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2006

2006 Publications

Adam Margolin, Kai Wang, Wei Lim, Manjunath Kustagi, Ilya Nemenman, Andrea Califano .  2006.   Reverse engineering cellular networks.. Nat Protoc. 1 (2) :662-71 ▶ Go to Pubmed
Teresa Palomero, Wei Lim, Duncan Odom, Maria Sulis, Pedro Real, Adam Margolin, Kelly Barnes, Jennifer O'Neil, Donna Neuberg, Andrew Weng, Jon Aster, Francois Sigaux, Jean Soulier, Thomas Look, Richard Young, Andrea Califano, Adolfo Ferrando .  2006.   NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth.. Proc Natl Acad Sci U S A. 103 (48) :18261-6 ▶ Go to Pubmed
Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark Gerstein, Yves Lussier .  2006.   An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.. PLoS Comput Biol. 2 (11) :e159 ▶ Go to Pubmed
Yves Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, Carol Friedman .  2006.   PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.. Pac Symp Biocomput. :64-75 ▶ Go to Pubmed
Raul Rodriguez-Esteban, Ivan Iossifov, Andrey Rzhetsky .  2006.   Imitating manual curation of text-mined facts in biomedicine.. PLoS Comput Biol. 2 (9) :e118 ▶ Go to Pubmed
Hans-Günther Döbereiner, Benjamin Dubin-Thaler, Jake Hofman, Harry Xenias, Tasha Sims, Grégory Giannone, Michael Dustin, Chris Wiggins, Michael Sheetz .  2006.   Lateral membrane waves constitute a universal dynamic pattern of motile cells.. Phys Rev Lett. 97 (3) :038102 ▶ Go to Pubmed
Celine Moorman, Ling Sun V, Junbai Wang, Elzo de Wit, Wendy Talhout, Lucas Ward, Frauke Greil, Xiang-Jun Lu, Kevin White, Harmen Bussemaker, Bas van Steensel .  2006.   Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.. Proc Natl Acad Sci U S A. 103 (32) :12027-32 ▶ Go to Pubmed
Vinay Varadan, David Miller, Dimitris Anastassiou .  2006.   Computational inference of the molecular logic for synaptic connectivity in C. elegans.. Bioinformatics. 22 (14) :e497-506 ▶ Go to Pubmed
Yanay Ofran, Guy Yachdav, Eyal Mozes, Ta-tsen Soong, Rajesh Nair, Burkhard Rost .  2006.   Create and assess protein networks through molecular characteristics of individual proteins.. Bioinformatics. 22 (14) :e402-7 ▶ Go to Pubmed
Barrett Foat, Alexandre Morozov V, Harmen Bussemaker .  2006.   Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.. Bioinformatics. 22 (14) :e141-9 ▶ Go to Pubmed
Carol Friedman, Tara Borlawsky, Lyudmila Shagina, Rosie Xing, Yves Lussier .  2006.   Bio-Ontology and text: bridging the modeling gap.. Bioinformatics. 22 (19) :2421-9 ▶ Go to Pubmed
Gabor Halasz, Marinus van Batenburg, Joelle Perusse, Sujun Hua, Xiang-Jun Lu, Kevin White, Harmen Bussemaker .  2006.   Detecting transcriptionally active regions using genomic tiling arrays.. Genome Biol. 7 (7) :R59 ▶ Go to Pubmed
Harmen Bussemaker .  2006.   Modeling gene expression control using Omes Law.. Mol Syst Biol. 2 :2006.0013 ▶ Go to Pubmed
Adam Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla-Favera, Andrea Califano .  2006.   ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.. BMC Bioinformatics. 7 Suppl 1 :S7 ▶ Go to Pubmed
Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina Leslie .  2006.   A classification-based framework for predicting and analyzing gene regulatory response.. BMC Bioinformatics. 7 Suppl 1 :S5 ▶ Go to Pubmed
Dimitris Anastassiou, Hairuo Liu, Vinay Varadan .  2006.   Variable window binding for mutually exclusive alternative splicing.. Genome Biol. 7 (1) :R2 ▶ Go to Pubmed
Daniel Koster, Chris Wiggins, Nynke Dekker .  2006.   Multiple events on single molecules: unbiased estimation in single-molecule biophysics.. Proc Natl Acad Sci U S A. 103 (6) :1750-5 ▶ Go to Pubmed