Skip to main content
Table of Contents

March 2013

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.

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


New Methods Section in PLOS Computational Biology

Thomas Lengauer, Ruth Nussinov

Related Articles

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

Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action

James B. Gilmore, Anthony D. Kelleher, David A. Cooper, John M. Murray

Automated Analysis of a Diverse Synapse Population

Brad Busse, Stephen Smith

Stability and Responsiveness in a Self-Organized Living Architecture

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

A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana

Christoph Schmal, Peter Reimann, Dorothee Staiger

A Model of Binocular Rivalry and Cross-orientation Suppression

Christopher P. Said, David J. Heeger

The Fate of Cooperation during Range Expansions

Kirill S. Korolev

Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain

Marta I. Garrido, Maneesh Sahani, Raymond J. Dolan

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

Related Articles

Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza

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

Bursts of Vertex Activation and Epidemics in Evolving Networks

Luis E. C. Rocha, Vincent D. Blondel

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment

Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, Rui Kuang

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

Neuronal Avalanches Differ from Wakefulness to Deep Sleep – Evidence from Intracranial Depth Recordings in Humans

Viola Priesemann, Mario Valderrama, Michael Wibral, Michel Le Van Quyen

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart

A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence

Andreas Handel, Justin Brown, David Stallknecht, Pejman Rohani

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase – Cytochrome c

Frank H. Wallrapp, Alexander A. Voityuk, Victor Guallar

Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids

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

Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins

Hyun-Jun Nam, Seong Kyu Han, James U. Bowie, Sanguk Kim

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

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering

Mehrdad Mehrbod, Mohammad R. K. Mofrad

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

Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity

BoHung Kim, Sarah L. Hawes, Fawad Gillani, Lane J. Wallace, Kim T. Blackwell

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

Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock

Stefanie Hertel, Christian Brettschneider, Ilka M. Axmann

Differential Expression Analysis for Pathways

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

Related Articles

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

Interpretation of Genomic Variants Using a Unified Biological Network Approach

Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein

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

Dual Coordination of Post Translational Modifications in Human Protein Networks

Jonathan Woodsmith, Atanas Kamburov, Ulrich Stelzl

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

Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems

Yuhan Chen, Shengjun Wang, Claus C. Hilgetag, Changsong Zhou

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

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

Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning

Tomoki Kurikawa, Kunihiko Kaneko

Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza

Chad R. Wells, Eili Y. Klein, Chris T. Bauch

Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks

Munia Amin, Steven L. Porter, Orkun S. Soyer

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

David Amar, Hershel Safer, Ron Shamir