Ten simple rules for successfully hosting an intern at a scientific software company

Kristine Briedis, Yi-Shiou Chen, Scott Markel

PLOS Computational Biology: published June 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007020

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors

Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard Laubenbacher, Jeffrey H. Chuang

PLOS Computational Biology: published June 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007026

Ten quick tips for effective dimensionality reduction

Lan Huong Nguyen, Susan Holmes

PLOS Computational Biology: published June 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006907

Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?

Angela C. Davies, Diane Harris, Amanda Banks-Gatenby, Andy Brass

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006746

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training

Annette McGrath, Katherine Champ, Catherine A. Shang, Ellen van Dam, Cath Brooksbank, Sarah L. Morgan

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006923

Telling ecological networks apart by their structure: A computational challenge

Matthew J. Michalska-Smith, Stefano Allesina

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1007076

Modern technologies and algorithms for scaffolding assembled genomes

Jay Ghurye, Mihai Pop

PLOS Computational Biology: published June 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006994

Protein ensembles link genotype to phenotype

Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang

PLOS Computational Biology: published June 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006648

Neural correlates of sparse coding and dimensionality reduction

Michael Beyeler, Emily L. Rounds, Kristofor D. Carlson, Nikil Dutt, Jeffrey L. Krichmar

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006908

Evolution of interface binding strengths in simplified model of protein quaternary structure

Alexander S. Leonard, Sebastian E. Ahnert

PLOS Computational Biology: published June 3, 2019 | https://doi.org/10.1371/journal.pcbi.1006886

Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies

Monica Civera, Francesca Vasile, Donatella Potenza, Cinzia Colombo, Sara Parente, Chiara Vettraino, Tommaso Prosdocimi, Emilio Parisini, Laura Belvisi

PLOS Computational Biology: published June 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007041

Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells

Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay, Marek Kimmel

PLOS Computational Biology: published June 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007054

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Chuankai Cheng, Edward J. O’Brien, Douglas McCloskey, Jose Utrilla, Connor Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, Zachary A. King

PLOS Computational Biology: published June 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007066

Emergent decision-making behaviour and rhythm generation in a computational model of the ventromedial nucleus of the hypothalamus

Duncan J. MacGregor, Gareth Leng

PLOS Computational Biology: published June 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007092

Multiscale model of integrin adhesion assembly

Tamara C. Bidone, Austin V. Skeeters, Patrick W. Oakes, Gregory A. Voth

PLOS Computational Biology: published June 4, 2019 | https://doi.org/10.1371/journal.pcbi.1007077

Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance

Yapeng Su, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H. C. Ng, Victoria Liu, Antoni Ribas, James R. Heath, Wei Wei

PLOS Computational Biology: published June 5, 2019 | https://doi.org/10.1371/journal.pcbi.1007034

Charting pathways to climate change mitigation in a coupled socio-climate model

Thomas M. Bury, Chris T. Bauch, Madhur Anand

PLOS Computational Biology: published June 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007000

Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis

Takaaki Yonekura, Akitoshi Iwamoto, Hironori Fujita, Munetaka Sugiyama

PLOS Computational Biology: published June 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007044

The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes

Hongjun Bai, Yifan Li, Nelson L. Michael, Merlin L. Robb, Morgane Rolland

PLOS Computational Biology: published June 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007056

Dynamic properties of internal noise probed by modulating binocular rivalry

Daniel H. Baker, Bruno Richard

PLOS Computational Biology: published June 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007071

Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes

Atsushi Kamimura, Yoshiya J. Matsubara, Kunihiko Kaneko, Nobuto Takeuchi

PLOS Computational Biology: published June 6, 2019 | https://doi.org/10.1371/journal.pcbi.1007094

A neural field model for color perception unifying assimilation and contrast

Anna Song, Olivier Faugeras, Romain Veltz

PLOS Computational Biology: published June 7, 2019 | https://doi.org/10.1371/journal.pcbi.1007050

Predicting three-dimensional genome organization with chromatin states

Yifeng Qi, Bin Zhang

PLOS Computational Biology: published June 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007024

How single neuron properties shape chaotic dynamics and signal transmission in random neural networks

Samuel P. Muscinelli, Wulfram Gerstner, Tilo Schwalger

PLOS Computational Biology: published June 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007122

Models that learn how humans learn: The case of decision-making and its disorders

Amir Dezfouli, Kristi Griffiths, Fabio Ramos, Peter Dayan, Bernard W. Balleine

PLOS Computational Biology: published June 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006903

Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model

Mahua Roy, Stacey D. Finley

PLOS Computational Biology: published June 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007053

Sequential exploration in the Iowa gambling task: Validation of a new computational model in a large dataset of young and old healthy participants

Romain Ligneul

PLOS Computational Biology: published June 13, 2019 | https://doi.org/10.1371/journal.pcbi.1006989

Disentangling juxtacrine from paracrine signalling in dynamic tissue

Hiroshi Momiji, Kirsty L. Hassall, Karen Featherstone, Anne V. McNamara, Amanda L. Patist, David G. Spiller, Helen C. Christian, Michael R. H. White, Julian R. E. Davis, Bärbel F. Finkenstädt, David A. Rand

PLOS Computational Biology: published June 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007030

Development of a physiologically-based pharmacokinetic pediatric brain model for prediction of cerebrospinal fluid drug concentrations and the influence of meningitis

Laurens F. M. Verscheijden, Jan B. Koenderink, Saskia N. de Wildt, Frans G. M. Russel

PLOS Computational Biology: published June 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007117

Integrative modeling of the HIV-1 ribonucleoprotein complex

David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli

PLOS Computational Biology: published June 13, 2019 | https://doi.org/10.1371/journal.pcbi.1007150

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

Kymberleigh A. Pagel, Danny Antaki, AoJie Lian, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

PLOS Computational Biology: published June 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007112

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Ingoo Lee, Jongsoo Keum, Hojung Nam

PLOS Computational Biology: published June 14, 2019 | https://doi.org/10.1371/journal.pcbi.1007129

Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology

Hansaim Lim, Di He, Yue Qiu, Patrycja Krawczuk, Xiaoru Sun, Lei Xie

PLOS Computational Biology: published June 17, 2019 | https://doi.org/10.1371/journal.pcbi.1006619

A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test

David Hasler, Pinelopi Anagnostopoulou, Sylvia Nyilas, Philipp Latzin, Johannes Schittny, Dominik Obrist

PLOS Computational Biology: published June 17, 2019 | https://doi.org/10.1371/journal.pcbi.1007079

Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies

Payam Piray, Amir Dezfouli, Tom Heskes, Michael J. Frank, Nathaniel D. Daw

PLOS Computational Biology: published June 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007043

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes

Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis

PLOS Computational Biology: published June 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007113

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or

PLOS Computational Biology: published June 19, 2019 | https://doi.org/10.1371/journal.pcbi.1007127

Coupling water fluxes with cell wall mechanics in a multicellular model of plant development

Ibrahim Cheddadi, Michel Génard, Nadia Bertin, Christophe Godin

PLOS Computational Biology: published June 20, 2019 | https://doi.org/10.1371/journal.pcbi.1007121

Modelling the transport of fluid through heterogeneous, whole tumours in silico

Paul W. Sweeney, Angela d’Esposito, Simon Walker-Samuel, Rebecca J. Shipley

PLOS Computational Biology: published June 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006751

Resurgent Na⁺ Current Offers Noise Modulation in Bursting Neurons

Sharmila Venugopal, Soju Seki, David H. Terman, Antonios Pantazis, Riccardo Olcese, Martina Wiedau-Pazos, Scott H. Chandler

PLOS Computational Biology: published June 21, 2019 | https://doi.org/10.1371/journal.pcbi.1007154

Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa

Anthony Hauser, Katharina Kusejko, Leigh F. Johnson, Gilles Wandeler, Julien Riou, Fardo Goldstein, Matthias Egger, Roger D. Kouyos

PLOS Computational Biology: published June 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007083

Learning to use past evidence in a sophisticated world model

Sanjeevan Ahilan, Rebecca B. Solomon, Yannick-André Breton, Kent Conover, Ritwik K. Niyogi, Peter Shizgal, Peter Dayan

PLOS Computational Biology: published June 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007093

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology: published June 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007128

A neural network model predicts community-level signaling states in a diverse microbial community

Kalinga Pavan T. Silva, James Q. Boedicker

PLOS Computational Biology: published June 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007166

A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model

Erlend Hodneland, Erik Hanson, Ove Sævareid, Geir Nævdal, Arvid Lundervold, Veronika Šoltészová, Antonella Z. Munthe-Kaas, Andreas Deistung, Jürgen R. Reichenbach, Jan M. Nordbotten

PLOS Computational Biology: published June 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007073

Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort

Mikael F. Forsgren, Markus Karlsson, Olof Dahlqvist Leinhard, Nils Dahlström, Bengt Norén, Thobias Romu, Simone Ignatova, Mattias Ekstedt, Stergios Kechagias, Peter Lundberg, Gunnar Cedersund

PLOS Computational Biology: published June 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007157

Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations

Hanne Hoitzing, Payam A. Gammage, Lindsey Van Haute, Michal Minczuk, Iain G. Johnston, Nick S. Jones

PLOS Computational Biology: published June 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007023

Optimization of surgical intervention outside the epileptogenic zone in the Virtual Epileptic Patient (VEP)

Sora An, Fabrice Bartolomei, Maxime Guye, Viktor Jirsa

PLOS Computational Biology: published June 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007051

Predicting gastrointestinal drug effects using contextualized metabolic models

Marouen Ben Guebila, Ines Thiele

PLOS Computational Biology: published June 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007100

Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales

Joshua M. Mueller, Primoz Ravbar, Julie H. Simpson, Jean M. Carlson

PLOS Computational Biology: published June 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007105

Augmenting subnetwork inference with information extracted from the scientific literature

Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006758

Modeling the temporal dynamics of the gut microbial community in adults and infants

Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D. Silverman, Itzhak Mizrahi, Eran Halperin

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006960

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

Rohan V. Koodli, Benjamin Keep, Katherine R. Coppess, Fernando Portela, Eterna participants, Rhiju Das

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1007059

Evidence accumulation is biased by motivation: A computational account

Filip Gesiarz, Donal Cahill, Tali Sharot

PLOS Computational Biology: published June 27, 2019 | https://doi.org/10.1371/journal.pcbi.1007089

Notification of Republication: Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy

The PLOS Computational Biology Staff

PLOS Computational Biology: published June 4, 2019 | https://doi.org/10.1371/journal.pcbi.1007110

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Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng

PLOS Computational Biology: published June 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007114

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Correction: A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana

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PLOS Computational Biology: published June 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007140

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Correction: Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence

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PLOS Computational Biology: published June 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007146

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Correction: Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria

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Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

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Correction: Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

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Correction: The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction

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Correction: Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action

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Correction: Ten Simple Rules for Taking Advantage of Git and GitHub

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Correction: Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics

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Correction: Geospatial characteristics of measles transmission in China during 2005−2014

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Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

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Correction: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

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Correction: From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses

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