Margolin A, Wang K, Lim WKeat, Kustagi M, Nemenman I, Califano A. 2006. Reverse engineering cellular networks.. Nat Protoc. 1(2):662-71.▶ Go to Pubmed
Palomero T, Lim WKeat, Odom DT, Sulis MLuisa, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, A Look T, Young RA, Califano A, Ferrando A. 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
Liu Y, Li J, Sam L, Goh C-S, Gerstein M, Lussier YA. 2006. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.. PLoS Comput Biol. 2(11):e159.▶ Go to Pubmed
Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C. 2006. PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.. Pac Symp Biocomput. :64-75.▶ Go to Pubmed
Rodriguez-Esteban R, Iossifov I, Rzhetsky A. 2006. Imitating manual curation of text-mined facts in biomedicine.. PLoS Comput Biol. 2(9):e118.▶ Go to Pubmed
Döbereiner H-G, Dubin-Thaler BJ, Hofman JM, Xenias HS, Sims TN, Giannone G, Dustin ML, Wiggins C, Sheetz MP. 2006. Lateral membrane waves constitute a universal dynamic pattern of motile cells.. Phys Rev Lett. 97(3):038102.▶ Go to Pubmed
Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu X-J, White KP, Bussemaker H, van Steensel B. 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
Varadan V, Miller DM, Anastassiou D. 2006. Computational inference of the molecular logic for synaptic connectivity in C. elegans.. Bioinformatics. 22(14):e497-506.▶ Go to Pubmed
Ofran Y, Yachdav G, Mozes E, Soong T-tsen, Nair R, Rost B. 2006. Create and assess protein networks through molecular characteristics of individual proteins.. Bioinformatics. 22(14):e402-7.▶ Go to Pubmed
Foat BC, Morozov AV, Bussemaker H. 2006. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.. Bioinformatics. 22(14):e141-9.▶ Go to Pubmed
Friedman C, Borlawsky T, Shagina L, H Xing R, Lussier Y. 2006. Bio-Ontology and text: bridging the modeling gap.. Bioinformatics. 22(19):2421-9.▶ Go to Pubmed
Halasz G, van Batenburg MF, Perusse J, Hua S, Lu X-J, White KP, Bussemaker H. 2006. Detecting transcriptionally active regions using genomic tiling arrays.. Genome Biol. 7(7):R59.▶ Go to Pubmed
Bussemaker H. 2006. Modeling gene expression control using Omes Law.. Mol Syst Biol. 2:2006.0013.▶ Go to Pubmed
Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla-Favera R, Califano A. 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
Kundaje A, Middendorf M, Shah M, Wiggins C, Freund Y, Leslie C. 2006. A classification-based framework for predicting and analyzing gene regulatory response.. BMC Bioinformatics. 7 Suppl 1:S5.▶ Go to Pubmed
Anastassiou D, Liu H, Varadan V. 2006. Variable window binding for mutually exclusive alternative splicing.. Genome Biol. 7(1):R2.▶ Go to Pubmed
Koster DA, Wiggins C, Dekker NH. 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