Table of Contents: August 2014

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Animal groups, such as the starling murmuration (Sturnus vulgaris) shown here, must frequently make consensus decisions. These collective decisions may be based on various environmental cues that individuals in the group observe, and these individual opinions must be integrated into a collective decision through movement dynamics. Associative learning, which is ubiquitous across animal taxa, can alter the degree to which group members rely on particular cues. The learned behavior can differ dramatically when learning within a group context compared to learning in isolation, which can lead to substantially enhanced collective wisdom. See Kao et al.

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Research Articles

Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions

Piero Dalle Pezze, Glyn Nelson, Elsje G. Otten, Viktor I. Korolchuk, Thomas B. L. Kirkwood, Thomas von Zglinicki, Daryl P. Shanley

Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth

Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M. L. Ebos, Lynn Hlatky, Philip Hahnfeldt

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution

Priscilla Ambrosi, Juan Sebastian Chahda, Hannah R. Koslen, Hillel J. Chiel, Claudia Mieko Mizutani

Communication through Resonance in Spiking Neuronal Networks

Gerald Hahn, Alejandro F. Bujan, Yves Frégnac, Ad Aertsen, Arvind Kumar

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

Geir Villy Isaksen, Johan Åqvist, Bjørn Olav Brandsdal

Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input

Jonathan Laudanski, Benjamin Torben-Nielsen, Idan Segev, Shihab Shamma

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

Andries J. van Tonder, Shilan Mistry, James E. Bray, Dorothea M. C. Hill, Alison J. Cody, Chris L. Farmer, Keith P. Klugman, Anne von Gottberg, Stephen D. Bentley, Julian Parkhill, Keith A. Jolley, Martin C. J. Maiden, Angela B. Brueggemann

A New Model for Pore Formation by Cholesterol-Dependent Cytolysins

Cyril F. Reboul, James C. Whisstock, Michelle A. Dunstone

Sparsity and Compressed Coding in Sensory Systems

Victor J. Barranca, Gregor Kovačič, Douglas Zhou, David Cai

Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions

Kanghoon Jung, Hyeran Jang, Jerald D. Kralik, Jaeseung Jeong

Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens

Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S. Lopes, Bruno Ceña, Cláudia T. Codeço, M. Gabriela M. Gomes

Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro

René F. M. van Oers, Elisabeth G. Rens, Danielle J. LaValley, Cynthia A. Reinhart-King, Roeland M. H. Merks

Optimal Behavioral Hierarchy

Alec Solway, Carlos Diuk, Natalia Córdova, Debbie Yee, Andrew G. Barto, Yael Niv, Matthew M. Botvinick

A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells

Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J. Sanderson, James Sneyd

Kinetic Memory Based on the Enzyme-Limited Competition

Tetsuhiro S. Hatakeyama, Kunihiko Kaneko

Dynamic Mechanisms of Neocortical Focal Seizure Onset

Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis

Seungyeul Yoo, Tao Huang, Joshua D. Campbell, Eunjee Lee, Zhidong Tu, Mark W. Geraci, Charles A. Powell, Eric E. Schadt, Avrum Spira, Jun Zhu

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding

Memory Capacity of Networks with Stochastic Binary Synapses

Alexis M. Dubreuil, Yali Amit, Nicolas Brunel

A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation

Erwan Hingant, Pascaline Fontes, Maria Teresa Alvarez-Martinez, Jacques-Damien Arnaud, Jean-Pierre Liautard, Laurent Pujo-Menjouet

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You

Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment

Johannes Textor, Sarah E. Henrickson, Judith N. Mandl, Ulrich H. von Andrian, Jürgen Westermann, Rob J. de Boer, Joost B. Beltman

Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus

Nik J. Cunniffe, Francisco F. Laranjeira, Franco M. Neri, R. Erik DeSimone, Christopher A. Gilligan

Collective Learning and Optimal Consensus Decisions in Social Animal Groups

Albert B. Kao, Noam Miller, Colin Torney, Andrew Hartnett, Iain D. Couzin

Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment

Eric L. Haseltine, Sandra De Meyer, Inge Dierynck, Doug J. Bartels, Anne Ghys, Andrew Davis, Eileen Z. Zhang, Ann M. Tigges, Joan Spanks, Gaston Picchio, Tara L. Kieffer, James C. Sullivan

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung'u