Table of Contents: RECOMB Regulatory Genomics and Systems Biology 2009


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In a joint venture between PLoS Computational Biology, PLoS ONE and the conference program committee, this collection draws together papers from the 6th Annual RECOMB Satellite on Regulatory Genomics and the 5th Annual RECOMB Satellite on Systems Biology, held jointly at MIT, December 2-6, 2009.

The meeting brought together computational and experimental scientists in the area of regulatory genomics and systems biology to discuss current research directions and the latest findings, and establish new collaborations towards a systems-level understanding of gene regulation. The full-length research articles presented in this collection were reviewed and selected for presentation by the RECOMB program committee before full peer review by the journal editors.

Image Credit: Song et al., PLoS Comput Biol 6(3): e1000699

Research Articles

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets

Manikandan Narayanan, Adrian Vetta, Eric E. Schadt, Jun Zhu

Estimating the Stochastic Bifurcation Structure of Cellular Networks

Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins

Characterizing Dynamic Changes in the Human Blood Transcriptional Network

Jun Zhu, Yanqing Chen, Amy S. Leonardson, Kai Wang, John R. Lamb, Valur Emilsson, Eric E. Schadt

Dynamic Networks from Hierarchical Bayesian Graph Clustering

Yongjin Park, Cristopher Moore, Joel S. Bader

Network-Free Inference of Knockout Effects in Yeast

Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan

How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch

Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo, Mario di Bernardo

Inferring Binding Energies from Selected Binding Sites

Yue Zhao, David Granas, Gary D. Stormo

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data

Xin He, Chieh-Chun Chen, Feng Hong, Fang Fang, Saurabh Sinha, Huck-Hui Ng, Sheng Zhong