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Table of Contents: March 2013

COVER

Ensemble conformations of human Chromosome 19 generated by computer simulations

Image Credit: Marco Di Stefano, Angelo Rosa, Cristian Micheletti
Issue Image

The yellow bundle in the foreground represents a coarse-grained, computer-generated conformation of human Chromosome 19. The structure was obtained by using steered molecular dynamics simulations to enforce a comprehensive set of knowledge-based constraints. Specifically, the simulations were used to promote the spatial proximity of hundreds of gene pairs that are known to be significantly co-regulated. Conformations were obtained with LAMMPS and visualized by VMD. See Di Stefano, et al.

Editorial

Topic Pages

Viral Phylodynamics

Erik M. Volz, Katia Koelle, Trevor Bedford

Evolving Digital Ecological Networks

Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria

Research Articles

The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks

Clive G. Bowsher, Margaritis Voliotis, Peter S. Swain

Stability and Responsiveness in a Self-Organized Living Architecture

Simon Garnier, Tucker Murphy, Matthew Lutz, Edward Hurme, Simon Leblanc, Iain D. Couzin

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd

Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity

Himadri Mukhopadhyay, Shaun-Paul Cordoba, Philip K. Maini, P. Anton van der Merwe, Omer Dushek

An Integrated Computational/Experimental Model of Lymphoma Growth

Hermann B. Frieboes, Bryan R. Smith, Yao-Li Chuang, Ken Ito, Allison M. Roettgers, Sanjiv S. Gambhir, Vittorio Cristini

Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit

Yuguo Yu, Thomas S. McTavish, Michael L. Hines, Gordon M. Shepherd, Cesare Valenti, Michele Migliore

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

Philip Stegmaier, Alexander Kel, Edgar Wingender, Jürgen Borlak

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward

Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza

Laura Matrajt, M. Elizabeth Halloran, Ira M. Longini Jr

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser, Francisco S. Domingues

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen

Angiogenesis: An Adaptive Dynamic Biological Patterning Problem

Timothy W. Secomb, Jonathan P. Alberding, Richard Hsu, Mark W. Dewhirst, Axel R. Pries

Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids

Alexander J. Stewart, Robert M. Seymour, Andrew Pomiankowski, Max Reuter

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

Jialiang Huang, Chaoqun Niu, Christopher D. Green, Lun Yang, Hongkang Mei, Jing-Dong J. Han

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

Silvio a Beccara, Tatjana Škrbić, Roberto Covino, Cristian Micheletti, Pietro Faccioli

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

Paul C. Whitford, Scott C. Blanchard, Jamie H. D. Cate, Karissa Y. Sanbonmatsu

Stimulus-dependent Maximum Entropy Models of Neural Population Codes

Einat Granot-Atedgi, Gašper Tkačik, Ronen Segev, Elad Schneidman

Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming

Robert W. Mill, Tamás M. Bőhm, Alexandra Bendixen, István Winkler, Susan L. Denham

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt

A Dynamical Role for Acetylcholine in Synaptic Renormalization

Christian G. Fink, Geoffrey G. Murphy, Michal Zochowski, Victoria Booth

Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling

Douglas E. White, Melissa A. Kinney, Todd C. McDevitt, Melissa L. Kemp

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars A. Bongo, Rebecca D. Burdine, Olga G. Troyanskaya

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model

Libin Rong, Jeremie Guedj, Harel Dahari, Daniel J. Coffield Jr, Micha Levi, Patrick Smith, Alan S. Perelson

Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, Jens Boch

Differential Expression Analysis for Pathways

Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren

Directional Summation in Non-direction Selective Retinal Ganglion Cells

Syed Y. Abbas, Khaldoun C. Hamade, Ellen J. Yang, Scott Nawy, Robert G. Smith, Diana L. Pettit

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David J. Gavaghan

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich

High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron

Bóris Marin, William H. Barnett, Anca Doloc-Mihu, Ronald L. Calabrese, Gennady S. Cymbalyuk

Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

Ron Stewart, Cynthia Alexander Rascón, Shulan Tian, Jeff Nie, Chris Barry, Li-Fang Chu, Hamisha Ardalani, Ryan J. Wagner, Mitchell D. Probasco, Jennifer M. Bolin, Ning Leng, Srikumar Sengupta, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey

Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise

R. Channing Moore, Tyler Lee, Frédéric E. Theunissen

Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model

Néstor Sepúlveda, Laurence Petitjean, Olivier Cochet, Erwan Grasland-Mongrain, Pascal Silberzan, Vincent Hakim