Ten simple rules for surviving an interdisciplinary PhD

Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J. Gavaghan, Charlotte M. Deane, Bernhard Knapp

PLOS Computational Biology: published May 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005512

Ten simple rules to make the most out of your undergraduate research career

Megan Yu, Yu-Min Kuo

PLOS Computational Biology: published May 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005484

Ten simple rules to consider regarding preprint submission

Philip E. Bourne, Jessica K. Polka, Ronald D. Vale, Robert Kiley

PLOS Computational Biology: published May 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005473

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko

PLOS Computational Biology: published May 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005425

Transcriptomics technologies

Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee

PLOS Computational Biology: published May 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005457

Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection

Wesley P. Clawson, Nathaniel C. Wright, Ralf Wessel, Woodrow L. Shew

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005574

On the effects of alternative optima in context-specific metabolic model predictions

Semidán Robaina-Estévez, Zoran Nikoloski

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005568

sourceR: Classification and source attribution of infectious agents among heterogeneous populations

Poppy Miller, Jonathan Marshall, Nigel French, Chris Jewell

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005564

Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile

Pierre Bonnin, Norbert Kern, Neil T. Young, Ian Stansfield, M. Carmen Romano

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005555

Dynamic decomposition of spatiotemporal neural signals

Luca Ambrogioni, Marcel A. J. van Gerven, Eric Maris

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005540

Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)

Yogi A. Patel, Ansel George, Alan D. Dorval, John A. White, David J. Christini, Robert J. Butera

PLOS Computational Biology: published May 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005430

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Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms

Florian Berger, A. J. Hudspeth

PLOS Computational Biology: published May 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005566

ROTS: An R package for reproducibility-optimized statistical testing

Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo

PLOS Computational Biology: published May 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005562

Predicting cryptic links in host-parasite networks

Tad Dallas, Andrew W Park, John M Drake

PLOS Computational Biology: published May 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005557

An agent-based model of leukocyte transendothelial migration during atherogenesis

Rita Bhui, Heather N. Hayenga

PLOS Computational Biology: published May 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005523

Spontaneous cortical activity is transiently poised close to criticality

Gerald Hahn, Adrian Ponce-Alvarez, Cyril Monier, Giacomo Benvenuti, Arvind Kumar, Frédéric Chavane, Gustavo Deco, Yves Frégnac

PLOS Computational Biology: published May 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005543

Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach

Raphaël Mourad, Lang Li, Olivier Cuvier

PLOS Computational Biology: published May 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005538

Protein charge distribution in proteomes and its impact on translation

Rodrigo D. Requião, Luiza Fernandes, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic, Fernando L. Palhano

PLOS Computational Biology: published May 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005549

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta

PLOS Computational Biology: published May 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005544

Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia

Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark Alber

PLOS Computational Biology: published May 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005533

PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data

Gabriel F. Dorlhiac, Clyde Fare, Jasper J. van Thor

PLOS Computational Biology: published May 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005528

Automatically tracking neurons in a moving and deforming brain

Jeffrey P. Nguyen, Ashley N. Linder, George S. Plummer, Joshua W. Shaevitz, Andrew M. Leifer

PLOS Computational Biology: published May 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005517

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

Don Klinkenberg, Jantien A. Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga

PLOS Computational Biology: published May 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005495

High-order epistasis shapes evolutionary trajectories

Zachary R. Sailer, Michael J. Harms

PLOS Computational Biology: published May 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005541

SteadyCom: Predicting microbial abundances while ensuring community stability

Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas

PLOS Computational Biology: published May 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005539

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci

Jin Hyun Ju, Sushila A. Shenoy, Ronald G. Crystal, Jason G. Mezey

PLOS Computational Biology: published May 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005537

A predictive coding account of bistable perception - a model-based fMRI study

Veith Weilnhammer, Heiner Stuke, Guido Hesselmann, Philipp Sterzer, Katharina Schmack

PLOS Computational Biology: published May 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005536

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates

Andreas Tuerk, Gregor Wiktorin, Serhat Güler

PLOS Computational Biology: published May 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005515

FIMTrack: An open source tracking and locomotion analysis software for small animals

Benjamin Risse, Dimitri Berh, Nils Otto, Christian Klämbt, Xiaoyi Jiang

PLOS Computational Biology: published May 11, 2017 | https://doi.org/10.1371/journal.pcbi.1005530

Short-term activity cycles impede information transmission in ant colonies

Thomas O. Richardson, Jonas I. Liechti, Nathalie Stroeymeyt, Sebastian Bonhoeffer, Laurent Keller

PLOS Computational Biology: published May 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005527

Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions

Thomas H. B. FitzGerald, Dorothea Hämmerer, Karl J. Friston, Shu-Chen Li, Raymond J. Dolan

PLOS Computational Biology: published May 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005418

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Single-molecule protein identification by sub-nanopore sensors

Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp, Pavel A. Pevzner

PLOS Computational Biology: published May 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005356

Post-transcriptional regulation across human tissues

Alexander Franks, Edoardo Airoldi, Nikolai Slavov

PLOS Computational Biology: published May 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005535

Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans

Nicolás Tomasini, Paula Gabriela Ragone, Sébastien Gourbière, Juan Pablo Aparicio, Patricio Diosque

PLOS Computational Biology: published May 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005532

The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning

Eghbal A. Hosseini, Katrina P. Nguyen, Wilsaan M. Joiner

PLOS Computational Biology: published May 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005492

Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott Emrich, Patricia L. Clark

PLOS Computational Biology: published May 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005531

A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration

Christopher M. Jakobson, Danielle Tullman-Ercek, Marilyn F. Slininger, Niall M. Mangan

PLOS Computational Biology: published May 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005525

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov

PLOS Computational Biology: published May 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005480

A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns

William R. Holmes, JinSeok Park, Andre Levchenko, Leah Edelstein-Keshet

PLOS Computational Biology: published May 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005524

Top-down control of cortical gamma-band communication via pulvinar induced phase shifts in the alpha rhythm

Silvan Quax, Ole Jensen, Paul Tiesinga

PLOS Computational Biology: published May 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005519

Mechanisms underlying different onset patterns of focal seizures

Yujiang Wang, Andrew J Trevelyan, Antonio Valentin, Gonzalo Alarcon, Peter N Taylor, Marcus Kaiser

PLOS Computational Biology: published May 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005475

Modelling of the cancer cell cycle as a tool for rational drug development: A systems pharmacology approach to cyclotherapy

Robert C. Jackson, Giovanni Y. Di Veroli, Siang-Boon Koh, Ian Goldlust, Frances M. Richards, Duncan I. Jodrell

PLOS Computational Biology: published May 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005529

phyC: Clustering cancer evolutionary trees

Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano, Teppei Shimamura

PLOS Computational Biology: published May 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005509

Slow diffusive dynamics in a chaotic balanced neural network

Nimrod Shaham, Yoram Burak

PLOS Computational Biology: published May 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005505

Co-occurring protein phosphorylation are functionally associated

Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li

PLOS Computational Biology: published May 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005502

Nucleotide-time alignment for molecular recorders

Thaddeus R. Cybulski, Edward S. Boyden, George M. Church, Keith E. J. Tyo, Konrad P. Kording

PLOS Computational Biology: published May 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005483