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Table of Contents: December 2013

COVER

Epidemic spread on weighted networks.

Image Credit: Andreas Bunten and clix
Issue Image

Epidemics spread along networks of infectious contacts, in particular those with high contact intensity or weight. Kamp et al. show that the preference of pathogens to travel along "highways" of high weight in the contact network strongly impacts epidemic dynamics.

Editorials

Education in Computational Biology Today and Tomorrow

Joanne A. Fox, B. F. Francis Ouellette

Message from ISCB

The Spirit of Competition: To Win or Not To Win

Teresa Szczepinska, Wataru Iwasaki, Thomas Abeel

Topic Page

Flow Cytometry Bioinformatics

Kieran O'Neill, Nima Aghaeepour, Josef Špidlen, Ryan Brinkman

Review

Research Articles

Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics

Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, Philippe Beaune, Patrice Degoulet, Anita Burgun, Marie-Anne Loriot, Paul Avillach

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas P. Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander

Structural Control of Metabolic Flux

Max Sajitz-Hermstein, Zoran Nikoloski

Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics

Geir Halnes, Ivar Østby, Klas H. Pettersen, Stig W. Omholt, Gaute T. Einevoll

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs

Patrick G. Blachly, César A. F. de Oliveira, Sarah L. Williams, J. Andrew McCammon

A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda

Artemis Koukounari, Christl A. Donnelly, Irini Moustaki, Edridah M. Tukahebwa, Narcis B. Kabatereine, Shona Wilson, Joanne P. Webster, André M. Deelder, Birgitte J. Vennervald, Govert J. van Dam

Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission

T. Alex Perkins, Thomas W. Scott, Arnaud Le Menach, David L. Smith

Epidemic Spread on Weighted Networks

Christel Kamp, Mathieu Moslonka-Lefebvre, Samuel Alizon

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

Tjaart A. P. de Beer, Roman A. Laskowski, Sarah L. Parks, Botond Sipos, Nick Goldman, Janet M. Thornton

Forward and Backward Inference in Spatial Cognition

Will D. Penny, Peter Zeidman, Neil Burgess

Modeling the Afferent Dynamics of the Baroreflex Control System

Adam Mahdi, Jacob Sturdy, Johnny T. Ottesen, Mette S. Olufsen

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier

Inferring Developmental Stage Composition from Gene Expression in Human Malaria

Regina Joice, Vagheesh Narasimhan, Jacqui Montgomery, Amar Bir Sidhu, Keunyoung Oh, Evan Meyer, Willythssa Pierre-Louis, Karl Seydel, Danny Milner, Kim Williamson, Roger Wiegand, Daouda Ndiaye, Johanna Daily, Dyann Wirth, Terrie Taylor, Curtis Huttenhower, Matthias Marti

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluís Gelpí, Modesto Orozco

Transformation of Stimulus Correlations by the Retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian

Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation

Mike Bonny, Elisabeth Fischer-Friedrich, Martin Loose, Petra Schwille, Karsten Kruse

Determinants of Cell-to-Cell Variability in Protein Kinase Signaling

Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie

Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions

Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei

Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybiło, Nicole N. Driessen, David Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett

Extrapolating Weak Selection in Evolutionary Games

Bin Wu, Julián García, Christoph Hauert, Arne Traulsen