DREAM Publications
October 29, 2010

2010 Publications

Gustafsson, M. and Hörnquist, M.
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge
PLoS ONE 5(2): e9134. doi:10.1371/journal.pone.0009134

Ruan, J.
A top-performing algorithm for the DREAM3 gene expression prediction challenge
PLoS ONE 5(2): e8944. doi:10.1371/journal.pone.0008944

Guex, N. Migliavacca, E. and Xenarios, I.
Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy
PLoS ONE 5(1): e8012. doi:10.1371/journal.pone.0008012

Madar, A. and Greenfield, A. and Vanden-eijnden, E. and Bonneau, R.
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator
PLoS ONE 5(3): e9803. doi:10.1371/journal.pone.0009803

Clarke, N.D. and Bourque, G.
Success in the DREAM3 signaling response challenge using simple weighted-average imputation: lessons for community-wide experiments in systems biology
PLoS ONE 5(1): e8417. doi:10.1371/journal.pone.0008417

Prill, R.J. and Marbach, D. Saez-rodriguez, J. and Sorger, P.K. and Alexopoulos, L.G. and Xue, X. and Clarke, N.D. and Altan-bonnet, G. and Stolovitzky, G.
Towards a rigorous assessment of systems biology models: the DREAM3 challenges
PLoS ONE 5(2): e9202. doi:10.1371/journal.pone.0009202

Menéndez, P. and Kourmpetis, Y.A.I. and Ter Braak, C.J.F. Van Eeuwijk, F.A.
Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge
PLoS ONE 5(12): e14147. doi:10.1371/journal.pone.0014147

Greenfield, Alex and Madar, Aviv and Ostrer, Harry and Bonneau, Richard,
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models
PLoS ONE 5(10): e13397. doi:10.1371/journal.pone.0013397

Hong, Seungpyo and Chung, Taesu and Kim, Dongsup,
SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates
PLoS ONE 5(9): e12654. doi:10.1371/journal.pone.0012654

Pinna, Andrea and Soranzo, Nicola and de la Fuente, Alberto,
From knockouts to networks: establishing direct cause-effect relationships through graph analysis
PLoS ONE 5(10): e12912. doi:10.1371/journal.pone.0012912

Huynh-Thu, Vân Anh and Irrthum, Alexandre and Wehenkel, Louis and Geurts, Pierre,
Inferring regulatory networks from expression data using tree-based methods
PLoS ONE 5(9): e12776. doi:10.1371/journal.pone.0012776

Küffner, Robert and Petri, Tobias and Windhager, Lukas and Zimmer, Ralf,
Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parameterization
PLoS ONE 5(9): e12807. doi:10.1371/journal.pone.0012807

Zaslavsky, Elena and Bradley, Philip and Yanover, Chen,
Inferring PDZ domain multi-mutant binding preferences from single-mutant data
PLoS ONE 5(9): e12787. doi:10.1371/journal.pone.0012787

Yip, Kevin Y and Alexander, Roger P and Yan, Koon-Kiu and Gerstein, Mark,
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data
PLoS ONE 5(1): e8121. doi:10.1371/journal.pone.0008121

Eduati, Federica and Corradin, Alberto and Di Camillo, Barbara and Toffolo, Gianna,
A Boolean approach to linear prediction for signaling network modeling
PLoS ONE 5(9): e12789. doi:10.1371/journal.pone.0012789

Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.
Revealing strengths and weaknesses of methods for gene network inference.
Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22.