December 2018

Two-dimensional projections of three-dimensional light sheet fluorescence microscropy images of gut bacteria in larval zebrafish. The right half consists of images hand-labeled as bacteria, the left half as noise or non-bacterial objects. These and thousands of other datasets were used to train a convolutional neural network, which achieves human-level classfication accuracy.

Image Credit: Edouard A Hay and Raghuveer Parthasarathy, The University of Oregon

Editorials

Ten simple rules for documenting scientific software

Benjamin D. Lee

PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006561

One thousand simple rules

Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin

PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006670

Education Articles

Eleven quick tips to build a usable REST API for life sciences

Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner, Robert D. Finn, Andrew D. Yates

PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006542

Ten quick tips for sharing open genomic data

Anne V. Brown, Jacqueline D. Campbell, Teshale Assefa, David Grant, Rex T. Nelson, Nathan T. Weeks, Steven B. Cannon

PLOS Computational Biology: published December 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006472

Perspectives

Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy

Wang Xi, Michael A. Beer

PLOS Computational Biology: published December 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006625

Harnessing formal concepts of biological mechanism to analyze human disease

Lindley Darden, Kunal Kundu, Lipika R. Pal, John Moult

PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006540

Research Articles

A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins

Luhao Zhang, Maodong Li, Zhirong Liu

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006393

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

Lei Liu, Guang Shi, D. Thirumalai, Changbong Hyeon

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006617

A stochastic framework to model axon interactions within growing neuronal populations

Agustina Razetti, Caroline Medioni, Grégoire Malandain, Florence Besse, Xavier Descombes

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006627

Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets

Edouard A. Hay, Raghuveer Parthasarathy

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006628

TAMMiCol: Tool for analysis of the morphology of microbial colonies

Hayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006629

Detection and analysis of spatiotemporal patterns in brain activity

Rory G. Townsend, Pulin Gong

PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006643

Regulation of harvester ant foraging as a closed-loop excitable system

Renato Pagliara, Deborah M. Gordon, Naomi Ehrich Leonard

PLOS Computational Biology: published December 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006200

The empirical characteristics of human pattern vision defy theoretically-driven expectations

Peter Neri

PLOS Computational Biology: published December 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006585

Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture

Shouryadipta Ghosh, Kenneth Tran, Lea M. D. Delbridge, Anthony J. R. Hickey, Eric Hanssen, Edmund J. Crampin, Vijay Rajagopal

PLOS Computational Biology: published December 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006640

Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson’s disease

Logan L. Grado, Matthew D. Johnson, Theoden I. Netoff

PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006606

Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection

Michiel W. H. Remme, John Rinzel, Susanne Schreiber

PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006612

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study

Anna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jiri Sponer, Paolo Carloni

PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006642

Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors

Mengrou Shan, David Dai, Arunodai Vudem, Jeffrey D. Varner, Abraham D. Stroock

PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006584

Deep convolutional networks do not classify based on global object shape

Nicholas Baker, Hongjing Lu, Gennady Erlikhman, Philip J. Kellman

PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006613

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development

Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman

PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006614

Projecting social contact matrices to different demographic structures

Sergio Arregui, Alberto Aleta, Joaquín Sanz, Yamir Moreno

PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006638

Predicting protein targets for drug-like compounds using transcriptomics

Nicolas A. Pabon, Yan Xia, Samuel K. Estabrooks, Zhaofeng Ye, Amanda K. Herbrand, Evelyn Süß, Ricardo M. Biondi, Victoria A. Assimon, Jason E. Gestwicki, Jeffrey L. Brodsky, Carlos J. Camacho, Ziv Bar-Joseph

PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006651

Odorant mixtures elicit less variable and faster responses than pure odorants

Ho Ka Chan, Fabian Hersperger, Emiliano Marachlian, Brian H. Smith, Fernando Locatelli, Paul Szyszka, Thomas Nowotny

PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006536

Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors

Isao T. Tokuda, Daisuke Ono, Sato Honma, Ken-Ichi Honma, Hanspeter Herzel

PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006607

Identifying (un)controllable dynamical behavior in complex networks

Jordan C. Rozum, Réka Albert

PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006630

Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development

Aleksandr V. Zhuravlev, Oleg V. Vetrovoy, Elena V. Savvateeva-Popova

PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006672

PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions

Ning Zhang, Yuting Chen, Feiyang Zhao, Qing Yang, Franco L. Simonetti, Minghui Li

PLOS Computational Biology: published December 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006615

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

Wen Zhang, Xiang Yue, Guifeng Tang, Wenjian Wu, Feng Huang, Xining Zhang

PLOS Computational Biology: published December 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006616

Coherent chaos in a recurrent neural network with structured connectivity

Itamar Daniel Landau, Haim Sompolinsky

PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006309

Full-Length Envelope Analyzer (`FLEA`): A tool for longitudinal analysis of viral amplicons

Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell

PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006498

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

Enrico Lavezzo, Michele Berselli, Ilaria Frasson, Rosalba Perrone, Giorgio Palù, Alessandra R. Brazzale, Sara N. Richter, Stefano Toppo

PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006675

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data

Danesh Moradigaravand, Martin Palm, Anne Farewell, Ville Mustonen, Jonas Warringer, Leopold Parts

PLOS Computational Biology: published December 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006258

Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading

Kellen Chen, Xiao Hu, Silvia S. Blemker, Jeffrey W. Holmes

PLOS Computational Biology: published December 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006652

A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies

Anne Cori, Pierre Nouvellet, Tini Garske, Hervé Bourhy, Emmanuel Nakouné, Thibaut Jombart

PLOS Computational Biology: published December 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006554

Bayesian inference of protein conformational ensembles from limited structural data

Wojciech Potrzebowski, Jill Trewhella, Ingemar Andre

PLOS Computational Biology: published December 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006641

Determinants of drug-target interactions at the single cell level

Vlad Elgart, Jia-Ren Lin, Joseph Loscalzo

PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006601

Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern

Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov

PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006637

Movement and conformity interact to establish local behavioural traditions in animal populations

Marius Somveille, Josh A. Firth, Lucy M. Aplin, Damien R. Farine, Ben C. Sheldon, Robin N. Thompson

PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006647

Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator

Daniel Blustein, Ahmed Shehata, Kevin Englehart, Jonathon Sensinger

PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006501

On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model

Brian C. Lee, Daniel J. Tward, Partha P. Mitra, Michael I. Miller

PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006610

Cover

Bacterium or noise?

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Research Articles

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