An edition of The challenges of systems biology
(2009)
The challenges of systems biology
community efforts to harness biological complexity
by Gustavo Stolovitzky
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The challenges of systems biology: community efforts to harness biological complexity
2009, Published by Blackwell Pub. on behalf of the New York Academy of Sciences
in English
1573317519 9781573317511
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Table of Contents
Ranking genes by their co-expression to subsets of pathway members / Priit Adler ... [et al.]
Creating reference datasets for systems biology applications using text mining / Martin Krallinger, Ana María Rojas, Alfonso Valencia
The condition-dependent transcriptional network in Escherichia coli / Karen Lemmens ... [et al.]
Reverse-engineering transcriptional modules from gene expression data / Tom Michoel ... [et al.]
Specification of spatial relationships in directed graphs of cell signaling networks / Azi Lipshtat, Susana R. Neves, Ravi Iyengar
Uncovering metabolic objectives pursued by changes of enzyme levels / Sabrina Hoffmann, Hermann-Georg Holzhütter
Modeling of gene regulatory network dynamics using threshold logic / Tejaswi Gowda, Sarma Vrudhula, Seungchan Kim
Global robustness and identifiability of random, scale-free, and small-world networks / Yunchen Gong, Zhaolei Zhang
The five-gene-network data analysis with local causal discovery algorithm using causal Bayesian networks / Changwon Yoo, Erik M. Brilz
Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge / Daniel Marbach, Claudio Mattiussi, Dario Floreano
Network inference by combining biologically motivated regulatory constraints with penalized regression / Fabio Parisi, Heinz Koeppl, Felix Naef
A gene network simulator to assess reverse engineering algorithms / Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli
A network inference workflow applied to virulence-related processes in Salmonella typhimurium / Ronald C. Taylor ... [et al.]
Lessons from the DREAM2 challenges : a community effort to assess biological network inference / Gustavo Stolovitzky, Robert J. Prill, Andrea Califano
DREAM2 challenge : integrated multi-array supervised learning algorithm for BCL6 transcriptional targets prediction / W.H. Lee ... [et al.]
A data integration framework for prediction of transcription factor targets : a BCL6 case study / Matti Nykter ... [et al.]
Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge / Vinsensius B. Vega ... [et al.]
A probabilistic graph-theoretic approach to integrate multiple predictions for the protein-protein subnetwork prediction challenge / Hon Nian Chua ... [et al.]
Replaying the evolutionary tape : biomimetic reverse engineering of gene networks / Daniel Marbach, Claudio Mattiussi, Dario Floreano
Inferring gene networks : dream or nightmare? : part 1: challenges 1 and 3 / Angela Baralla, Wieslawa I. Mentzen, Alberto de la Fuente
NIRest : a tool for gene network and mode of action inference / Mario Lauria, Francesco Iorio, Diego di Bernardo
Reverse engineering of gene networks with LASSO and nonlinear basis functions / Mika Gustafsson ... [et al.]
Prediction of pairwise gene interaction using threshold logic / Tejaswi Gowda, Sarma Vrudhula, Seungchan Kim
Inferring gene networks : dream or nightmare? : part 2: challenges 4 and 5 / Alan Scheinine ... [et al.]
Inference of regulatory gene interactions from expression data using three-way mutual information / John Watkinson ... [et al.].
Edition Notes
"The volume is the result of the Second Dialogue on Reverse Engineering Assessment and Methods (DREAM2) Challenges, posed to the systems biology community between July and October, 2007; the DREAM2 Conference, held on December 3-4, 2007 at the New York Academy of Sciences in New York; and the ENFIN-DREAM Conference, Assessment of Computational Methods in Systems Biology, held on April 28-29, 2008 in Madrid, Spain"--P. v.
Includes bibliographical references and index.
Issued also online.
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