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PCA visualization of LSTM hidden layer activity of an example 7-hidden-unit RNN while performing a 2-back working memory task. Visualized are the representations of different input stimuli (each represented with a different color) when in an unprioritized state in working memory. Solid gray arrow denotes the stimulus coding axis, which will rotate counterclockwise in the image plane (defined by the 1st and 2nd PCs) as the stimulus transitions to a prioritized state (indicated by the dashed gray arrow).

Image Credit: Quan Wan, Po'stl'ab, University of Wisconsin-Madison

Editorials

Advancing code sharing in the computational biology community

Lauren Cadwallader, Feilim Mac Gabhann, Jason Papin, Virginia E. Pitzer

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010193

Ten simple rules for succeeding as an underrepresented STEM undergraduate

Melanie Duc Bo Massey, Suchinta Arif, Shanukie Embuldeniya, Karma Nanglu, Joseph Bielawski

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010101

Ten simple rules for good research practice

Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia M. Palagi, Lars G. Hemkens, Meike Ramon, Nicolas Rothen, Stephen Senn, Eva Furrer, Leonhard Held

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010139

Education

Ten simple rules for managing communications with a large number of coauthors

Robert Muscarella, Lourens Poorter

PLOS Computational Biology: published June 30, 2022 | https://doi.org/10.1371/journal.pcbi.1010185

Perspectives

Ten simple rules for good leadership

Philip E. Bourne

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010133

Ten simple rules for improving communication among scientists

Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010130

Research Articles

Developmental shifts in computations used to detect environmental controllability

Hillary A. Raab, Careen Foord, Romain Ligneul, Catherine A. Hartley

PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010120

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Alaina Shumate, Brandon Wong, Geo Pertea, Mihaela Pertea

PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009730

Spatial modelling for population replacement of mosquito vectors at continental scale

Nicholas J. Beeton, Andrew Wilkins, Adrien Ickowicz, Keith R. Hayes, Geoffrey R. Hosack

PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009526

Role of water-bridged interactions in metal ion coupled protein allostery

Xingyue Guan, Cheng Tan, Wenfei Li, Wei Wang, D. Thirumalai

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010195

sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics

Nadezhda M. Belonogova, Gulnara R. Svishcheva, Anatoly V. Kirichenko, Irina V. Zorkoltseva, Yakov A. Tsepilov, Tatiana I. Axenovich

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010172

fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions

Natalia A. Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009783

Priority-based transformations of stimulus representation in visual working memory

Quan Wan, Jorge A. Menendez, Bradley R. Postle

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009062

Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model

Aranyak Chakravarty, Mahesh V. Panchagnula, Alladi Mohan, Neelesh A. Patankar

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010143

Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis

Rishabh Rishabh, Hadi Zadeh-Haghighi, Dennis Salahub, Christoph Simon

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010198

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak, Thierry Mora

PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010167

scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics

Anne Bertolini, Michael Prummer, Mustafa Anil Tuncel, Ulrike Menzel, María Lourdes Rosano-González, Jack Kuipers, Daniel Johannes Stekhoven, Tumor Profiler consortium, Niko Beerenwinkel, Franziska Singer

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010097

CellDynaMo–stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly

Evgenii Kliuchnikov, Artem Zhmurov, Kenneth A. Marx, Alex Mogilner, Valeri Barsegov

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010165

Addressing delayed case reporting in infectious disease forecast modeling

Lauren J. Beesley, Dave Osthus, Sara Y. Del Valle

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010115

From affinity selection to kinetic selection in Germinal Centre modelling

Danial Lashgari, Elena Merino Tejero, Michael Meyer-Hermann, Mathieu A. F. Claireaux, Marit J. van Gils, Huub C. J. Hoefsloot, Antoine H. C. van Kampen

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010168

A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait

Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009398

Strain design optimization using reinforcement learning

Maryam Sabzevari, Sandor Szedmak, Merja Penttilä, Paula Jouhten, Juho Rousu

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010177

Quantifying the impact of ecological memory on the dynamics of interacting communities

Moein Khalighi, Guilhem Sommeria-Klein, Didier Gonze, Karoline Faust, Leo Lahti

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009396

Induced fit with replica exchange improves protein complex structure prediction

Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray

PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010124

Fluid mechanics of the zebrafish embryonic heart trabeculation

Adriana Gaia Cairelli, Renee Wei-Yan Chow, Julien Vermot, Choon Hwai Yap

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010142

Characterizing collaborative transcription regulation with a graph-based deep learning approach

Zhenhao Zhang, Fan Feng, Jie Liu

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010162

Finding landmarks - An investigation of viewing behavior during spatial navigation in VR using a graph-theoretical analysis approach

Jasmin L. Walter, Lucas Essmann, Sabine U. König, Peter König

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009485

Non-monotonic effects of GABAergic synaptic inputs on neuronal firing

Aghil Abed Zadeh, Brandon D. Turner, Nicole Calakos, Nicolas Brunel

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010226

Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics

Hyun Kim, Cheolhong Min, Byeongha Jeong, Kyoung J. Lee

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010213

Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks

María Hernández Mesa, Jonas van den Brink, William E. Louch, Kimberly J. McCabe, Padmini Rangamani

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010126

Model-checking ecological state-transition graphs

Colin Thomas, Maximilien Cosme, Cédric Gaucherel, Franck Pommereau

PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009657

Whole community invasions and the integration of novel ecosystems

Colin Campbell, Laura Russo, Réka Albert, Angus Buckling, Katriona Shea

PLOS Computational Biology: published June 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010151

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics

Tinghua Huang, Hong Xiao, Qi Tian, Zhen He, Cheng Yuan, Zezhao Lin, Xuejun Gao, Min Yao

PLOS Computational Biology: published June 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009773

An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise

Tom Van Wouwe, Lena H. Ting, Friedl De Groote

PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009338

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Florian Auer, Simone Mayer, Frank Kramer

PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010205

Annotation-free delineation of prokaryotic homology groups

Yongze Yin, Huw A. Ogilvie, Luay Nakhleh

PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010216

Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors

Niranjan Sarpangala, Ajay Gopinathan

PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010217

Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge

PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010228

Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission

Israel Ukawuba, Jeffrey Shaman

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010161

The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition

Benjamin Gagl, Fabio Richlan, Philipp Ludersdorfer, Jona Sassenhagen, Susanne Eisenhauer, Klara Gregorova, Christian J. Fiebach

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009995

Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data

Pratik Mullick, Sylvain Fontaine, Cécile Appert-Rolland, Anne-Hélène Olivier, William H. Warren, Julien Pettré

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010210

Contextual cues are not unique for motor learning: Task-dependant switching of feedback controllers

Justinas Česonis, David W. Franklin

PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010192

Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice

Elke Smith, Jan Peters

PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010096

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

Maksim Zakhartsev, Filip Rotnes, Marie Gulla, Ove Øyås, Jesse C. J. van Dam, Maria Suarez-Diez, Fabian Grammes, Róbert Anton Hafþórsson, Wout van Helvoirt, Jasper J. Koehorst, Peter J. Schaap, Yang Jin, Liv Torunn Mydland, Arne B. Gjuvsland, Simen R. Sandve, Vitor A. P. Martins dos Santos, Jon Olav Vik

PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010194

Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)

Anika Liu, Namshik Han, Jordi Munoz-Muriedas, Andreas Bender

PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010148

HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data

Qing Xie, Chenggong Han, Victor Jin, Shili Lin

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010129

Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation

Alfonso Santiago, Constantine Butakoff, Beatriz Eguzkitza, Richard A. Gray, Karen May-Newman, Pras Pathmanathan, Vi Vu, Mariano Vázquez

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010141

Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue

Sang-Woo Lee, Yoshihiro Morishita

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010178

Differential methods for assessing sensitivity in biological models

Rachel Mester, Alfonso Landeros, Chris Rackauckas, Kenneth Lange

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009598

cytoNet: Spatiotemporal network analysis of cell communities

Arun S. Mahadevan, Byron L. Long, Chenyue W. Hu, David T. Ryan, Nicolas E. Grandel, George L. Britton, Marisol Bustos, Maria A. Gonzalez Porras, Katerina Stojkova, Andrew Ligeralde, Hyeonwi Son, John Shannonhouse, Jacob T. Robinson, Aryeh Warmflash, Eric M. Brey, Yu Shin Kim, Amina A. Qutub

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009846

Discrete modeling for integration and analysis of large-scale signaling networks

Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010175

A mechanism for punctuating equilibria during mammalian vocal development

Thiago T. Varella, Yisi S. Zhang, Daniel Y. Takahashi, Asif A. Ghazanfar

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010173

Modeling cell biological features of meiotic chromosome pairing to study interlock resolution

Erik J. Navarro, Wallace F. Marshall, Jennifer C. Fung

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010252

Computational simulations and Ca²⁺ imaging reveal that slow synaptic depolarizations (slow EPSPs) inhibit fast EPSP evoked action potentials for most of their time course in enteric neurons

Parvin Zarei Eskikand, Katerina Koussoulas, Rachel M. Gwynne, Joel C. Bornstein

PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009717

Direct reciprocity between individuals that use different strategy spaces

Laura Schmid, Christian Hilbe, Krishnendu Chatterjee, Martin A. Nowak

PLOS Computational Biology: published June 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010149

Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning

Beatriz Eymi Pimentel Mizusaki, Sally Si Ying Li, Rui Ponte Costa, Per Jesper Sjöström

PLOS Computational Biology: published June 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009409

Explainable detection of adverse drug reaction with imbalanced data distribution

Jin Wang, Liang-Chih Yu, Xuejie Zhang

PLOS Computational Biology: published June 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010144

SPF: A spatial and functional data analytic approach to cell imaging data

Thao Vu, Julia Wrobel, Benjamin G. Bitler, Erin L. Schenk, Kimberly R. Jordan, Debashis Ghosh

PLOS Computational Biology: published June 15, 2022 | https://doi.org/10.1371/journal.pcbi.1009486

Orchestrated neuronal migration and cortical folding: A computational and experimental study

Shuolun Wang, Kengo Saito, Hiroshi Kawasaki, Maria A. Holland

PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010190

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach

Mahmudul Hasan Rifat, Jamil Ahmed, Milad Ahmed, Foeaz Ahmed, Airin Gulshan, Mahmudul Hasan

PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009539

A weighted constraint satisfaction approach to human goal-directed decision making

Yuxuan Li, James L. McClelland

PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009553

Active inference unifies intentional and conflict-resolution imperatives of motor control

Antonella Maselli, Pablo Lanillos, Giovanni Pezzulo

PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010095

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Shengbo Wang, David García-Seisdedos, Ananth Prakash, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Silvie Fexova, Pablo Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno

PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010174

Size regulation of multiple organelles competing for a limiting subunit pool

Deb Sankar Banerjee, Shiladitya Banerjee

PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010253

Metastable spiking networks in the replica-mean-field limit

Luyan Yu, Thibaud O. Taillefumier

PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010215

Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain

Kayson Fakhar, Claus C. Hilgetag

PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010250

Efficient Bayesian inference for mechanistic modelling with high-throughput data

Simon Martina Perez, Heba Sailem, Ruth E. Baker

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010191

Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data

Toshitake Asabuki, Prajakta Kokate, Tomoki Fukai

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010214

Towards a more general understanding of the algorithmic utility of recurrent connections

Brett W. Larsen, Shaul Druckmann

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010227

Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance

Mikahl Banwarth-Kuhn, Kevin Rodriguez, Christian Michael, Calvin-Khang Ta, Alexander Plong, Eric Bourgain-Chang, Ali Nematbakhsh, Weitao Chen, Amit Roy-Chowdhury, G. Venugopala Reddy, Mark Alber

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010199

Error-based or target-based? A unified framework for learning in recurrent spiking networks

Cristiano Capone, Paolo Muratore, Pier Stanislao Paolucci

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010221

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

Christos Maniatis, Catalina A. Vallejos, Guido Sanguinetti

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010163

Sequence learning, prediction, and replay in networks of spiking neurons

Younes Bouhadjar, Markus Diesmann, Dirk J. Wouters, Tom Tetzlaff

PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010233

Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks

Timon Wittenstein, Nava Leibovich, Andreas Hilfinger

PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010183

A method for the inference of cytokine interaction networks

Joanneke E. Jansen, Dominik Aschenbrenner, Holm H. Uhlig, Mark C. Coles, Eamonn A. Gaffney

PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010112

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases

Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman

PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009414

Topological Sholl descriptors for neuronal clustering and classification

Reem Khalil, Sadok Kallel, Ahmad Farhat, Pawel Dlotko

PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010229

Tracking the contribution of inductive bias to individualised internal models

Balázs Török, David G. Nagy, Mariann Kiss, Karolina Janacsek, Dezső Németh, Gergő Orbán

PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010182

Epidemic management and control through risk-dependent individual contact interventions

Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas Böttcher, Dmitry Burov, Alfredo Garbuno-Inigo, Gregory L. Wagner, Sen Pei, Chiara Daraio, Raffaele Ferrari, Jeffrey Shaman

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010171

Image-based parameter inference for epithelial mechanics

Goshi Ogita, Takefumi Kondo, Keisuke Ikawa, Tadashi Uemura, Shuji Ishihara, Kaoru Sugimura

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010209

Interpretable pairwise distillations for generative protein sequence models

Christoph Feinauer, Barthelemy Meynard-Piganeau, Carlo Lucibello

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010219

Modeling cortical synaptic effects of anesthesia and their cholinergic reversal

Bolaji P. Eniwaye, Victoria Booth, Anthony G. Hudetz, Michal Zochowski

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009743

LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production

Hasini R. Weerathunge, Gabriel A. Alzamendi, Gabriel J. Cler, Frank H. Guenther, Cara E. Stepp, Matías Zañartu

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010159

Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit

Catalina Vich, Matthew Clapp, Jonathan E. Rubin, Timothy Verstynen

PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010255

Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study

Naomi R. Waterlow, Michiko Toizumi, Edwin van Leeuwen, Hien-Anh Thi Nguyen, Lay Myint-Yoshida, Rosalind M. Eggo, Stefan Flasche

PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010234

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Hamid Alinejad-Rokny, Rassa Ghavami Modegh, Hamid R. Rabiee, Ehsan Ramezani Sarbandi, Narges Rezaie, Kin Tung Tam, Alistair R. R. Forrest

PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010241

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale

Vítor Vieira, Jorge Ferreira, Miguel Rocha

PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009294

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design

Jeremy Grignard, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval, François Fages

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010236

Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling

Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Loewer, Mária Lukáčová-Medvid’ová, Stefan Legewie

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010266

Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data

Jair Andrade, Jim Duggan

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010206

An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China

Yuliang Chen, Tao Liu, Xiaolin Yu, Qinghui Zeng, Zixi Cai, Haisheng Wu, Qingying Zhang, Jianpeng Xiao, Wenjun Ma, Sen Pei, Pi Guo

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010218

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology

Laurynas Kalesinskas, Sanjana Gupta, Purvesh Khatri

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010260

Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIα and MeCP2

Yili Zhang, Paul Smolen, Cristina M. Alberini, Douglas A. Baxter, John H. Byrne

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010239

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

Raphael R. Eguchi, Christian A. Choe, Po-Ssu Huang

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010271

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase

Gabriel Monteiro da Silva, Jordan Yang, Bunlong Leang, Jessie Huang, Daniel M. Weinreich, Brenda M. Rubenstein

PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1009944

June 2022

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