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Table of Contents: May 2017

Image of an artery with atherosclerotic plaque as illustrated using agent based modeling. Various white blood cells (blue, cyan, and red) are adhered to the endothelial cells (green) based on their receptor-ligand affinity and blood hemodynamics. Bhui et al.

Image Credit: Original image by Rita Bhui

Editorials

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

Ten simple rules to consider regarding preprint submission

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

Education

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

Topic Page

Transcriptomics technologies

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

Research Articles

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

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

Semidán Robaina-Estévez, Zoran Nikoloski

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

Poppy Miller, Jonathan Marshall, Nigel French, Chris Jewell

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

Dynamic decomposition of spatiotemporal neural signals

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

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

ROTS: An R package for reproducibility-optimized statistical testing

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

Predicting cryptic links in host-parasite networks

Tad Dallas, Andrew W Park, John M Drake

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

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

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

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

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

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

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

Automatically tracking neurons in a moving and deforming brain

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

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

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

High-order epistasis shapes evolutionary trajectories

Zachary R. Sailer, Michael J. Harms

SteadyCom: Predicting microbial abundances while ensuring community stability

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

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

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

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

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

Short-term activity cycles impede information transmission in ant colonies

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

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

Single-molecule protein identification by sub-nanopore sensors

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

Post-transcriptional regulation across human tissues

Alexander Franks, Edoardo Airoldi, Nikolai Slavov

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

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

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

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

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

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

Mechanisms underlying different onset patterns of focal seizures

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

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

phyC: Clustering cancer evolutionary trees

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

Slow diffusive dynamics in a chaotic balanced neural network

Nimrod Shaham, Yoram Burak

Co-occurring protein phosphorylation are functionally associated

Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li

Nucleotide-time alignment for molecular recorders

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