April 2017

Depiction of oncodomain hotspots found to be significantly overlapping with the active site of the protein kinase domain. Peterson et al.

Image Credit: Original image by Thomas Peterson

Editorial

Ten simple rules for making research software more robust

Morgan Taschuk, Greg Wilson

PLOS Computational Biology: published April 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005412

Review

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller

PLOS Computational Biology: published April 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005409

Research Articles

When do correlations increase with firing rates in recurrent networks?

Andrea K. Barreiro, Cheng Ly

PLOS Computational Biology: published April 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005506

Variable habitat conditions drive species covariation in the human microbiota

Charles K. Fisher, Thierry Mora, Aleksandra M. Walczak

PLOS Computational Biology: published April 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005435

Personalized glucose forecasting for type 2 diabetes using data assimilation

David J. Albers, Matthew Levine, Bruce Gluckman, Henry Ginsberg, George Hripcsak, Lena Mamykina

PLOS Computational Biology: published April 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005232

ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time

Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun

PLOS Computational Biology: published April 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005518

An aggregation-removal model for the formation and size determination of post-synaptic scaffold domains

Jonas Ranft, Leandro G. Almeida, Pamela C. Rodriguez, Antoine Triller, Vincent Hakim

PLOS Computational Biology: published April 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005516

Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis

Jörn Diedrichsen, Nikolaus Kriegeskorte

PLOS Computational Biology: published April 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005508

Predicting explorative motor learning using decision-making and motor noise

Xiuli Chen, Kieran Mohr, Joseph M. Galea

PLOS Computational Biology: published April 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005503

Intrinsically-generated fluctuating activity in excitatory-inhibitory networks

Francesca Mastrogiuseppe, Srdjan Ostojic

PLOS Computational Biology: published April 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005498

Exhaustive search of linear information encoding protein-peptide recognition

Abdellali Kelil, Benjamin Dubreuil, Emmanuel D. Levy, Stephen W. Michnick

PLOS Computational Biology: published April 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005499

A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana

Mónica L. García-Gómez, Eugenio Azpeitia, Elena R. Álvarez-Buylla

PLOS Computational Biology: published April 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005488

Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples

Thomas A. Peterson, Iris Ivy M. Gauran, Junyong Park, DoHwan Park, Maricel G. Kann

PLOS Computational Biology: published April 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005428

Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)

Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias

PLOS Computational Biology: published April 20, 2017 | https://doi.org/10.1371/journal.pcbi.1005372

Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size

Tilo Schwalger, Moritz Deger, Wulfram Gerstner

PLOS Computational Biology: published April 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005507

Robust information propagation through noisy neural circuits

Joel Zylberberg, Alexandre Pouget, Peter E. Latham, Eric Shea-Brown

PLOS Computational Biology: published April 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005497

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal

Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J. Lercher

PLOS Computational Biology: published April 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005494

Semantic prioritization of novel causative genomic variants

Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf

PLOS Computational Biology: published April 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005500

Probabilistic fluorescence-based synapse detection

Anish K. Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T. Vogelstein, Kristina D. Micheva, Richard J. Weinberg, Stephen J. Smith, Guillermo Sapiro

PLOS Computational Biology: published April 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005493

Effect of transcription factor resource sharing on gene expression noise

Dipjyoti Das, Supravat Dey, Robert C. Brewster, Sandeep Choubey

PLOS Computational Biology: published April 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005491

Dynamics of adaptive immunity against phage in bacterial populations

Serena Bradde, Marija Vucelja, Tiberiu Teşileanu, Vijay Balasubramanian

PLOS Computational Biology: published April 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005486

Achieving global perfect homeostasis through transporter regulation

Yonatan Savir, Alexander Martynov, Michael Springer

PLOS Computational Biology: published April 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005458

Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor

Vijay Singh, Ilya Nemenman

PLOS Computational Biology: published April 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005490

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

Mireya Plass, Simon H. Rasmussen, Anders Krogh

PLOS Computational Biology: published April 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005460

Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons

Yann Zerlaut, Alain Destexhe

PLOS Computational Biology: published April 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005452

Inferring modulators of genetic interactions with epistatic nested effects models

Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz

PLOS Computational Biology: published April 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005496

Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging

Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Lingling Geng, Qiaojun Fang

PLOS Computational Biology: published April 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005441

Human behavioral complexity peaks at age 25

Nicolas Gauvrit, Hector Zenil, Fernando Soler-Toscano, Jean-Paul Delahaye, Peter Brugger

PLOS Computational Biology: published April 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005408

Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD)

Tobias U. Hauser, Michael Moutoussis, Reto Iannaccone, Silvia Brem, Susanne Walitza, Renate Drechsler, Peter Dayan, Raymond J. Dolan

PLOS Computational Biology: published April 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005440

Modeling disordered protein interactions from biophysical principles

Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara

PLOS Computational Biology: published April 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005485

Amino acid composition predicts prion activity

Fayyaz ul Amir Afsar Minhas, Eric D. Ross, Asa Ben-Hur

PLOS Computational Biology: published April 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005465

Dose-response relationships for environmentally mediated infectious disease transmission models

Andrew F. Brouwer, Mark H. Weir, Marisa C. Eisenberg, Rafael Meza, Joseph N. S. Eisenberg

PLOS Computational Biology: published April 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005481

Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating

Mindaugas Snipas, Lina Rimkute, Tadas Kraujalis, Kestutis Maciunas, Feliksas F. Bukauskas

PLOS Computational Biology: published April 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005464

Dynamic compensation, parameter identifiability, and equivariances

Eduardo D. Sontag

PLOS Computational Biology: published April 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005447

How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation

Kostas Kouvaris, Jeff Clune, Loizos Kounios, Markus Brede, Richard A. Watson

PLOS Computational Biology: published April 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005358

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data

Ofir Shukron, David Holcman

PLOS Computational Biology: published April 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005469

Cover

Oncodomain Hotspots Overlap with the Active Site of Protein Kinases

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