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2006 Publications

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 et al.  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 et al.  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