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PLoS Computational Biology, Volume 17
Volume 17, Number 1, January 2021
- 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.
- Mehmet Aziz Yirik
, Christoph Steinbeck
:
Chemical graph generators.
- 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. - 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
- 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.
- 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.
- Johannes Bracher
, Evan L. Ray, Tilmann Gneiting
, Nicholas G. Reich
:
Evaluating epidemic forecasts in an interval format.
- 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.
- 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
- 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.
- 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.
- 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 Días
:
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.
- 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
- 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.
- 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
- 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.
- 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?
- 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.
- 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
- 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.
- 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.
- Jitao David Zhang
:
Ten simple rules for doing a postdoc in pharma.
- 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.
- 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.
- PLOS Computational Biology Staff:
Correction: A new model for simultaneous dimensionality reduction and time-varying functional connectivity estimation.
Volume 17, Number 7, July 2021
- 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.
- 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.