July 2019

Cai et al present genes that are aligned according to their chromosome locations in the most inner track, with chromosome number indicated. Different types of SGA events are shown in tracks: copy number deletion (blue), copy number amplification (orange), mutation (green). The outmost track (red) shows the number of tumors in which an SGA is deemed as a candidate driver.

Image Credit: Cai et al. Cai used the open-access software Circos plot is used to generate the plot.

Editorials

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose

PLOS Computational Biology: published July 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007007

Ten simple rules for giving an effective academic job talk

Shayna A. Sura, Lauren L. Smith, Monique R. Ambrose, C. Eduardo Guerra Amorim, Annabel C. Beichman, Ana C. R. Gomez, Mark Juhn, Gaurav S. Kandlikar, Julie S. Miller, Jazlyn Mooney, Riley O. Mummah, Kirk E. Lohmueller, James O. Lloyd-Smith

PLOS Computational Biology: published July 25, 2019 | https://doi.org/10.1371/journal.pcbi.1007163

Perspective

Think: Theory for Africa

Christopher B. Currin, Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P. Vogels, Joseph V. Raimondo

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007049

Review

Machine and deep learning meet genome-scale metabolic modeling

Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007084

Research Articles

DART-ID increases single-cell proteome coverage

Albert Tian Chen, Alexander Franks, Nikolai Slavov

PLOS Computational Biology: published July 1, 2019 | https://doi.org/10.1371/journal.pcbi.1007082

The invasion of de-differentiating cancer cells into hierarchical tissues

Da Zhou, Yue Luo, David Dingli, Arne Traulsen

PLOS Computational Biology: published July 1, 2019 | https://doi.org/10.1371/journal.pcbi.1007167

Molecular noise of innate immunity shapes bacteria-phage ecologies

Jakob Ruess, Maroš Pleška, Cǎlin C. Guet, Gašper Tkačik

PLOS Computational Biology: published July 2, 2019 | https://doi.org/10.1371/journal.pcbi.1007168

Cross-species functional modules link proteostasis to human normal aging

Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson-Rechavi

PLOS Computational Biology: published July 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007162

Modelling the mechanics of exploration in larval Drosophila

Jane Loveless, Konstantinos Lagogiannis, Barbara Webb

PLOS Computational Biology: published July 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006635

Disease gene prediction for molecularly uncharacterized diseases

Juan J. Cáceres, Alberto Paccanaro

PLOS Computational Biology: published July 5, 2019 | https://doi.org/10.1371/journal.pcbi.1007078

Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference

Chunhui Cai, Gregory F. Cooper, Kevin N. Lu, Xiaojun Ma, Shuping Xu, Zhenlong Zhao, Xueer Chen, Yifan Xue, Adrian V. Lee, Nathan Clark, Vicky Chen, Songjian Lu, Lujia Chen, Liyue Yu, Harry S. Hochheiser, Xia Jiang, Q. Jane Wang, Xinghua Lu

PLOS Computational Biology: published July 5, 2019 | https://doi.org/10.1371/journal.pcbi.1007088

With an eye on uncertainty: Modelling pupillary responses to environmental volatility

Peter Vincent, Thomas Parr, David Benrimoh, Karl J Friston

PLOS Computational Biology: published July 5, 2019 | https://doi.org/10.1371/journal.pcbi.1007126

Human online adaptation to changes in prior probability

Elyse H. Norton, Luigi Acerbi, Wei Ji Ma, Michael S. Landy

PLOS Computational Biology: published July 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006681

Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling

Aravind Chandrasekaran, Arpita Upadhyaya, Garegin A. Papoian

PLOS Computational Biology: published July 9, 2019 | https://doi.org/10.1371/journal.pcbi.1007156

ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages

Chun Chan, Xiaoyun Pang, Yan Zhang, Tongxin Niu, Shengjiang Yang, Daohui Zhao, Jian Li, Lanyuan Lu, Victor W. Hsu, Jian Zhou, Fei Sun, Jun Fan

PLOS Computational Biology: published July 10, 2019 | https://doi.org/10.1371/journal.pcbi.1007081

Identifying determinants of persistent MRSA bacteremia using mathematical modeling

Tsuyoshi Mikkaichi, Michael R. Yeaman, Alexander Hoffmann, MRSA Systems Immunobiology Group

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007087

Modeling the daily rhythm of human pain processing in the dorsal horn

Jennifer Crodelle, Sofia H. Piltz, Megan Hastings Hagenauer, Victoria Booth

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007106

Sensorimotor maps can be dynamically calibrated using an adaptive-filter model of the cerebellum

Emma D. Wilson, Sean R. Anderson, Paul Dean, John Porrill

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007187

PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting

Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau

PLOS Computational Biology: published July 11, 2019 | https://doi.org/10.1371/journal.pcbi.1007206

Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity

Stefano Recanatesi, Gabriel Koch Ocker, Michael A. Buice, Eric Shea-Brown

PLOS Computational Biology: published July 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006446

Information-theoretic analysis of multivariate single-cell signaling responses

Tomasz Jetka, Karol Nienałtowski, Tomasz Winarski, Sławomir Błoński, Michał Komorowski

PLOS Computational Biology: published July 12, 2019 | https://doi.org/10.1371/journal.pcbi.1007132

Reservoir computing model of prefrontal cortex creates novel combinations of previous navigation sequences from hippocampal place-cell replay with spatial reward propagation

Nicolas Cazin, Martin Llofriu Alonso, Pablo Scleidorovich Chiodi, Tatiana Pelc, Bruce Harland, Alfredo Weitzenfeld, Jean-Marc Fellous, Peter Ford Dominey

PLOS Computational Biology: published July 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006624

Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas

Víctor M. Pérez-García, Luis E. Ayala-Hernández, Juan Belmonte-Beitia, Philippe Schucht, Michael Murek, Andreas Raabe, Juan Sepúlveda

PLOS Computational Biology: published July 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006778

Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction

Maarten H. G. Heusinkveld, Wouter Huberts, Joost Lumens, Theo Arts, Tammo Delhaas, Koen D. Reesink

PLOS Computational Biology: published July 15, 2019 | https://doi.org/10.1371/journal.pcbi.1007173

Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks

Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf, Thomas Dandekar

PLOS Computational Biology: published July 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007075

Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential

Aleksandra Karolak, Sharan Poonja, Katarzyna A. Rejniak

PLOS Computational Biology: published July 16, 2019 | https://doi.org/10.1371/journal.pcbi.1007214

From skylight input to behavioural output: A computational model of the insect polarised light compass

Evripidis Gkanias, Benjamin Risse, Michael Mangan, Barbara Webb

PLOS Computational Biology: published July 18, 2019 | https://doi.org/10.1371/journal.pcbi.1007123

Assessment of the cardiovascular adverse effects of drug-drug interactions through a combined analysis of spontaneous reports and predicted drug-target interactions

Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006851

Recombinant vector vaccine evolution

James J. Bull, Scott L. Nuismer, Rustom Antia

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1006857

Propagation of orientation selectivity in a spiking network model of layered primary visual cortex

Benjamin Merkt, Friedrich Schüßler, Stefan Rotter

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1007080

Assessing key decisions for transcriptomic data integration in biochemical networks

Anne Richelle, Chintan Joshi, Nathan E. Lewis

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1007185

Primacy coding facilitates effective odor discrimination when receptor sensitivities are tuned

David Zwicker

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1007188

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

Elizabeth A. Proctor, David D. Mowrey, Nikolay V. Dokholyan

PLOS Computational Biology: published July 19, 2019 | https://doi.org/10.1371/journal.pcbi.1007225

Aberrant DNA methylation defines isoform usage in cancer, with functional implications

Yun-Ching Chen, Laura Elnitski

PLOS Computational Biology: published July 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007095

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data

Duncan K. Ralph, Frederick A. Matsen IV

PLOS Computational Biology: published July 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007133

Why do eukaryotic proteins contain more intrinsically disordered regions?

Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson

PLOS Computational Biology: published July 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007186

Ensemble of decision tree reveals potential miRNA-disease associations

Xing Chen, Chi-Chi Zhu, Jun Yin

PLOS Computational Biology: published July 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007209

Modeling human intuitions about liquid flow with particle-based simulation

Christopher J. Bates, Ilker Yildirim, Joshua B. Tenenbaum, Peter Battaglia

PLOS Computational Biology: published July 22, 2019 | https://doi.org/10.1371/journal.pcbi.1007210

Biophysics and population size constrains speciation in an evolutionary model of developmental system drift

Bhavin S. Khatri, Richard A. Goldstein

PLOS Computational Biology: published July 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007177

A case study in the functional consequences of scaling the sizes of realistic cortical models

Madhura R. Joglekar, Logan Chariker, Robert Shapley, Lai-Sang Young

PLOS Computational Biology: published July 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007198

Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation

Enrico Seiler, Kathrin Trappe, Bernhard Y. Renard

PLOS Computational Biology: published July 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007208

Mathematical model predicts anti-adhesion–antibiotic–debridement combination therapies can clear an antibiotic resistant infection

Paul A. Roberts, Ryan M. Huebinger, Emma Keen, Anne-Marie Krachler, Sara Jabbari

PLOS Computational Biology: published July 23, 2019 | https://doi.org/10.1371/journal.pcbi.1007211

Foraging as an evidence accumulation process

Jacob D. Davidson, Ahmed El Hady

PLOS Computational Biology: published July 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007060

Syntrophy emerges spontaneously in complex metabolic systems

Eric Libby, Laurent Hébert-Dufresne, Sayed-Rzgar Hosseini, Andreas Wagner

PLOS Computational Biology: published July 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007169

Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers

Jessica M. Conway, Alan S. Perelson, Jonathan Z. Li

PLOS Computational Biology: published July 24, 2019 | https://doi.org/10.1371/journal.pcbi.1007229

Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications

Joseph A. Lewnard, Benjamin A. Lopman, Umesh D. Parashar, Aisleen Bennett, Naor Bar-Zeev, Nigel A. Cunliffe, Prasanna Samuel, M. Lourdes Guerrero, Guillermo Ruiz-Palacios, Gagandeep Kang, Virginia E. Pitzer

PLOS Computational Biology: published July 26, 2019 | https://doi.org/10.1371/journal.pcbi.1007014

Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism

Jan R. Wessel, David E. Huber

PLOS Computational Biology: published July 29, 2019 | https://doi.org/10.1371/journal.pcbi.1006927

Identifying important parameters in the inflammatory process with a mathematical model of immune cell influx and macrophage polarization

Marcella Torres, Jing Wang, Paul J. Yannie, Shobha Ghosh, Rebecca A. Segal, Angela M. Reynolds

PLOS Computational Biology: published July 31, 2019 | https://doi.org/10.1371/journal.pcbi.1007172

Corrections

Correction: From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm

Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Bastian Hoesel, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabě de Angelis

PLOS Computational Biology: published July 2, 2019 | https://doi.org/10.1371/journal.pcbi.1007191

Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Yoram Zarai, Tamir Tuller

PLOS Computational Biology: published July 2, 2019 | https://doi.org/10.1371/journal.pcbi.1007192

Correction: Temporal Gillespie algorithm: Fast simulation of contagion processes on time-varying networks

Christian L. Vestergaard, Mathieu Génois

PLOS Computational Biology: published July 3, 2019 | https://doi.org/10.1371/journal.pcbi.1007190

Cover

A Circos plot showing the landscape of somatic genome alterations (SGA) events and candidate cancer driver genes along the chromosomes

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