The challenges of systems biology : community efforts to harness biological complexity /
The challenges of systems biology : community efforts to harness biological complexity /
edited by Gustavo Stolovitzky, Pascal Kahlem, and Andrea Califano
- Boston, Mass. : Published by Blackwell Pub. on behalf of the New York Academy of Sciences, c2009
- xii, 316 p. : ill. (some col.) ; 25 cm.
- Annals of the New York Academy of Sciences, v. 1158 0077-8923 ; .
- Annals of the New York Academy of Sciences, v. 1158 .
"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
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.]
9781573317511 1573317519
Systems biology--Congresses
Systems Biology--Congresses
Gene Regulatory Networks--Congresses
"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
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.]
9781573317511 1573317519
Systems biology--Congresses
Systems Biology--Congresses
Gene Regulatory Networks--Congresses