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Table of Contents

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

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

Perspective

Think: Theory for Africa

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

Review

Machine and deep learning meet genome-scale metabolic modeling

Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione

Research Articles

DART-ID increases single-cell proteome coverage

Albert Tian Chen, Alexander Franks, Nikolai Slavov

The invasion of de-differentiating cancer cells into hierarchical tissues

Da Zhou, Yue Luo, David Dingli, Arne Traulsen

Molecular noise of innate immunity shapes bacteria-phage ecologies

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

Cross-species functional modules link proteostasis to human normal aging

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

Modelling the mechanics of exploration in larval Drosophila

Jane Loveless, Konstantinos Lagogiannis, Barbara Webb

Disease gene prediction for molecularly uncharacterized diseases

Juan J. Cáceres, Alberto Paccanaro

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

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

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

Human online adaptation to changes in prior probability

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

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

Identifying determinants of persistent MRSA bacteremia using mathematical modeling

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

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

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

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

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

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

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

Information-theoretic analysis of multivariate single-cell signaling responses

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

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

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

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

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

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

Aleksandra Karolak, Sharan Poonja, Katarzyna A. Rejniak

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

Evripidis Gkanias, Benjamin Risse, Michael Mangan, Barbara Webb

Recombinant vector vaccine evolution

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

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

Benjamin Merkt, Friedrich Schüßler, Stefan Rotter

Assessing key decisions for transcriptomic data integration in biochemical networks

Anne Richelle, Chintan Joshi, Nathan E. Lewis

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

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

Duncan K. Ralph, Frederick A. Matsen IV

Why do eukaryotic proteins contain more intrinsically disordered regions?

Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson

Ensemble of decision tree reveals potential miRNA-disease associations

Xing Chen, Chi-Chi Zhu, Jun Yin

Modeling human intuitions about liquid flow with particle-based simulation

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

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

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

Foraging as an evidence accumulation process

Jacob D. Davidson, Ahmed El Hady

Syntrophy emerges spontaneously in complex metabolic systems

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

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

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

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

A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth

Shiva Rudraraju, Derek E. Moulton, Régis Chirat, Alain Goriely, Krishna Garikipati

Depressive symptoms are associated with blunted reward learning in social contexts

Lou Safra, Coralie Chevallier, Stefano Palminteri

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Trevor A. Graham, Andrea Sottoriva

The impact of DNA methylation on the cancer proteome

Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan, Olivier Gevaert

Robustness of respiratory rhythm generation across dynamic regimes

Jonathan E. Rubin, Jeffrey C. Smith

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