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Table of Contents: 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

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

Research Articles

When do correlations increase with firing rates in recurrent networks?

Andrea K. Barreiro, Cheng Ly

Variable habitat conditions drive species covariation in the human microbiota

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

Personalized glucose forecasting for type 2 diabetes using data assimilation

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

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

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

Predicting explorative motor learning using decision-making and motor noise

Xiuli Chen, Kieran Mohr, Joseph M. Galea

Intrinsically-generated fluctuating activity in excitatory-inhibitory networks

Francesca Mastrogiuseppe, Srdjan Ostojic

Exhaustive search of linear information encoding protein-peptide recognition

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

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

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

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

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

Tilo Schwalger, Moritz Deger, Wulfram Gerstner

Robust information propagation through noisy neural circuits

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

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

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

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

Effect of transcription factor resource sharing on gene expression noise

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

Dynamics of adaptive immunity against phage in bacterial populations

Serena Bradde, Marija Vucelja, Tiberiu Teşileanu, Vijay Balasubramanian

Achieving global perfect homeostasis through transporter regulation

Yonatan Savir, Alexander Martynov, Michael Springer

Inferring modulators of genetic interactions with epistatic nested effects models

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

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

Human behavioral complexity peaks at age 25

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

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

Modeling disordered protein interactions from biophysical principles

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

Amino acid composition predicts prion activity

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

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

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

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

Computation and measurement of cell decision making errors using single cell data

Iman Habibi, Raymond Cheong, Tomasz Lipniacki, Andre Levchenko, Effat S. Emamian, Ali Abdi

Geospatial characteristics of measles transmission in China during 2005−2014

Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-Yi Zhang, Jeffrey Shaman

Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock

Tom Sumner, Richard J. Orton, Darren M. Green, Rowland R. Kao, Simon Gubbins

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

Wen-Ting Chu, Jane Clarke, Sarah L. Shammas, Jin Wang

Sequence dependency of canonical base pair opening in the DNA double helix

Viveca Lindahl, Alessandra Villa, Berk Hess

The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation

Anne-Claire M. F. Martines, Karen van Eunen, Dirk-Jan Reijngoud, Barbara M. Bakker

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling

Irene Otero-Muras, Pencho Yordanov, Joerg Stelling

Polarization and migration in the zebrafish posterior lateral line system

Hildur Knutsdottir, Cole Zmurchok, Dhananjay Bhaskar, Eirikur Palsson, Damian Dalle Nogare, Ajay B. Chitnis, Leah Edelstein-Keshet