Table of Contents

December 2010

Th1 and Th2 lymphocytes are thought to be counter-regulatory. A network model of genes that regulate Th1 and Th2 cells was constructed by automated mining of 18 million abstracts in Medline. Analysis of the dynamics of this model using in silico knock-outs suggested a synergistic, rather than a counter-regulatory, relationship between Th1 and Th2 cells. This was supported by analysis of public gene expression microarray data from different inflammatory diseases. Network modeling using public data may be generally applicable to understand complex regulatory networks in health and disease. (See Pedicini et al., doi:10.1371/journal.pcbi.1001032.)

Image Credit: Filippo Castiglione

Research Articles

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay

Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway

Andreja Jovic, Bryan Howell, Michelle Cote, Susan M. Wade, Khamir Mehta, Atsushi Miyawaki, Richard R. Neubig, Jennifer J. Linderman, Shuichi Takayama

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

John Archer, Andrew Rambaut, Bruce E. Taillon, P. Richard Harrigan, Marilyn Lewis, David L. Robertson

How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations

Tilo Schwalger, Karin Fisch, Jan Benda, Benjamin Lindner

Kinetics of Rhodopsin Deactivation and Its Role in Regulating Recovery and Reproducibility of Rod Photoresponse

Giovanni Caruso, Paolo Bisegna, Leonardo Lenoci, Daniele Andreucci, Vsevolod V. Gurevich, Heidi E. Hamm, Emmanuele DiBenedetto

Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation

Marco Pedicini, Fredrik Barrenäs, Trevor Clancy, Filippo Castiglione, Eivind Hovig, Kartiek Kanduri, Daniele Santoni, Mikael Benson

Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait

Jie Zhang, Kai Zhang, Jianfeng Feng, Michael Small

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells

Florian Markowetz, Klaas W. Mulder, Edoardo M. Airoldi, Ihor R. Lemischka, Olga G. Troyanskaya

Mathematical Model of a Cell Size Checkpoint

Marco Vilela, Jeffrey J. Morgan, Paul A. Lindahl

Encoding of Spatio-Temporal Input Characteristics by a CA1 Pyramidal Neuron Model

Eleftheria Kyriaki Pissadaki, Kyriaki Sidiropoulou, Martin Reczko, Panayiota Poirazi

Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus

Richard Reeve, Belinda Blignaut, Jan J. Esterhuysen, Pamela Opperman, Louise Matthews, Elizabeth E. Fry, Tjaart A. P. de Beer, Jacques Theron, Elizabeth Rieder, Wilna Vosloo, Hester G. O'Neill, Daniel T. Haydon, Francois F. Maree

A Scalable Approach for Discovering Conserved Active Subnetworks across Species

Raamesh Deshpande, Shikha Sharma, Catherine M. Verfaillie, Wei-Shou Hu, Chad L. Myers

Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases

Robert J. Fieldhouse, Zachari Turgeon, Dawn White, A. Rod Merrill

Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics

Maarten Chris Boerlijst, Willem Marijn van Ballegooijen

Self-Organized Criticality in Developing Neuronal Networks

Christian Tetzlaff, Samora Okujeni, Ulrich Egert, Florentin Wörgötter, Markus Butz

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto López-Rendón, John Zintsmaster, Maria Ercsey-Ravasz, Christopher R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, Jesús A. Izaguirre

Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing

C. David Williams, Michael Regnier, Thomas L. Daniel

Modeling Mechanisms of In Vivo Variability in Methotrexate Accumulation and Folate Pathway Inhibition in Acute Lymphoblastic Leukemia Cells

John C. Panetta, Alex Sparreboom, Ching-Hon Pui, Mary V. Relling, William E. Evans

Assessing Computational Methods of Cis-Regulatory Module Prediction

Jing Su, Sarah A. Teichmann, Thomas A. Down

Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data

Fabrizio Iozzi, Francesco Trusiano, Matteo Chinazzi, Francesco C. Billari, Emilio Zagheni, Stefano Merler, Marco Ajelli, Emanuele Del Fava, Piero Manfredi

Gambling in the Visual Periphery: A Conjoint-Measurement Analysis of Human Ability to Judge Visual Uncertainty

Hang Zhang, Camille Morvan, Laurence T. Maloney

A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin

Najl V. Valeyev, Christian Hundhausen, Yoshinori Umezawa, Nikolay V. Kotov, Gareth Williams, Alex Clop, Crysanthi Ainali, Christos Ouzounis, Sophia Tsoka, Frank O. Nestle

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Eugene V. Davydov, David L. Goode, Marina Sirota, Gregory M. Cooper, Arend Sidow, Serafim Batzoglou

Structure Learning in Human Sequential Decision-Making

Daniel E. Acuña, Paul Schrater

A Minimal Model of Metabolism-Based Chemotaxis

Matthew D. Egbert, Xabier E. Barandiaran, Ezequiel A. Di Paolo