Amundadottir:
  Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals.
• 
  Adrienne C. Kinney, Sean Current, Joceline Lega:
  Aedes-AI: Neural network models of mosquito abundance.
• 
  Takeru Fujii, Kazumitsu Maehara, Masatoshi Fujita, Yasuyuki Ohkawa:
  Discriminative feature of cells characterizes cell populations of interest by a small subset of genes.
• 
  Xiaoxuan Wu, Kakit Kong, Wenlei Xiao, Feng Liu:
  Attractive internuclear force drives the collective behavior of nuclear arrays in Drosophila embryos.
• 
  Diego Barra Avila, Juan Ramon Melendez-Alvarez, Xiao-Jun Tian:
  Control of tissue homeostasis, tumorigenesis, and degeneration by coupled bidirectional bistable switches.
• 
  Melody Walker, Karthikeyan Chandrasegaran, Clément Vinauger, Michael A. Robert, Lauren M. Childs:
  Modeling the effects of Aedes aegypti's larval environment on adult body mass at emergence.
• 
  Tanner C. Dixon, Christina M. Merrick, Joni D. Wallis, Richard B. Ivry, Jose M. Carmena:
  Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals.
• 
  Xingjie Pan, Tanja Kortemme:
  De novo protein fold families expand the designable ligand binding site space.
• 
  Ryan T. Schroeder, Arthur D. Kuo:
  Elastic energy savings and active energy cost in a simple model of running.
• 
  Raquel Linheiro, John P. Archer:
  CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
• 
  Willem Jespers, Laura H. Heitman, Adriaan P. IJzerman, Eddy Sotelo, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez-de-Terán:
  Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations.
• 
  Shun Wang, Mengqian Hao, Zishu Pan, Jinzhi Lei, Xiufen Zou:
  Data-driven multi-scale mathematical modeling of SARS-CoV-2 infection reveals heterogeneity among COVID-19 patients.
• 
  Ege Altan, Sara A. Solla, Lee E. Miller, Eric J. Perreault:
  Estimating the dimensionality of the manifold underlying multi-electrode neural recordings.
• 
  Ernesto A. B. F. Lima, Danial Faghihi, Russell Philley, Jianchen Yang, John Virostko, Caleb M. Phillips, Thomas E. Yankeelov:
  Bayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth.
• 
  Niksa Praljak, Shamreen Iram, Utku Goreke, Gundeep Singh, Ailis Hill, Umut A. Gurkan, Michael Hinczewski:
  Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin.
• 
  Tunca Dogan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Jesus Martin, Rengül Çetin-Atalay:
  Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases.
• 
  Richard D. Lange, Ankani Chattoraj, Jeffrey M. Beck, Jacob L. Yates, Ralf M. Haefner:
  A confirmation bias in perceptual decision-making due to hierarchical approximate inference.
• 
  René Larisch, Lorenz Gönner, Michael Teichmann, Fred H. Hamker:
  Sensory coding and contrast invariance emerge from the control of plastic inhibition over emergent selectivity.
• 
  Bertrand Jayles, Clément Sire, Ralf H. J. M. Kurvers:
  Crowd control: Reducing individual estimation bias by sharing biased social information.
• 
  Upinder S. Bhalla:
  HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks.
• 
  Danial Pourjafar-Dehkordi, Martin Zacharias:
  Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling.
• 
  Shanshan Jia, Dajun Xing, Zhaofei Yu, Jian K. Liu:
  Dissecting cascade computational components in spiking neural networks.

Volume 17, Number 12, December 2021

Editorials

• 
  Kristen M. Naegle:
  Ten simple rules for effective presentation slides.
• 
  Stephen Pompea, Pedro Russo:
  Ten simple rules for scientists getting started in science education.
• 
  Shaun Aron, C. Victor Jongeneel, Paballo Abel Chauke, Melek Chaouch, Judit Kumuthini, Lyndon Zass, Fouzia Radouani, Samar Kamal Kassim, Faisal M. Fadlelmola, Nicola J. Mulder:
  Ten simple rules for developing bioinformatics capacity at an academic institution.

Perspectives

• 
  Jessica Burnett, Renee Dale, Chung-Yi Hou, Gabriela Palomo-Muñoz, Kaitlin Stack Whitney, Steve Aulenbach, Robert Sky Bristol, Denis Valle, Tristan P. Wellman:
  Ten simple rules for creating a scientific web application.
• 
  Jordan J. Baker, Christopher J. P. Mathy, Julia Schaletzky:
  A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design.

Research Articles

• 
  Jiajun Qiu, Xiao Ma, Fanyi Zeng, Jingbin Yan:
  RNA editing regulates lncRNA splicing in human early embryo development.
• 
  Lee Benson, Ross S. Davidson, Darren M. Green, Andrew Hoyle, Mike R. Hutchings, Glenn Marion:
  When and why direct transmission models can be used for environmentally persistent pathogens.
• 
  Katarína Bodová, Eniko Szép, Nicholas H. Barton:
  Dynamic maximum entropy provides accurate approximation of structured population dynamics.
• 
  Yanan Long, Qi Chen, Henrik Larsson, Andrey Rzhetsky:
  Observable variations in human sex ratio at birth.
• 
  Stephen Zhang, Anton Afanassiev, Laura Greenstreet, Tetsuya Matsumoto, Geoffrey Schiebinger:
  Optimal transport analysis reveals trajectories in steady-state systems.
• 
  Kaitlin E. Frasier:
  A machine learning pipeline for classification of cetacean echolocation clicks in large underwater acoustic datasets.
• 
  Suchana Chakravarty, Attila Csikász-Nagy:
  Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops.
• 
  Jacob Cook, Samraat Pawar, Robert G. Endres:
  Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium.
• 
  Icíar Civantos-Gómez, Javier García-Algarra, David García-Callejas, Javier Galeano, Oscar Godoy, Ignasi Bartomeus:
  Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble.
• 
  Ondrej Maxian, Raúl P. Peláez, Alex Mogilner, Aleksandar Donev:
  Simulations of dynamically cross-linked actin networks: Morphology, rheology, and hydrodynamic interactions.
• 
  Fu-Lai Wen, Chun Wai Kwan, Yu-Chiun Wang, Tatsuo Shibata:
  Autonomous epithelial folding induced by an intracellular mechano-polarity feedback loop.
• 
  Francesco Mottes, Chiara Villa, Matteo Osella, Michele Caselle:
  The impact of whole genome duplications on the human gene regulatory networks.
• 
  Lou Zonca, David Holcman:
  Emergence and fragmentation of the alpha-band driven by neuronal network dynamics.
• 
  Md. Ashfaq Ahmed, Sharmila Venugopal, Ranu Jung:
  Engaging biological oscillators through second messenger pathways permits emergence of a robust gastric slow-wave during peristalsis.
• 
  Stefano Longobardi, Anna Sher, Steven A. Niederer:
  In silico identification of potential calcium dynamics and sarcomere targets for recovering left ventricular function in rat heart failure with preserved ejection fraction.
• 
  Lei Liu, Bokai Zhang, Changbong Hyeon:
  Extracting multi-way chromatin contacts from Hi-C data.
• 
  Lior Lebovich, Michael Yunerman, Viviana Scaiewicz, Yonatan Loewenstein, Dan Rokni:
  Paradoxical relationship between speed and accuracy in olfactory figure-background segregation.
• 
  Michiel W. H. Remme, Urs Bergmann, Denis Alevi, Susanne Schreiber, Henning Sprekeler, Richard Kempter:
  Hebbian plasticity in parallel synaptic pathways: A circuit mechanism for systems memory consolidation.
• 
  Aviv Dotan, Oren Shriki:
  Tinnitus-like "hallucinations" elicited by sensory deprivation in an entropy maximization recurrent neural network.
• 
  Mario Rubio-Teves, Sergio Diez-Hermano, César Porrero, Abel Sanchez-Jimenez, Lucía Prensa, Francisco Clascá, María García-Amado, José Antonio Villacorta-Atienza:
  Benchmarking of tools for axon length measurement in individually-labeled projection neurons.
• 
  Ankit Gupta, Christoph Schwab, Mustafa Khammash:
  DeepCME: A deep learning framework for computing solution statistics of the chemical master equation.
• 
  Valentin Schneider-Lunitz, Jorge Ruiz-Orera, Norbert Hübner, Sebastiaan van Heesch:
  Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
• 
  Guoyang Zou, Yang Zou, Chenglong Ma, Jiaojiao Zhao, Lei Li:
  Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example.
• 
  Xu Zhang, Roeland Hancock, Sabato Santaniello:
  Transcranial direct current stimulation of cerebellum alters spiking precision in cerebellar cortex: A modeling study of cellular responses.
• 
  Lei Li, Yu-Tian Wang, Cunmei Ji, Chun-Hou Zheng, Jian-Cheng Ni, Yan-Sen Su:
  GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder.
• 
  Mario Pannunzi, Thomas Nowotny:
  Non-synaptic interactions between olfactory receptor neurons, a possible key feature of odor processing in flies.
• 
  Jan Ewald, Flora Rivieccio, Lukás Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta:
  Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis.
• 
  Han Zhuang, Tzu-Yang Huang, Daniel E. Acuna:
  Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations.
• 
  Andrea Ferrario, Andrey Palyanov, Stella Koutsikou, Wen-Chang Li, Stephen R. Soffe, Alan Roberts, Roman Borisyuk:
  From decision to action: Detailed modelling of frog tadpoles reveals neuronal mechanisms of decision-making and reproduces unpredictable swimming movements in response to sensory signals.
• 
  Assaf Amitai:
  Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure.
• 
  Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar:
  CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data.
• 
  Sarah A. Robinson, Matthew I. J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane:
  Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.
• 
  Ana C. Estrada, Linda Irons, Bruno V. Rego, Guangxin Li, George Tellides, Jay D. Humphrey:
  Roles of mTOR in thoracic aortopathy understood by complex intracellular signaling interactions.
• 
  Fuminari Miura, Ka Yin Leung, Don Klinkenberg, Kylie E. C. Ainslie, Jacco Wallinga:
  Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization.
• 
  Thomas W. Christy, Catherine A. Giannetti, Alain Laederach, Kevin M. Weeks:
  Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper.
• 
  Michael R. Traner, Ethan S. Bromberg-Martin, Ilya E. Monosov:
  How the value of the environment controls persistence in visual search.
• 
  Miguel Piñeiro, Wilson Mena, John Ewer, Patricio Orio:
  Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior.
• 
  Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel:
  Statistical tests for intra-tumour clonal co-occurrence and exclusivity.
• 
  Joseph R. Larsen, Margaret R. Martin, John D. Martin, James B. Hicks, Peter Kuhn:
  Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant.
• 
  Yeonju Sin, Hee Young Seon, Yun Kyoung Shin, Oh-Sang Kwon, Dongil Chung:
  Subjective optimality in finite sequential decision-making.
• 
  Ralph Simon, Karol Bakunowski, Angel Eduardo Reyes-Vasques, Marco Tschapka, Mirjam Knörnschild, Jan Steckel, Dan Stowell:
  Acoustic traits of bat-pollinated flowers compared to flowers of other pollination syndromes and their echo-based classification using convolutional neural networks.
• 
  Ruby Kim, H. Frederik Nijhout, Michael C. Reed:
  One-carbon metabolism during the menstrual cycle and pregnancy.
• 
  Rashida Nayeem, Salah Bazzi, Mohsen Sadeghi, Neville Hogan, Dagmar Sternad:
  Preparing to move: Setting initial conditions to simplify interactions with complex objects.
• 
  Måns Unosson, Marco Brancaccio, Michael Hastings, Adam M. Johansen, Bärbel Finkenstädt:
  A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells.
• 
  Pratha Sah, Michael C. Otterstatter, Stephan T. Leu, Sivan Leviyang, Shweta Bansal:
  Revealing mechanisms of infectious disease spread through empirical contact networks.
• 
  Shanel C. Pickard, David J. Bertsch, Zoe Le Garrec, Roy E. Ritzmann, Roger D. Quinn, Nicholas S. Szczecinski:
  Internal state effects on behavioral shifts in freely behaving praying mantises (Tenodera sinensis).
• 
  Priit Paluoja, Hindrek Teder, Amin Ardeshirdavani, Baran Bayindir, Joris Robert Vermeesch, Andres Salumets, Kaarel Krjutskov, Priit Palta:
  Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples.
• 
  Juan Diaz-Colunga, Ramón Díaz-Uriarte:
  Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
• 
  Michael Famulare, Wesley Wong, Rashidul Haque, James A. Platts-Mills, Parimalendu Saha, Asma B. Aziz, Tahmina Ahmed, Md Ohedul Islam, Md Jashim Uddin, Ananda S. Bandyopadhyay, Mohammed Yunus, Khalequ Zaman, Mami Taniuchi:
  Multiscale model for forecasting Sabin 2 vaccine virus household and community transmission.
• 
  Huaming Yan, Daniel Ramirez-Guerrero, John S. Lowengrub, Min Wu:
  Stress generation, relaxation and size control in confined tumor growth.
• 
  Akshaya V. Annapragada, Joseph L. Greenstein, Sanjukta N. Bose, Bradford D. Winters, Sridevi V. Sarma, Raimond L. Winslow:
  SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction.
• 
  Alexander E. Downie, Andreas Mayer, C. Jessica E. Metcalf, Andrea L. Graham:
  Optimal immune specificity at the intersection of host life history and parasite epidemiology.
• 
  Jesse Kreger, Natalia L. Komarova, Dominik Wodarz:
  A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV.
• 
  Lanxin Zhang, Junyu Wang, Max von Kleist:
  Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes.
• 
  Deus Thindwa, Nicole Wolter, Amy Pinsent, Maimuna Carrim, John Ojal, Stefano Tempia, Jocelyn Moyes, Meredith McMorrow, Jackie Kleynhans, Anne von Gottberg, Neil French, PHIRST group, Cheryl Cohen, Stefan Flasche:
  Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study.
• 
  Zhuo-Cheng Xiao, Kevin K. Lin, Lai-Sang Young:
  A data-informed mean-field approach to mapping of cortical parameter landscapes.
• 
  Melanie E. Moses, Steven A. Hofmeyr, Judy L. Cannon, Akil Andrews, Rebekah Gridley, Monica Hinga, Kirtus G. Leyba, Abigail Pribisova, Vanessa Surjadidjaja, Humayra Tasnim, Stephanie Forrest:
  Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection.
• 
  Matthew N. McCall, Chin-Yi Chu, Lu Wang, Lauren Benoodt, Juilee Thakar, Anthony Corbett, Jeanne Holden-Wiltse, Christopher Slaunwhite, Alex Grier, Steven R. Gill, Ann R. Falsey, David J. Topham, Mary T. Caserta, Edward E. Walsh, Xing Qiu, Thomas J. Mariani:
  A systems genomics approach uncovers molecular associates of RSV severity.
• 
  Jessica R. Parker, Alexander N. Klishko, Boris I. Prilutsky, Gennady S. Cymbalyuk:
  Asymmetric and transient properties of reciprocal activity of antagonists during the paw-shake response in the cat.
• 
  Robin Schmucker, Gabriele Farina, James R. Faeder, Fabian Fröhlich, Ali Sinan Saglam, Tuomas Sandholm:
  Combination treatment optimization using a pan-cancer pathway model.
• 
  Takashi Morita, Hiroki Koda, Kazuo Okanoya, Ryosuke Tachibana:
  Measuring context dependency in birdsong using artificial neural networks.
• 
  Daniel Müller-Komorowska, Ana Parabucki, Gal Elyasaf, Yonatan Katz, Heinz Beck, Ilan Lampl:
  A novel theoretical framework for simultaneous measurement of excitatory and inhibitory conductances.
• 
  Marta Zaffaroni, Loup Rimbaud, Ludovic Mailleret, Nik J. Cunniffe, Daniele Bevacqua:
  Modelling interference between vectors of non-persistently transmitted plant viruses to identify effective control strategies.
• 
  Xiamin Leng, Debbie Yee, Harrison Ritz, Amitai Shenhav:
  Dissociable influences of reward and punishment on adaptive cognitive control.
• 
  Samuel E. Champer, Nathan Oakes, Ronin Sharma, Pablo García-Díaz, Jackson Champer, Philipp W. Messer:
  Modeling CRISPR gene drives for suppression of invasive rodents using a supervised machine learning framework.
• 
  Benjamin G. Weiner, Andrew G. T. Pyo, Yigal Meir, Ned S. Wingreen:
  Motif-pattern dependence of biomolecular phase separation driven by specific interactions.
• 
  Lara Connolley, Joanna Szczepaniak, Colin Kleanthous, Seán M. Murray:
  The quantitative basis for the redistribution of immobile bacterial lipoproteins to division septa.
• 
  Yuzhen Liang, Chunwu Yu, Wentao Ma:
  The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life.
• 
  Phuc Nguyen, Sylvia Chien, Jin Dai, Raymond J. Monnat Jr., Pamela S. Becker, Hao Yuan Kueh:
  Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies.
• 
  Chiara Gastaldi, Tilo Schwalger, Emanuela De Falco, Rodrigo Quian Quiroga, Wulfram Gerstner:
  When shared concept cells support associations: Theory of overlapping memory engrams.
• 
  Elishai Ezra Tsur, Oren Amsalem, Lea Ankri, Pritish Patil, Idan Segev, Michal Rivlin-Etzion:
  Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity.
• 
  Nik J. Cunniffe, Nick P. Taylor, Frédéric M. Hamelin, Michael J. Jeger:
  Epidemiological and ecological consequences of virus manipulation of host and vector in plant virus transmission.
• 
  Ariel Zylberberg:
  Decision prioritization and causal reasoning in decision hierarchies.

Corrections

• 
  Zhenxing Wu, Kai Zhao:
  Correction: Taste of time: A porous-medium model for human tongue surface with implications for early taste perception.
• 
  Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherratt, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey:
  Correction: Practical considerations for measuring the effective reproductive number, Rt.
• 
  Pascal F. Hagolani, Roland Zimm, Renske M. A. Vroomans, Isaac Salazar-Ciudad:
  Correction: On the evolution and development of morphological complexity: A view from gene regulatory networks.
• 
  Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, David Vallenet:
  Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
• 
  Jonathan Cannon:
  Correction: Expectancy-based rhythmic entrainment as continuous Bayesian inference.
• 
  Alejandro Tabas, Martin Andermann, Valeria Schuberth, Helmut Riedel, Emili Balaguer-Ballester, André Rupp:
  Correction: Modeling and MEG evidence of early consonance processing in auditory cortex.
• 
  Fillipe Georgiou, Jérôme Buhl, J. Edward F. Green, Bishnu P. Lamichhane, Ngamta Thamwattana:
  Correction: Modelling locust foraging: How and why food affects group formation.
• 
  Tomasz Pienko, Joanna Trylska:
  Correction: Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli.
• 
  Jichao Pan, Yan Cai, Liang Wang, Akiko Maehara, Gary S. Mintz, Dalin Tang, Zhiyong Li:
  Correction: A prediction tool for plaque progression based on patient-specific multi-physical modeling.
• 
  Emili Balaguer-Ballester, Ramon Nogueira, Juan M. Abolafia, Rubén Moreno-Bote, Maria V. Sanchez-Vives:
  Correction: Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions.