Biology & Life Sciences

RECOMB Regulatory Genomics and Systems Biology 2009

Published May 25, 2018 Partnered Collections, Special Issues

In a joint venture between PLOS 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 at MIT in December 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

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Reseach Articles

Reseach Articles

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10.1371/journal.pcbi.1000832

PLOS Computational Biology RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
July 1, 2010 Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris
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10.1371/journal.pcbi.1000742

PLOS Computational Biology Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets
April 15, 2010 Manikandan Narayanan, Adrian Vetta, Eric E. Schadt, Jun Zhu
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10.1371/journal.pcbi.1000699

PLOS Computational Biology Estimating the Stochastic Bifurcation Structure of Cellular Networks
March 5, 2010 Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins
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10.1371/journal.pcbi.1000671

PLOS Computational Biology Characterizing Dynamic Changes in the Human Blood Transcriptional Network
February 12, 2010 Jun Zhu, Yanqing Chen, Amy S. Leonardson, Kai Wang, John R. Lamb, Valur Emilsson, Eric E. Schadt
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10.1371/journal.pone.0008118

PLOS ONE Dynamic Networks from Hierarchical Bayesian Graph Clustering
January 11, 2010 Yongjin Park, Cristopher Moore, Joel S. Bader
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10.1371/journal.pcbi.1000635

PLOS Computational Biology Network-Free Inference of Knockout Effects in Yeast
January 8, 2010 Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan
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Song et al., PLoS Comput Biol 6(3): e1000699

PLOS ONE Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models
December 7, 2009 Xiaoning Qian, Byung-Jun Yoon
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10.1371/journal.pone.0008083

PLOS ONE How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch
December 7, 2009 Lucia Marucci, David A. W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, Stefania Santini, Diego di Bernardo, Mario di Bernardo
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10.1371/journal.pone.0008161

PLOS ONE Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity
December 7, 2009 Junjie Su, Byung-Jun Yoon, Edward R. Dougherty
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10.1371/journal.pcbi.1000590

PLOS Computational Biology Inferring Binding Energies from Selected Binding Sites
December 4, 2009 Yue Zhao, David Granas, Gary D. Stormo
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10.1371/journal.pcbi.1000591

PLOS Computational Biology Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
December 4, 2009 Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos
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10.1371/journal.pone.0007992

PLOS ONE Scalable Steady State Analysis of Boolean Biological Regulatory Networks
December 1, 2009 Ferhat Ay, Fei Xu, Tamer Kahveci
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10.1371/journal.pone.0008001

PLOS ONE Ground State Robustness as an Evolutionary Design Principle in Signaling Networks
December 1, 2009 Önder Kartal, Oliver Ebenhöh
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10.1371/journal.pone.0008040

PLOS ONE A Dynamic Analysis of IRS-PKR Signaling in Liver Cells: A Discrete Modeling Approach
December 1, 2009 Ming Wu, Xuerui Yang, Christina Chan
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10.1371/journal.pone.0008155

PLOS ONE A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data
December 1, 2009 Xin He, Chieh-Chun Chen, Feng Hong, Fang Fang, Saurabh Sinha, Huck-Hui Ng, Sheng Zhong