Ten simple rules for scientists: Improving your writing productivity

Todd C. Peterson, Sofie R. Kleppner, Crystal M. Botham

PLOS Computational Biology: published October 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006379

Ten simple rules when considering retirement

Philip E. Bourne

PLOS Computational Biology: published October 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006411

Ten simple rules for developing good reading habits during graduate school and beyond

Marcos Méndez

PLOS Computational Biology: published October 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006467

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain

PLOS Computational Biology: published October 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006468

Ten quick tips for getting the most scientific value out of numerical data

Lars Ole Schwen, Sabrina Rueschenbaum

PLOS Computational Biology: published October 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006141

What to know before forecasting the flu

Prithwish Chakraborty, Bryan Lewis, Stephen Eubank, John S. Brownstein, Madhav Marathe, Naren Ramakrishnan

PLOS Computational Biology: published October 12, 2018 | https://doi.org/10.1371/journal.pcbi.1005964

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine

Francisco Y. Cai, Thomas Fussell, Sarah Cobey, Marc Lipsitch

PLOS Computational Biology: published October 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006333

Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data

Fabian A. Soto, Lauren E. Vucovich, F. Gregory Ashby

PLOS Computational Biology: published October 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006470

Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing

Michael F. Staddon, Dapeng Bi, A. Pasha Tabatabai, Visar Ajeti, Michael P. Murrell, Shiladitya Banerjee

PLOS Computational Biology: published October 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006502

Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Andreas Handel, Yan Li, Brian McKay, Kasia A. Pawelek, Veronika Zarnitsyna, Rustom Antia

PLOS Computational Biology: published October 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006505

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays

Sahar Gelfman, Quanli Wang, Yi-Fan Lu, Diana Hall, Christopher D. Bostick, Ryan Dhindsa, Matt Halvorsen, K. Melodi McSweeney, Ellese Cotterill, Tom Edinburgh, Michael A. Beaumont, Wayne N. Frankel, Slavé Petrovski, Andrew S. Allen, Michael J. Boland, David B. Goldstein, Stephen J. Eglen

PLOS Computational Biology: published October 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006506

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

Ling Chen, Alexandra E. Fish, John A. Capra

PLOS Computational Biology: published October 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006484

A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons

Andreas Solbrå, Aslak Wigdahl Bergersen, Jonas van den Brink, Anders Malthe-Sørenssen, Gaute T. Einevoll, Geir Halnes

PLOS Computational Biology: published October 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006510

Noise propagation in an integrated model of bacterial gene expression and growth

Istvan T. Kleijn, Laurens H. J. Krah, Rutger Hermsen

PLOS Computational Biology: published October 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006386

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals

Iksoo Huh, Isabel Mendizabal, Taesung Park, Soojin V. Yi

PLOS Computational Biology: published October 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006451

Interactive reservoir computing for chunking information streams

Toshitake Asabuki, Naoki Hiratani, Tomoki Fukai

PLOS Computational Biology: published October 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006400

In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability

Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne

PLOS Computational Biology: published October 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006460

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Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function

Robin Moss, Frank B. Sachse, Eloy G. Moreno-Galindo, Ricardo A. Navarro-Polanco, Martin Tristani-Firouzi, Gunnar Seemann

PLOS Computational Biology: published October 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006438

Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells

Ernest C. Y. Ho, Juan Nicolas Malagón, Abha Ahuja, Rama Singh, Ellen Larsen

PLOS Computational Biology: published October 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006455

Seizure pathways: A model-based investigation

Philippa J. Karoly, Levin Kuhlmann, Daniel Soudry, David B. Grayden, Mark J. Cook, Dean R. Freestone

PLOS Computational Biology: published October 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006403

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern

Huy Tran, Jonathan Desponds, Carmina Angelica Perez Romero, Mathieu Coppey, Cecile Fradin, Nathalie Dostatni, Aleksandra M. Walczak

PLOS Computational Biology: published October 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006513

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Self-organized traffic via priority rules in leaf-cutting ants

Daniel Strömbom, Audrey Dussutour

PLOS Computational Biology: published October 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006523

State dependence of stimulus-induced variability tuning in macaque MT

Joseph A. Lombardo, Matthew V. Macellaio, Bing Liu, Stephanie E. Palmer, Leslie C. Osborne

PLOS Computational Biology: published October 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006527

Internal but not external noise frees working memory resources

Ivan Tomić, Paul M. Bays

PLOS Computational Biology: published October 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006488

Predicting B cell receptor substitution profiles using public repertoire data

Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin

PLOS Computational Biology: published October 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006388

Genomic data integration systematically biases interactome mapping

Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster

PLOS Computational Biology: published October 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006474

Data-driven brain network models differentiate variability across language tasks

Kanika Bansal, John D. Medaglia, Danielle S. Bassett, Jean M. Vettel, Sarah F. Muldoon

PLOS Computational Biology: published October 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006487

A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas

Maximilian Schmidt, Rembrandt Bakker, Kelly Shen, Gleb Bezgin, Markus Diesmann, Sacha Jennifer van Albada

PLOS Computational Biology: published October 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006359

Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques

Dominik Wodarz, Pamela J. Skinner, David N. Levy, Elizabeth Connick

PLOS Computational Biology: published October 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006461

Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque

Song Xu, Sanggu Kim, Irvin S. Y. Chen, Tom Chou

PLOS Computational Biology: published October 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006489

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang, Simonas Marcišauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven

PLOS Computational Biology: published October 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006541

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria

Erki Aun, Age Brauer, Veljo Kisand, Tanel Tenson, Maido Remm

PLOS Computational Biology: published October 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006434

Predicting how and when hidden neurons skew measured synaptic interactions

Braden A. W. Brinkman, Fred Rieke, Eric Shea-Brown, Michael A. Buice

PLOS Computational Biology: published October 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006490

Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents

Sandra Giuliani, Arthur C. Silva, Joyce V. V. B. Borba, Pablo I. P. Ramos, Ross A. Paveley, Eugene N. Muratov, Carolina Horta Andrade, Nicholas Furnham

PLOS Computational Biology: published October 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006515

An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids

Xinjian Mao, Sarah McManaway, Jagdish K. Jaiswal, Priyanka B. Patel, William R. Wilson, Kevin O. Hicks, Gib Bogle

PLOS Computational Biology: published October 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006469

Quantum chemistry reveals thermodynamic principles of redox biochemistry

Adrian Jinich, Avi Flamholz, Haniu Ren, Sung-Jin Kim, Benjamin Sanchez-Lengeling, Charles A. R. Cotton, Elad Noor, Alán Aspuru-Guzik, Arren Bar-Even

PLOS Computational Biology: published October 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006471

Dilution and titration of cell-cycle regulators may control cell size in budding yeast

Frank S. Heldt, Reece Lunstone, John J. Tyson, Béla Novák

PLOS Computational Biology: published October 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006548

Modeling sensory-motor decisions in natural behavior

Ruohan Zhang, Shun Zhang, Matthew H. Tong, Yuchen Cui, Constantin A. Rothkopf, Dana H. Ballard, Mary M. Hayhoe

PLOS Computational Biology: published October 25, 2018 | https://doi.org/10.1371/journal.pcbi.1006518

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)

Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang

PLOS Computational Biology: published October 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006511

Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments

Ioannis Kalfas, Kasper Vinken, Rufin Vogels

PLOS Computational Biology: published October 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006557

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data

Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski

PLOS Computational Biology: published October 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006538

Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions

Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena C. Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham A. Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L. Myers

PLOS Computational Biology: published October 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006532

Modeling and subtleties of K-Ras and Calmodulin interaction

Eduardo Garrido, Juan Lázaro, Montserrat Jaumot, Neus Agell, Jaime Rubio-Martinez

PLOS Computational Biology: published October 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006552

Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota

Michael A. Henson, Poonam Phalak

PLOS Computational Biology: published October 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006558

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis

Tycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels

PLOS Computational Biology: published October 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006520

Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase

Daniel S. Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova

PLOS Computational Biology: published October 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006525

A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments

Katharina Nöh, Sebastian Niedenführ, Martin Beyß, Wolfgang Wiechert

PLOS Computational Biology: published October 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006533

Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina

PLOS Computational Biology: published October 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006539

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