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Table of Contents

November 2015

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. Maesani et al.

Image Credit: Maesani et al.

Education

Research Articles

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

Shuyi Ma, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, Nathan D. Price

Multiscale Embedded Gene Co-expression Network Analysis

Won-Min Song, Bin Zhang

Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics

Jonathan W. Armond, Edward F. Harry, Andrew D. McAinsh, Nigel J. Burroughs

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitriy M. Chudakov

Reputation Effects in Public and Private Interactions

Hisashi Ohtsuki, Yoh Iwasa, Martin A. Nowak

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

Silvia Lovera, Maria Morando, Encarna Pucheta-Martinez, Jorge L. Martinez-Torrecuadrada, Giorgio Saladino, Francesco L. Gervasio

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu

A Model of Drosophila Larva Chemotaxis

Alex Davies, Matthieu Louis, Barbara Webb

A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation

Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu

Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes

Maciej Jan Ejsmond, Jacek Radwan

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns

Andrea Maesani, Pavan Ramdya, Steeve Cruchet, Kyle Gustafson, Richard Benton, Dario Floreano

Computational Modelling of Metastasis Development in Renal Cell Carcinoma

Etienne Baratchart, Sébastien Benzekry, Andreas Bikfalvi, Thierry Colin, Lindsay S. Cooley, Raphäel Pineau, Emeline J Ribot, Olivier Saut, Wilfried Souleyreau

A Systematic Bayesian Integration of Epidemiological and Genetic Data

Max S. Y. Lau, Glenn Marion, George Streftaris, Gavin Gibson

Quantifying Stochastic Noise in Cultured Circadian Reporter Cells

Peter C. St. John, Francis J. Doyle III

Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling

Robert P. Jenkins, Anja Hanisch, Cristian Soza-Ried, Erik Sahai, Julian Lewis

Finding New Order in Biological Functions from the Network Structure of Gene Annotations

Kimberly Glass, Michelle Girvan

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

Jia Li, Marie-Anne Poursat, Damien Drubay, Arnaud Motz, Zohra Saci, Antonin Morillon, Stefan Michiels, Daniel Gautheret

Parsimony, Exhaustivity and Balanced Detection in Neocortex

Alberto Romagnoni, Jérôme Ribot, Daniel Bennequin, Jonathan Touboul

A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes

Olivier J. N. Bertrand, Jens P. Lindemann, Martin Egelhaaf

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

Satohiro Tajima, Toru Yanagawa, Naotaka Fujii, Taro Toyoizumi

Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach

Joanne L. Dunster, Francoise Mazet, Michael J. Fry, Jonathan M. Gibbins, Marcus J. Tindall

Learning of Chunking Sequences in Cognition and Behavior

Jordi Fonollosa, Emre Neftci, Mikhail Rabinovich

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction

Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing

Donatien F. Chedom, Pablo R. Murcia, Chris D. Greenman

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alex Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton

Neuromechanistic Model of Auditory Bistability

James Rankin, Elyse Sussman, John Rinzel

Dynamic Redox Regulation of IL-4 Signaling

Gaurav Dwivedi, Margaret A. Gran, Pritha Bagchi, Melissa L. Kemp

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

Dmitry Svetlichnyy, Hana Imrichova, Mark Fiers, Zeynep Kalender Atak, Stein Aerts

Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model

Guido Gigante, Gustavo Deco, Shimon Marom, Paolo Del Giudice

The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex

Marina Martinez-Garcia, Andrea Insabato, Mario Pannunzi, Jose L. Pardo-Vazquez, Carlos Acuña, Gustavo Deco

Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics

Tri Hieu Nim, Le Luo, Jacob K. White, Marie-Véronique Clément, Lisa Tucker-Kellogg

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States

Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

Sandeep Choubey, Jane Kondev, Alvaro Sanchez

Network Plasticity as Bayesian Inference

David Kappel, Stefan Habenschuss, Robert Legenstein, Wolfgang Maass

On the Adjacency Matrix of RyR2 Cluster Structures

Mark A. Walker, Tobias Kohl, Stephan E. Lehnart, Joseph L. Greenstein, W. J. Lederer, Raimond L. Winslow

A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli

Kristin J. Adolfsen, Mark P. Brynildsen

Mechanism of Focal Adhesion Kinase Mechanosensing

Jing Zhou, Camilo Aponte-Santamaría, Sebastian Sturm, Jakob Tómas Bullerjahn, Agnieszka Bronowska, Frauke Gräter

A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ

Daniel Yakubovich, Shai Berlin, Uri Kahanovitch, Moran Rubinstein, Isabella Farhy-Tselnicker, Boaz Styr, Tal Keren-Raifman, Carmen W. Dessauer, Nathan Dascal

Lévy Walks Suboptimal under Predation Risk

Masato S. Abe, Masakazu Shimada

Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates

Max Hinne, Ronald J. Janssen, Tom Heskes, Marcel A.J. van Gerven

Learning to Estimate Dynamical State with Probabilistic Population Codes

Joseph G. Makin, Benjamin K. Dichter, Philip N. Sabes

Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition

Jonathan Cannon, Nancy Kopell, Timothy Gardner, Jeffrey Markowitz

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jiri Damborsky

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone