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ORCIDPLoS Computational Biology, Volume 19
Volume 19, Number 1, January 2023
- Vishal H. Oza
, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina E. Uno-Antonison, Brandon M. Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, Brittany N. Lasseigne:
Ten simple rules for using public biological data for your research. - Davide Chicco, Rakesh Shiradkar:
Ten quick tips for computational analysis of medical images. - Saskia D. Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J. Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina P. Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi A. Bacon, Fotis E. Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, The Galaxy Team, Björn A. Grüning, Bérénice Batut:
Galaxy Training: A powerful framework for teaching!
- William Stafford Noble:
Ten simple rules for defining a computational biology project.
- Verena Heise, Constance Holman, Hung Lo, Ekaterini Maria Lyras, Mark Christopher Adkins, Maria Raisa Jessica Aquino, Konstantinos I. Bougioukas, Katherine O. Bray, Martyna Gajos, Xuanzong Guo, Corinna Hartling, Rodrigo Huerta-Gutierrez, Miroslava Jindrová, Joanne P. M. Kenney, Adrianna P. Kepinska, Laura Kneller, Elena Lopez-Rodriguez, Felix Mühlensiepen, Angela Richards, Gareth Richards, Maximilian Siebert, James A. Smith, Natalie Smith, Nicolai Stransky, Sirpa Tarvainen, Daniela Sofia Valdes, Kayleigh L. Warrington, Nina-Maria Wilpert, Disa Witkowska, Mirela Zaneva, Jeanette Zanker, Tracey L. Weissgerber:
Ten simple rules for implementing open and reproducible research practices after attending a training course.
- Migle Gabrielaite, Marc Bennedbæk, Malthe Sebro Rasmussen, Virginia Kan, Hansjakob Furrer, Robert Flisiak, Marcelo Losso, Jens D. Lundgren, INSIGHT START Study Group, Rasmus L. Marvig:
Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load. - Polina A. Lakrisenko, Paul Stapor, Stephan Grein, Lukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer:
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. - Frédéric Labbé, Qixin He, Qi Zhan, Kathryn E. Tiedje, Dionne C. Argyropoulos, Mun Hua Tan, Anita Ghansah, Karen P. Day, Mercedes Pascual:
Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections. - Yann Roussel, Csaba Verasztó, Dimitri Rodarie, Tanguy Damart, Michael W. Reimann, Srikanth Ramaswamy, Henry Markram, Daniel Keller:
Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons. - Connor Brennan, Adeeti Aggarwal, Rui Pei, David Sussillo, Alex Proekt:
One dimensional approximations of neuronal dynamics reveal computational strategy. - Sebastian Sten, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, Gunnar Cedersund:
A quantitative model for human neurovascular coupling with translated mechanisms from animals. - Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina J. Kechris:
RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks. - Hongxuan Zhai, Julia Fukuyama:
A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures. - Nicola Catenacci Volpi, Martin Greaves, Dari Trendafilov, Christoph Salge, Giovanni Pezzulo, Daniel Polani:
Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions. - Jason Asher, Annabelle Lemenuel-Diot, Matthew Clay, David P. Durham, Luis Mier-y-Teran-Romero, Carlos J. Arguello, Sébastien Jolivet, Diana Y. Wong, Klaus Kuhlbusch, Barry Clinch, Jean-Eric Charoin:
Novel modelling approaches to predict the role of antivirals in reducing influenza transmission. - Lujun Shen, Jinqing Mo, Changsheng Yang, Yiquan Jiang, Liangru Ke, Dan Hou, Jingdong Yan, Tao Zhang, Weijun Fan:
SurvivalPath:A R package for conducting personalized survival path mapping based on time-series survival data. - Junping Li, Lin Gao, Yusen Ye:
HiSV: A control-free method for structural variation detection from Hi-C data. - Gian Luca Lancia, Mattia Eluchans, Marco D'Alessandro, Hugo J. Spiers, Giovanni Pezzulo:
Humans account for cognitive costs when finding shortcuts: An information-theoretic analysis of navigation. - Theresa Ullmann, Stefanie Peschel, Philipp F. M. Baumann, Christian L. Müller, Anne-Laure Boulesteix:
Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering. - Jiani Chen, Swan Tan, Vasanthi Avadhanula, Leonard Moise, Pedro A. Piedra, Anne S. De Groot, Justin Bahl:
Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. - Artem S. Kasianov, Anna V. Klepikova, Alexey V. Mayorov, Gleb S. Buzanov, Maria D. Logacheva, Aleksey A. Penin:
Interspecific comparison of gene expression profiles using machine learning. - Ashish B. George, Kirill S. Korolev:
Ecological landscapes guide the assembly of optimal microbial communities. - Noga Mosheiff, Bard Ermentrout, Chengcheng Huang:
Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability. - Ivan Lazarevich, Ilya Prokin, Boris Gutkin, Victor B. Kazantsev:
Spikebench: An open benchmark for spike train time-series classification. - Ryan J. Murphy, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson:
Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability. - Kai Siedenburg, Jackson E. Graves, Daniel Pressnitzer:
A unitary model of auditory frequency change perception. - Kahlan E. Newman, Syma Khalid:
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. - Garima Singh, Mehmet A. Orman, Jacinta C. Conrad, Michael Nikolaou:
Systematic design of pulse dosing to eradicate persister bacteria. - Adrianne L. Jenner, Wayne Kelly, Michael Dallaston, Robyn Araujo, Isobelle Parfitt, Dominic Steinitz, Pantea Pooladvand, Peter S. Kim, Samantha J. Wade, Kara L. Vine:
Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model. - Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie:
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. - Caleb M. Phillips, Ernesto A. B. F. Lima, Manasa Gadde, Angela M. Jarrett, Marissa Nichole Rylander, Thomas E. Yankeelov:
Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis. - Timo Flesch, David G. Nagy, Andrew M. Saxe, Christopher Summerfield:
Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals. - Yuki Sugiyama, Kohei Uno, Yusuke Matsui:
Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments. - Omri David Gilday, Benedikt Praegel, Ido Maor, Tav Cohen, Israel Nelken, Adi Mizrahi:
Surround suppression in mouse auditory cortex underlies auditory edge detection. - Oshane O. Thomas, Hongyu Shen, Ryan L. Raaum, William E. H. Harcourt-Smith, John D. Polk, Mark Hasegawa-Johnson:
Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics. - Alexander P. Browning, Matthew J. Simpson:
Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates. - Daipeng Chen, Zary Forghany, Xinxin Liu, Haijiang Wang, Roeland M. H. Merks, David A. Baker:
A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers. - Carlos Gueto-Tettay, Di Tang, Lotta Happonen, Moritz Heusel, Hamed Khakzad, Johan Malmström, Lars Malmström:
Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics. - Solveig Engebretsen, Alfonso Diz-Lois Palomares, Gunnar Rø, Anja Bråthen Kristoffersen, Jonas Christoffer Lindstrøm, Kenth Engø-Monsen, Meghana Kamineni, Louis Yat Hin Chan, Ørjan Dale, Jørgen Eriksson Midtbø, Kristian Lindalen Stenerud, Francesco Di Ruscio, Richard White, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting. - Gregory J. Kimmel, Richard J. Beck, Xiaoqing Yu, Thomas Veith, Samuel Bakhoum, Philipp M. Altrock, Noemi Andor:
Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction. - Arash Mehrjou, Ashkan Soleymani, Amin Abyaneh, Samir Bhatt, Bernhard Schölkopf, Stefan Bauer:
Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases. - Yuxiu Shao, Srdjan Ostojic:
Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks. - Joel Roca-Martínez, Hrishikesh Dhondge, Michael Sattler, Wim F. Vranken:
Deciphering the RRM-RNA recognition code: A computational analysis. - Eric C. Dykeman:
Modelling ribosome kinetics and translational control on dynamic mRNA. - Fabian A. Soto, Sanjay Narasiwodeyar:
Improving the validity of neuroimaging decoding tests of invariant and configural neural representation. - Cristoforo Simonetto, Ulrich Mansmann, Jan Christian Kaiser:
Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models. - David J. Jörg, Doris H. Fuertinger, Peter Kotanko:
Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents. - Malte Schilling, Holk Cruse:
neuroWalknet, a controller for hexapod walking allowing for context dependent behavior. - Sören von Bülow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer:
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. - Joonas P. Kosonen, Atte S. A. Eskelinen, Gustavo A. Orozco, Petteri Nieminen, Donald D. Anderson, Alan J. Grodzinsky, Rami K. Korhonen, Petri Tanska:
Injury-related cell death and proteoglycan loss in articular cartilage: Numerical model combining necrosis, reactive oxygen species, and inflammatory cytokines. - Mei Ma, Xiujuan Lei:
A dual graph neural network for drug-drug interactions prediction based on molecular structure and interactions. - Edoardo Pinzuti, Patricia Wollstadt, Oliver Tüscher, Michael Wibral:
Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia. - Sebastian Goldt, Florent Krzakala, Lenka Zdeborová, Nicolas Brunel:
Bayesian reconstruction of memories stored in neural networks from their connectivity. - Jacob D. O'Sullivan, J. Christopher D. Terry, Ramesh Wilson, Axel G. Rossberg:
Community composition exceeds area as a predictor of long-term conservation value. - Diana Burk, Bruno B. Averbeck:
Environmental uncertainty and the advantage of impulsive choice strategies. - Yibo Zhao, Nikoleta Vavouraki, Ruth C. Lovering, Valentina Escott-Price, Kirsten Harvey, Patrick A. Lewis, Claudia Manzoni:
Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit. - Tareian A. Cazares, Faiz W. Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T. Bejjani, Joseph A. Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C. Kottyan, Artem Barski, Matthew T. Weirauch, V. B. Surya Prasath, Emily R. Miraldi:
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
- Daniel Cresta, Donald C. Warren, Christian Quirouette, Amanda P. Smith, Lindey C. Lane, Amber M. Smith, Catherine A. A. Beauchemin:
Correction: Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration.
Volume 19, Number 2, February 2023
- Roberto Marangoni, Vitoantonio Bevilacqua, Mario Cannataro, Bruno Hay Mele, Giancarlo Mauri, Anna Marabotti:
An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS.
- Liberata A. Mwita, William F. Mawalla, Frank R. Mtiiye, Daniel Kandonga, Jill Kent, Julie Makani, Raphael Zozimus Sangeda:
Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme.
- Mojtaba Madadi Asl, Alireza Valizadeh, Peter A. Tass:
Decoupling of interacting neuronal populations by time-shifted stimulation through spike-timing-dependent plasticity. - Hippolyte Verdier, François Laurent, Alhassan Cassé, Christian L. Vestergaard, Christian G. Specht, Jean-Baptiste Masson:
Simulation-based inference for non-parametric statistical comparison of biomolecule dynamics. - Jérôme Tubiana, Lucia Adriana-Lifshits, Michael Nissan, Matan Gabay, Inbal Sher, Marina Sova, Haim J. Wolfson, Maayan Gal:
Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions. - Francesca A. Lovell-Read, Stephen Parnell, Nik J. Cunniffe, Robin N. Thompson:
Using 'sentinel' plants to improve early detection of invasive plant pathogens. - Giulio Ruffini, Giada Damiani, Diego Lozano-Soldevilla, Nikolas Deco, Fernando E. Rosas, Narsis A. Kiani, Adrián Ponce-Alvarez, Morten L. Kringelbach, Robin L. Carhart-Harris, Gustavo Deco:
LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics. - Rossana Bettoni, Clare Hudson, Géraldine Williaume, Cathy Sirour, Hitoyoshi Yasuo, Sophie de Buyl, Geneviève Dupont:
Model of neural induction in the ascidian embryo. - David Lipshutz, Aneesh Kashalikar, Shiva Farashahi, Dmitri B. Chklovskii:
A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment. - Liam Lang, Giancarlo La Camera, Alfredo Fontanini:
Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex. - S. Amin Moosavi, Wilson Truccolo:
Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures. - Jue Tao Lim, Kelvin Bryan Tan, John Arputhan Abisheganaden, Borame L. Dickens:
Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations. - Chenxi Liao, Masataka Sawayama, Bei Xiao:
Unsupervised learning reveals interpretable latent representations for translucency perception. - Irene Elices, Anirudh Kulkarni, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Michel Prevost, Romain Brette:
An electrophysiological and kinematic model of Paramecium, the "swimming neuron". - Ke Li, James M. McCaw, Pengxing Cao:
Enhanced viral infectivity and reduced interferon production are associated with high pathogenicity for influenza viruses. - Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft:
iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. - Gerald K. Cooray, Richard Rosch, Karl John Friston:
Global dynamics of neural mass models. - Tamara Raschka, Meemansa Sood, Bruce Schultz, Aybuge Altay, Christian Ebeling, Holger Fröhlich:
AI reveals insights into link between CD33 and cognitive impairment in Alzheimer's Disease. - Mohammad Dehghani-Habibabadi, Klaus Pawelzik:
Synaptic self-organization of spatio-temporal pattern selectivity. - Francesca Callegari, Martina Brofiga, Paolo Massobrio:
Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays. - Fengrong He, Ian H. Stevenson, Monty A. Escabí:
Two stages of bandwidth scaling drives efficient neural coding of natural sounds. - Takayuki Niizato, Hisashi Murakami, Takuya Musha:
Functional duality in group criticality via ambiguous interactions. - Julia Deichmann, Sara Bachmann, Marie-Anne Burckhardt, Marc Pfister, Gabor Szinnai, Hans-Michael Kaltenbach:
New model of glucose-insulin regulation characterizes effects of physical activity and facilitates personalized treatment evaluation in children and adults with type 1 diabetes. - Karoline Horgmo Jæger, Ena Ivanovic, Jan P. Kucera, Aslak Tveito:
Nano-scale solution of the Poisson-Nernst-Planck (PNP) equations in a fraction of two neighboring cells reveals the magnitude of intercellular electrochemical waves. - Bjarke Frost Nielsen, Chadi M. Saad-Roy, Yimei Li, Kim Sneppen, Lone Simonsen, Cécile Viboud, Simon A. Levin, Bryan T. Grenfell:
Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. - Brian Nils Lundstrom, Thomas J. Richner:
Neural adaptation and fractional dynamics as a window to underlying neural excitability. - Matthew E. Berginski, Chinmaya U. Joisa, Brian T. Golitz, Shawn M. Gomez:
Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. - Maryl Lambros, Yehonatan Sella, Aviv Bergman:
Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms. - Aaditya V. Rangan, Caroline C. McGrouther, Nivedita Bhadra, Stephanie Venn-Watson, Eric D. Jensen, Nicholas J. Schork:
A time-series analysis of blood-based biomarkers within a 25-year longitudinal dolphin cohort. - Samuel Goldman, Maximino Aldana, Philippe Cluzel:
Resonant learning in scale-free networks. - Philipp Fey, Daniel Ludwig Weber, Jannik Stebani, Philipp Mörchel, Peter Jakob, Jan Hansmann, Karl-Heinz Hiller, Daniel Haddad:
Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence. - Yichen He, Christopher R. Cooney, Steve Maddock, Gavin H. Thomas:
Using pose estimation to identify regions and points on natural history specimens. - Jake M. Ferguson, Andrea González-González, Johnathan A. Kaiser, Sara M. Winzer, Justin M. Anast, Ben Ridenhour, Tanya A. Miura, Christine E. Parent:
Hidden variable models reveal the effects of infection from changes in host survival. - Rion Brattig Correia, Alain Barrat, Luis M. Rocha:
Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs. - Madison S. Krieger:
Evolutionary dynamics of hyperbolic language. - Rocky Diegmiller, Jasmin Imran Alsous, Duojia Li, Yukiko M. Yamashita, Stanislav Y. Shvartsman:
Fusome topology and inheritance during insect gametogenesis. - John G. Holman, Winnie W. K. Lai, Paul Pichler, Daniel Saska, Leon Lagnado, Christopher L. Buckley:
A behavioral and modeling study of control algorithms underlying the translational optomotor response in larval zebrafish with implications for neural circuit function. - Weicheng Qian, Kevin Gordon Stanley, Nathaniel David Osgood:
Impacts of observation frequency on proximity contact data and modeled transmission dynamics. - David J. Haw, Matthew Biggerstaff, Pragati Prasad, Joseph Walker, Bryan T. Grenfell, Nimalan Arinaminpathy:
Using real-time data to guide decision-making during an influenza pandemic: A modelling analysis. - Boya Yang, Jiaxu Li, Michael J. Haller, Desmond A. Schatz, Libin Rong:
Modeling the progression of Type 2 diabetes with underlying obesity. - Inge M. N. Wortel, Johannes Textor:
Interpreting T-cell search "strategies" in the light of evolution under constraints. - Luke Trinity, Ian Wark, Lance Lansing, Hosna Jabbari, Ulrike Stege:
Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.
Volume 19, Number 3, March 2023
- Ryan R. Wick, Louise M. Judd, Kathryn E. Holt:
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. - Ruth Nanjala, Festus Nyasimi, Daniel Masiga, Caleb Kipkurui Kibet:
A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya. - Cameron Mura, Philip E. Bourne:
Ten simple rules for serving as an editor. - David Moreau, Kristina Wiebels:
Ten simple rules for designing and conducting undergraduate replication projects. - Alon Zivony, Rasha Kardosh, Liadh Timmins, Niv Reggev:
Ten simple rules for socially responsible science.
- Darya Pokutnaya, Bruce Childers, Alice E. Arcury-Quandt, Harry Hochheiser, Willem G. Van Panhuis:
An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases.
- Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chrétien, Eric Rosenthal, Gérard Le Goff, David Moher, John P. A. Ioannidis, Florian Naudet:
Ten (not so) simple rules for clinical trial data-sharing.
- Karina Arias-Calluari, Theotime Colin, Tanya Latty, Mary Myerscough, Eduardo G. Altmann:
Modelling daily weight variation in honey bee hives.