February 2020

The arrangement of stimulus representations in neural population response space determines how robust these representations are to noise, as their arrangement determines which noise perturbations (grey arrows) can be corrected by a decoder (green arrow) and which cannot (red arrow). Johnston et al. shows that nonlinear mixed selectivity for multiple stimulus features produces stimulus representations that are well separated in response space and, as a result, far more robust to noise than selectivity that encodes different stimulus features either separately or with only linear mixing – even when both encodings use the same amount of metabolic resources.

Image Credit: W. Jeffrey Johnston, The University of Chicago

Editorials

Ten simple rules for getting started on Twitter as a scientist

Veronika Cheplygina, Felienne Hermans, Casper Albers, Natalia Bielczyk, Ionica Smeets

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007513

Ten Simple Rules to becoming a principal investigator

John S. Tregoning, Jason E. McDermott

PLOS Computational Biology: published February 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007448

Research Articles

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

Janine Arloth, Gökcen Eraslan, Till F. M. Andlauer, Jade Martins, Stella Iurato, Brigitte Kühnel, Melanie Waldenberger, Josef Frank, Ralf Gold, Bernhard Hemmer, Felix Luessi, Sandra Nischwitz, Friedemann Paul, Heinz Wiendl, Christian Gieger, Stefanie Heilmann-Heimbach, Tim Kacprowski, Matthias Laudes, Thomas Meitinger, Annette Peters, Rajesh Rawal, Konstantin Strauch, Susanne Lucae, Bertram Müller-Myhsok, Marcella Rietschel, Fabian J. Theis, Elisabeth B. Binder, Nikola S. Mueller

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007616

Changes-of-mind in the absence of new post-decision evidence

Nadim A. A. Atiya, Arkady Zgonnikov, Denis O’Hora, Martin Schoemann, Stefan Scherbaum, KongFatt Wong-Lin

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007149

Optimality of sparse olfactory representations is not affected by network plasticity

Collins Assisi, Mark Stopfer, Maxim Bazhenov

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007461

Surprise response as a probe for compressed memory states

Hadar Levi-Aharoni, Oren Shriki, Naftali Tishby

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007065

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

Flavia Corsi, Richard Lavery, Elodie Laine, Alessandra Carbone

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007624

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

Aleksandr Ianevski, Sanna Timonen, Alexander Kononov, Tero Aittokallio, Anil K. Giri

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007604

Navigable maps of structural brain networks across species

Antoine Allard, M. Ángeles Serrano

PLOS Computational Biology: published February 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007584

Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition

Ana Moyano, Gila Lustig, Hylton E. Rodel, Tibor Antal, Alex Sigal

PLOS Computational Biology: published February 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007482

Predicting colorectal cancer risk from adenoma detection via a two-type branching process model

Brian M. Lang, Jack Kuipers, Benjamin Misselwitz, Niko Beerenwinkel

PLOS Computational Biology: published February 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007552

Opponent processes in visual memories: A model of attraction and repulsion in navigating insects’ mushroom bodies

Florent Le Möel, Antoine Wystrach

PLOS Computational Biology: published February 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007631

Orbit Image Analysis: An open-source whole slide image analysis tool

Manuel Stritt, Anna K. Stalder, Enrico Vezzali

PLOS Computational Biology: published February 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007313

What makes or breaks a campaign to stop an invading plant pathogen?

Alice E. Milne, Tim Gottwald, Stephen R. Parnell, Vasthi Alonso Chavez, Frank van den Bosch

PLOS Computational Biology: published February 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007570

The hourglass organization of the Caenorhabditis elegans connectome

Kaeser M. Sabrin, Yongbin Wei, Martijn Pieter van den Heuvel, Constantine Dovrolis

PLOS Computational Biology: published February 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007526

Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic

Susanne Reimering, Sebastian Muñoz, Alice C. McHardy

PLOS Computational Biology: published February 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007101

Multi-state design of flexible proteins predicts sequences optimal for conformational change

Marion F. Sauer, Alexander M. Sevy, James E. Crowe Jr., Jens Meiler

PLOS Computational Biology: published February 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007339

SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases

Paul Hager, Hans-Werner Mewes, Meino Rohlfs, Christoph Klein, Tim Jeske

PLOS Computational Biology: published February 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007613

A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells

Shubham Tripathi, Priyanka Chakraborty, Herbert Levine, Mohit Kumar Jolly

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007619

The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model

Ernesto Segredo-Otero, Rafael Sanjuán

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007656

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq

Xiangying Sun, Zhezhen Wang, Johnathon M. Hall, Carlos Perez-Cervantes, Alexander J. Ruthenburg, Ivan P. Moskowitz, Michael Gribskov, Xinan H. Yang

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007119

A model for time interval learning in the Purkinje cell

Daniel Majoral, Ajmal Zemmar, Raul Vicente

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007601

Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation

Simon Dirmeier, Christopher Dächert, Martijn van Hemert, Ali Tas, Natacha S. Ogando, Frank van Kuppeveld, Ralf Bartenschlager, Lars Kaderali, Marco Binder, Niko Beerenwinkel

PLOS Computational Biology: published February 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007587

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies

Shuang Song, Wei Jiang, Lin Hou, Hongyu Zhao

PLOS Computational Biology: published February 11, 2020 | https://doi.org/10.1371/journal.pcbi.1007565

A stochastic model for simulating ribosome kinetics in vivo

Eric Charles Dykeman

PLOS Computational Biology: published February 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007618

CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer

Paco Derouault, Jasmine Chauzeix, David Rizzo, Federica Miressi, Corinne Magdelaine, Sylvie Bourthoumieu, Karine Durand, Hélène Dzugan, Jean Feuillard, Franck Sturtz, Stéphane Mérillou, Anne-Sophie Lia

PLOS Computational Biology: published February 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007503

Neurogranin stimulates Ca²⁺/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies

Lu Li, Massimo Lai, Stephen Cole, Nicolas Le Novère, Stuart J. Edelstein

PLOS Computational Biology: published February 12, 2020 | https://doi.org/10.1371/journal.pcbi.1006991

A generative growth model for thalamocortical axonal branching in primary visual cortex

Pegah Kassraian-Fard, Michael Pfeiffer, Roman Bauer

PLOS Computational Biology: published February 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007315

SuperFreq: Integrated mutation detection and clonal tracking in cancer

Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J. Majewski

PLOS Computational Biology: published February 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007603

Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis

Qian-Yuan Tang, Kunihiko Kaneko

PLOS Computational Biology: published February 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007670

Coding with transient trajectories in recurrent neural networks

Giulio Bondanelli, Srdjan Ostojic

PLOS Computational Biology: published February 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007655

Bayesian inference and comparison of stochastic transcription elongation models

Jordan Douglas, Richard Kingston, Alexei J. Drummond

PLOS Computational Biology: published February 14, 2020 | https://doi.org/10.1371/journal.pcbi.1006717

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method

Kosuke Hamazaki, Hiroyoshi Iwata

PLOS Computational Biology: published February 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007663

From whole-organ imaging to in-silico blood flow modeling: A new multi-scale network analysis for revisiting tissue functional anatomy

Pol Kennel, Jules Dichamp, Corinne Barreau, Christophe Guissard, Lise Teyssedre, Jacques Rouquette, Julien Colombelli, Anne Lorsignol, Louis Casteilla, Franck Plouraboué

PLOS Computational Biology: published February 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007322

Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein

Joël R. Pradines, Victor Farutin, Nicholas A. Cilfone, Abouzar Ghavami, Elma Kurtagic, Jamey Guess, Anthony M. Manning, Ishan Capila

PLOS Computational Biology: published February 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007684

The role of adaptation in generating monotonic rate codes in auditory cortex

Jong Hoon Lee, Xiaoqin Wang, Daniel Bendor

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007627

Inferring TF activation order in time series scRNA-Seq studies

Chieh Lin, Jun Ding, Ziv Bar-Joseph

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007644

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007636

Deep Learning-driven research for drug discovery: Tackling Malaria

Bruno J. Neves, Rodolpho C. Braga, Vinicius M. Alves, Marília N. N. Lima, Gustavo C. Cassiano, Eugene N. Muratov, Fabio T. M. Costa, Carolina Horta Andrade

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007025

Nonlinear mixed selectivity supports reliable neural computation

W. Jeffrey Johnston, Stephanie E. Palmer, David J. Freedman

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007544

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

Andrei Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007652

Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit

Florian Ott, Dimitrije Marković, Alexander Strobel, Stefan J. Kiebel

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007685

Early prediction of antigenic transitions for influenza A/H3N2

Lauren A. Castro, Trevor Bedford, Lauren Ancel Meyers

PLOS Computational Biology: published February 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007683

Realistic assumptions about spatial locations and clustering of premises matter for models of foot-and-mouth disease spread in the United States

Stefan Sellman, Michael J. Tildesley, Christopher L. Burdett, Ryan S. Miller, Clayton Hallman, Colleen T. Webb, Uno Wennergren, Katie Portacci, Tom Lindström

PLOS Computational Biology: published February 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007641

Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells

Toshinori Namba, Shuji Ishihara

PLOS Computational Biology: published February 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007649

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution

Hao Hong, Shuai Jiang, Hao Li, Guifang Du, Yu Sun, Huan Tao, Cheng Quan, Chenghui Zhao, Ruijiang Li, Wanying Li, Xiaoyao Yin, Yangchen Huang, Cheng Li, Hebing Chen, Xiaochen Bo

PLOS Computational Biology: published February 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007287

Graph-based description of tertiary lymphoid organs at single-cell level

Nadine S. Schaadt, Ralf Schönmeyer, Germain Forestier, Nicolas Brieu, Peter Braubach, Katharina Nekolla, Michael Meyer-Hermann, Friedrich Feuerhake

PLOS Computational Biology: published February 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007385

Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy

Natacha Comandante-Lou, Mehwish Khaliq, Divya Venkat, Mohan Manikkam, Mohammad Fallahi-Sichani

PLOS Computational Biology: published February 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007688

Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials

Daniel B. Reeves, Yunda Huang, Elizabeth R. Duke, Bryan T. Mayer, E. Fabian Cardozo-Ojeda, Florencia A. Boshier, David A. Swan, Morgane Rolland, Merlin L. Robb, John R. Mascola, Myron S. Cohen, Lawrence Corey, Peter B. Gilbert, Joshua T. Schiffer

PLOS Computational Biology: published February 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007626

A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks

M. Ali Al-Radhawi, David Angeli, Eduardo D. Sontag

PLOS Computational Biology: published February 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007681

The SONATA data format for efficient description of large-scale network models

Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James G. King, Werner A. H. Van Geit, Arseny V. Povolotsky, Eilif Muller, Jean-Denis Courcol, Anton Arkhipov

PLOS Computational Biology: published February 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007696

Reprogramming of macrophages employing gene regulatory and metabolic network models

Franziska Hörhold, David Eisel, Marcus Oswald, Amol Kolte, Daniela Röll, Wolfram Osen, Stefan B. Eichmüller, Rainer König

PLOS Computational Biology: published February 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007657

In silico investigation of the mechanisms underlying atrial fibrillation due to impaired Pitx2

Jieyun Bai, Andy Lo, Patrick A. Gladding, Martin K. Stiles, Vadim V. Fedorov, Jichao Zhao

PLOS Computational Biology: published February 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007678

Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions

Daniel E. Hurtado, Javiera Jilberto, Grigory Panasenko

PLOS Computational Biology: published February 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007232

Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors

Cristina Vaghi, Anne Rodallec, Raphaëlle Fanciullino, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sébastien Benzekry

PLOS Computational Biology: published February 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007178

A biophysical model of striatal microcircuits suggests gamma and beta oscillations interleaved at delta/theta frequencies mediate periodicity in motor control

Julia A. K. Chartove, Michelle M. McCarthy, Benjamin R. Pittman-Polletta, Nancy J. Kopell

PLOS Computational Biology: published February 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007300

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Nonlinear mixed selectivity supports reliable neural computation

Editorials

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