April 2019

The top three gecko patterns were generated with simulations of pattern formation using identical parameters. Differences in these patterns are due only to random effects in the patterning process. Kiskowski et al. use computational models to understand the role of random effects in a set of naturally occurring gecko patterns. Are the differences between similar gecko patterns attributable to random effects alone, or is variation in genes and environment required to explain these differences? Simulation parameters represent genetic and environmental influences on patterns. Variation of these parameters can produce very distinct patterns (bottom row).

Image Credit: Kiskowski et al.

Editorials

Ten simple rules for organizing a webinar series

Faisal M. Fadlelmola, Sumir Panji, Azza E. Ahmed, Amel Ghouila, Wisdom A. Akurugu, Jean-Baka Domelevo Entfellner, Oussema Souiai, Nicola Mulder, H3ABioNet Research working group as members of the H3Africa Consortium

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006671

Ten simple rules towards healthier research labs

Fernando T. Maestre

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006914

Ten simple rules for providing a meaningful research experience to high school students

Emily A. Lescak, Kate M. O’Neill, Giovanna M. Collu, Subhamoy Das

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006920

Education Articles

A quick guide for student-driven community genome annotation

Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores-Gonzalez, Lukas A. Mueller, Helen Wiersma-Koch, Tom D’Elia, Susan J. Brown, Surya Saha

PLOS Computational Biology: published April 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006682

Ten quick tips for creating an effective lesson

Greg Wilson

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006915

Perspective

Network motifs and their origins

Lewi Stone, Daniel Simberloff, Yael Artzy-Randrup

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006749

Research Articles

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins

Arumay Pal, Yaakov Levy

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006768

Inferring rates of metastatic dissemination using stochastic network models

Philip Gerlee, Mia Johansson

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006868

Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs

Cheng Liang, Shengpeng Yu, Jiawei Luo

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006931

Evolutionary multiplayer games on graphs with edge diversity

Qi Su, Lei Zhou, Long Wang

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006947

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features

Craig A. Magaret, David C. Benkeser, Brian D. Williamson, Bhavesh R. Borate, Lindsay N. Carpp, Ivelin S. Georgiev, Ian Setliff, Adam S. Dingens, Noah Simon, Marco Carone, Christopher Simpkins, David Montefiori, Galit Alter, Wen-Han Yu, Michal Juraska, Paul T. Edlefsen, Shelly Karuna, Nyaradzo M. Mgodi, Srilatha Edugupanti, Peter B. Gilbert

PLOS Computational Biology: published April 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006952

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)

Hailong Meng, Gur Yaari, Christopher R. Bolen, Stefan Avey, Steven H. Kleinstein

PLOS Computational Biology: published April 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006899

Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits

Yifan Gu, Yang Qi, Pulin Gong

PLOS Computational Biology: published April 2, 2019 | https://doi.org/10.1371/journal.pcbi.1006902

Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors

Giovanni Minervini, Federica Quaglia, Francesco Tabaro, Silvio C. E. Tosatto

PLOS Computational Biology: published April 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006478

Conservation of conformational dynamics across prokaryotic actins

Natalie Ng, Handuo Shi, Alexandre Colavin, Kerwyn Casey Huang

PLOS Computational Biology: published April 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006683

Multiple factors influence the morphology of the bipolar electrogram: An in silico modeling study

Minki Hwang, Jaehyuk Kim, Byounghyun Lim, Jun-Seop Song, Boyoung Joung, Eun Bo Shim, Hui-Nam Pak

PLOS Computational Biology: published April 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006765

Modeling neuronal avalanches and long-range temporal correlations at the emergence of collective oscillations: Continuously varying exponents mimic M/EEG results

Leonardo Dalla Porta, Mauro Copelli

PLOS Computational Biology: published April 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006924

Model diagnostics and refinement for phylodynamic models

Max S. Y. Lau, Bryan T. Grenfell, Colin J. Worby, Gavin J. Gibson

PLOS Computational Biology: published April 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006955

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms

Kyriaki Kalimeri, Matteo Delfino, Ciro Cattuto, Daniela Perrotta, Vittoria Colizza, Caroline Guerrisi, Clement Turbelin, Jim Duggan, John Edmunds, Chinelo Obi, Richard Pebody, Ana O. Franco, Yamir Moreno, Sandro Meloni, Carl Koppeschaar, Charlotte Kjelsø, Ricardo Mexia, Daniela Paolotti

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006173

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006650

Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices

Andrea Malandrino, Xavier Trepat, Roger D. Kamm, Michael Mak

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006684

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments

Vilim Štih, Luigi Petrucco, Andreas M. Kist, Ruben Portugues

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006699

The intrinsic dimension of protein sequence evolution

Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006767

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

Jose Manuel Martí

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006967

Contextual influence on confidence judgments in human reinforcement learning

Maël Lebreton, Karin Bacily, Stefano Palminteri, Jan B. Engelmann

PLOS Computational Biology: published April 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006973

Confidence resets reveal hierarchical adaptive learning in humans

Micha Heilbron, Florent Meyniel

PLOS Computational Biology: published April 9, 2019 | https://doi.org/10.1371/journal.pcbi.1006972

Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning

Simone Conti, Martin Karplus

PLOS Computational Biology: published April 10, 2019 | https://doi.org/10.1371/journal.pcbi.1006954

Physical constraints on accuracy and persistence during breast cancer cell chemotaxis

Julien Varennes, Hye-ran Moon, Soutick Saha, Andrew Mugler, Bumsoo Han

PLOS Computational Biology: published April 10, 2019 | https://doi.org/10.1371/journal.pcbi.1006961

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

Anna S. Blazier, Jason A. Papin

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006507

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder

Abrar E. Al-Shaer, George R. Flentke, Mark E. Berres, Ana Garic, Susan M. Smith

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006937

Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth

Tanja Laske, Mandy Bachmann, Melanie Dostert, Alexander Karlas, Dagmar Wirth, Timo Frensing, Thomas F. Meyer, Hansjörg Hauser, Udo Reichl

PLOS Computational Biology: published April 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006944

Microstimulation in a spiking neural network model of the midbrain superior colliculus

Bahadir Kasap, A. John van Opstal

PLOS Computational Biology: published April 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006522

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size

Daniel I. S. Rosenbloom, Peter Bacchetti, Mars Stone, Xutao Deng, Ronald J. Bosch, Douglas D. Richman, Janet D. Siliciano, John W. Mellors, Steven G. Deeks, Roger G. Ptak, Rebecca Hoh, Sheila M. Keating, Melanie Dimapasoc, Marta Massanella, Jun Lai, Michele D. Sobolewski, Deanna A. Kulpa, Michael P. Busch, for the Reservoir Assay Validation and Evaluation Network (RAVEN) Study Group

PLOS Computational Biology: published April 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006849

The relative contribution of color and material in object selection

Ana Radonjić, Nicolas P. Cottaris, David H. Brainard

PLOS Computational Biology: published April 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006950

A global map of the protein shape universe

Xusi Han, Atilla Sit, Charles Christoffer, Siyang Chen, Daisuke Kihara

PLOS Computational Biology: published April 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006969

Competing evolutionary paths in growing populations with applications to multidrug resistance

Michael D. Nicholson, Tibor Antal

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006866

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

Anne Richelle, Austin W. T. Chiang, Chih-Chung Kuo, Nathan E. Lewis

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006867

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity

Lex E. Flagel, Benjamin K. Blackman, Lila Fishman, Patrick J. Monnahan, Andrea Sweigart, John K. Kelly

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006949

Passenger mutations accurately classify human tumors

Marina Salvadores, David Mas-Ponte, Fran Supek

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006953

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Ivan Juric, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Ming Hu

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006982

Approximate Bayesian estimation of coevolutionary arms races

Scott L. Nuismer, Bob Week

PLOS Computational Biology: published April 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006988

Neural control of body-plan axis in regenerating planaria

Alexis Pietak, Johanna Bischof, Joshua LaPalme, Junji Morokuma, Michael Levin

PLOS Computational Biology: published April 16, 2019 | https://doi.org/10.1371/journal.pcbi.1006904

Learning and forgetting using reinforced Bayesian change detection

Vincent Moens, Alexandre Zénon

PLOS Computational Biology: published April 17, 2019 | https://doi.org/10.1371/journal.pcbi.1006713

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks

Graeme Benstead-Hume, Xiangrong Chen, Suzanna R. Hopkins, Karen A. Lane, Jessica A. Downs, Frances M. G. Pearl

PLOS Computational Biology: published April 17, 2019 | https://doi.org/10.1371/journal.pcbi.1006888

Imperfect Bayesian inference in visual perception

Elina Stengård, Ronald van den Berg

PLOS Computational Biology: published April 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006465

Bet-hedging strategies in expanding populations

Paula Villa Martín, Miguel A. Muñoz, Simone Pigolotti

PLOS Computational Biology: published April 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006529

Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism

Félix P. Hartmann, Pierre Barbier de Reuille, Cris Kuhlemeier

PLOS Computational Biology: published April 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006896

SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species

Đorđe Miladinović, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian Baumann, Antoine Adamantidis, Steven A. Brown, Joachim M. Buhmann

PLOS Computational Biology: published April 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006968

Fluctuating environments select for short-term phenotypic variation leading to long-term exploration

Rosangela Canino-Koning, Michael J. Wiser, Charles Ofria

PLOS Computational Biology: published April 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006445

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vikash Pandey, Vassily Hatzimanikatis

PLOS Computational Biology: published April 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006760

Inferring neural circuit structure from datasets of heterogeneous tuning curves

Takafumi Arakaki, G. Barello, Yashar Ahmadian

PLOS Computational Biology: published April 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006816

Stability of working memory in continuous attractor networks under the control of short-term plasticity

Alexander Seeholzer, Moritz Deger, Wulfram Gerstner

PLOS Computational Biology: published April 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006928

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

Thomas D. Sherman, Luciane T. Kagohara, Raymon Cao, Raymond Cheng, Matthew Satriano, Michael Considine, Gabriel Krigsfeld, Ruchira Ranaweera, Yong Tang, Sandra A. Jablonski, Genevieve Stein-O'Brien, Daria A. Gaykalova, Louis M. Weiner, Christine H. Chung, Elana J. Fertig

PLOS Computational Biology: published April 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006935

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

Marko Järvenpää, Mohamad R. Abdul Sater, Georgia K. Lagoudas, Paul C. Blainey, Loren G. Miller, James A. McKinnell, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006534

Finding the balance between model complexity and performance: Using ventral striatal oscillations to classify feeding behavior in rats

Lucas L. Dwiel, Jibran Y. Khokhar, Michael A. Connerney, Alan I. Green, Wilder T. Doucette

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006838

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

Spencer E. Bliven, Aleix Lafita, Peter W. Rose, Guido Capitani, Andreas Prlić, Philip E. Bourne

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006842

Temporal pattern separation in hippocampal neurons through multiplexed neural codes

Antoine D. Madar, Laura A. Ewell, Mathew V. Jones

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006932

A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism

Oveis Jamialahmadi, Sameereh Hashemi-Najafabadi, Ehsan Motamedian, Stefano Romeo, Fatemeh Bagheri

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006936

Isolating and quantifying the role of developmental noise in generating phenotypic variation

Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble, Ylenia Chiari

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006943

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand V. Sastry, Yara Seif, Bernhard O. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006971

Weak electric fields promote resonance in neuronal spiking activity: Analytical results from two-compartment cell and network models

Josef Ladenbauer, Klaus Obermayer

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006974

Neural crest streaming as an emergent property of tissue interactions during morphogenesis

András Szabó, Eric Theveneau, Melissa Turan, Roberto Mayor

PLOS Computational Biology: published April 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007002

Deep convolutional models improve predictions of macaque V1 responses to natural images

Santiago A. Cadena, George H. Denfield, Edgar Y. Walker, Leon A. Gatys, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker

PLOS Computational Biology: published April 23, 2019 | https://doi.org/10.1371/journal.pcbi.1006897

Synchronization dependent on spatial structures of a mesoscopic whole-brain network

Hannah Choi, Stefan Mihalas

PLOS Computational Biology: published April 23, 2019 | https://doi.org/10.1371/journal.pcbi.1006978

A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP

Sergio M. G. Solinas, Elke Edelmann, Volkmar Leßmann, Michele Migliore

PLOS Computational Biology: published April 24, 2019 | https://doi.org/10.1371/journal.pcbi.1006975

Revealing evolutionary constraints on proteins through sequence analysis

Shou-Wen Wang, Anne-Florence Bitbol, Ned S. Wingreen

PLOS Computational Biology: published April 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007010

Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length

Kai Liu, Brian Chu, Jay Newby, Elizabeth L. Read, John Lowengrub, Jun Allard

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006352

Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits

Renato Duarte, Abigail Morrison

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006781

Chemical features mining provides new descriptive structure-odor relationships

Carmen C. Licon, Guillaume Bosc, Mohammed Sabri, Marylou Mantel, Arnaud Fournel, Caroline Bushdid, Jerome Golebiowski, Celine Robardet, Marc Plantevit, Mehdi Kaytoue, Moustafa Bensafi

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006945

TASmania: A bacterial Toxin-Antitoxin Systems database

Hatice Akarsu, Patricia Bordes, Moise Mansour, Donna-Joe Bigot, Pierre Genevaux, Laurent Falquet

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006946

A Bayesian framework for the analysis of systems biology models of the brain

Joshua Russell-Buckland, Christopher P. Barnes, Ilias Tachtsidis

PLOS Computational Biology: published April 26, 2019 | https://doi.org/10.1371/journal.pcbi.1006631

Integrated computational and Drosophila cancer model platform captures previously unappreciated chemicals perturbing a kinase network

Peter M. U. Ung, Masahiro Sonoshita, Alex P. Scopton, Arvin C. Dar, Ross L. Cagan, Avner Schlessinger

PLOS Computational Biology: published April 26, 2019 | https://doi.org/10.1371/journal.pcbi.1006878

I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment

Stelios Pavlidis, Calixte Monast, Matthew J. Loza, Patrick Branigan, Kiang F. Chung, Ian M. Adcock, Yike Guo, Anthony Rowe, Frédéric Baribaud

PLOS Computational Biology: published April 30, 2019 | https://doi.org/10.1371/journal.pcbi.1006951

Formal Comment

Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang

Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou

PLOS Computational Biology: published April 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006916

Cover

Gecko skin patterning and random versus genetic and environmental effects

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