March 2017

The autism awareness ribbon symbolizes the diverse experiences of people and families living with autism spectrum disorder. Here, it also represents the various genetic and environmental effects on the pathophysiology of autism spectrum disorder. The white pieces represent currently unknown effects. However, the piece illustrating folate-dependent one-carbon metabolism and transsulfuration contributes important information to our knowledge of autism spectrum disorder. Howsmon et al.

Image Credit: Daniel P. Howsmon

Editorials

Ten simple rules for responsible big data research

Matthew Zook, Solon Barocas, danah boyd, Kate Crawford, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara A. Koenig, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005399

Ten simple rules for short and swift presentations

Christopher J. Lortie

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005373

Ten simple rules for forming a scientific professional society

Bruno A. Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola Mulder, Paolo Romano, Lonnie Welch

PLOS Computational Biology: published March 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005226

PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You

PLOS Computational Biology: published March 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005442

Research Articles

The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes

Jeffrey Chen, Thomas MacCarthy

PLOS Computational Biology: published March 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005471

ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing

Sergey G. Aleksin, Kaiyu Zheng, Dmitri A. Rusakov, Leonid P. Savtchenko

PLOS Computational Biology: published March 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005467

Interrogating the topological robustness of gene regulatory circuits by randomization

Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, Jose N. Onuchic

PLOS Computational Biology: published March 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005456

Effects of contact structure on the transient evolution of HIV virulence

Sang Woo Park, Benjamin M. Bolker

PLOS Computational Biology: published March 31, 2017 | https://doi.org/10.1371/journal.pcbi.1005453

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005459

Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N

Polydefkis Diamantis, Oliver T. Unke, Markus Meuwly

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005450

Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment

Marie Devaine, Jean Daunizeau

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005422

Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrome

Daniele Caligiore, Francesco Mannella, Michael A. Arbib, Gianluca Baldassarre

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005395

A critical analysis of computational protein design with sparse residue interaction graphs

Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce R. Donald

PLOS Computational Biology: published March 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005346

High GC content causes orphan proteins to be intrinsically disordered

Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson

PLOS Computational Biology: published March 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005375

Phylodynamics on local sexual contact networks

David A. Rasmussen, Roger Kouyos, Huldrych F. Günthard, Tanja Stadler

PLOS Computational Biology: published March 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005448

Systematic identification of phosphorylation-mediated protein interaction switches

Matthew J. Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P. Roth, Anne-Claude Gavin, Peer Bork, Robert B. Russell

PLOS Computational Biology: published March 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005462

Geometry can provide long-range mechanical guidance for embryogenesis

Mahamar Dicko, Pierre Saramito, Guy B. Blanchard, Claire M. Lye, Bénédicte Sanson, Jocelyn Étienne

PLOS Computational Biology: published March 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005443

PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction

Zhu-Hong You, Zhi-An Huang, Zexuan Zhu, Gui-Ying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen

PLOS Computational Biology: published March 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005455

Network perturbation by recurrent regulatory variants in cancer

Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi

PLOS Computational Biology: published March 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005449

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis

PLOS Computational Biology: published March 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005397

Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide

Binwu Zhao, Martien A. Cohen Stuart, Carol K. Hall

PLOS Computational Biology: published March 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005446

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

Michiel J. M. Niesen, Connie Y. Wang, Reid C. Van Lehn, Thomas F. Miller III

PLOS Computational Biology: published March 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005427

A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands

Lindsay E. Clegg, Feilim Mac Gabhann

PLOS Computational Biology: published March 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005445

A general model for metabolic scaling in self-similar asymmetric networks

Alexander Byers Brummer, Van M. Savage, Brian J. Enquist

PLOS Computational Biology: published March 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005394

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu

PLOS Computational Biology: published March 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005432

Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability

Cibele V. Falkenberg, Evren U. Azeloglu, Mark Stothers, Thomas J. Deerinck, Yibang Chen, John C. He, Mark H. Ellisman, James C. Hone, Ravi Iyengar, Leslie M. Loew

PLOS Computational Biology: published March 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005433

Classification and adaptive behavior prediction of children with autism spectrum disorder based upon multivariate data analysis of markers of oxidative stress and DNA methylation

Daniel P. Howsmon, Uwe Kruger, Stepan Melnyk, S. Jill James, Juergen Hahn

PLOS Computational Biology: published March 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005385

A thermodynamically consistent model of the post-translational Kai circadian clock

Joris Paijmans, David K. Lubensky, Pieter Rein ten Wolde

PLOS Computational Biology: published March 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005415

Fast online deconvolution of calcium imaging data

Johannes Friedrich, Pengcheng Zhou, Liam Paninski

PLOS Computational Biology: published March 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005423

Stimulus-specific adaptation in a recurrent network model of primary auditory cortex

Tohar S. Yarden, Israel Nelken

PLOS Computational Biology: published March 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005437

Dynamics robustness of cascading systems

Jonathan T. Young, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko

PLOS Computational Biology: published March 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005434

Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis

Andrew F. Brouwer, Rafael Meza, Marisa C. Eisenberg

PLOS Computational Biology: published March 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005431

Patient-specific modeling of individual sickle cell behavior under transient hypoxia

Xuejin Li, E. Du, Ming Dao, Subra Suresh, George Em Karniadakis

PLOS Computational Biology: published March 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005426

Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background

Julien Vibert, Véronique Thomas-Vaslin

PLOS Computational Biology: published March 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005417

A human judgment approach to epidemiological forecasting

David C. Farrow, Logan C. Brooks, Sangwon Hyun, Ryan J. Tibshirani, Donald S. Burke, Roni Rosenfeld

PLOS Computational Biology: published March 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005248

A model for brain life history evolution

Mauricio González-Forero, Timm Faulwasser, Laurent Lehmann

PLOS Computational Biology: published March 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005380

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, Alexander Li Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack

PLOS Computational Biology: published March 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005209

Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions

Rashmi Priya, Guillermo A. Gomez, Srikanth Budnar, Bipul R. Acharya, Andras Czirok, Alpha S. Yap, Zoltan Neufeld

PLOS Computational Biology: published March 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005411

Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study

Erick A. Perez Alday, Michael A. Colman, Philip Langley, Henggui Zhang

PLOS Computational Biology: published March 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005270

Cover

Uncovering Mechanisms Underlying Autism Spectrum Disorder Piece by Piece

Editorials

Research Articles

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