Search Publications

2009 Publications

Mugler A, Ziv E, Nemenman I, Wiggins CH.  2009.  Quantifying evolvability in small biological networks. IET Syst Biol. 3(5):379-87. Go to Pubmed
Pantazatos SP, Li J, Pavlidis P, Lussier YA.  2009.  Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Inform. 8:75-94. Go to Pubmed
Alvarez M, Sumazin P, Rajbhandari P, Califano A.  2009.  Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol. 10(12):R143. Go to Pubmed
Khiabanian H, Trifonov V, Rabadan R.  2009.  Reassortment patterns in Swine influenza viruses. PLoS Curr. 1:RRN1008. Go to Pubmed
Effraim PR, Wang J, Englander MT, Avins J, Leyh TS, Gonzalez RL, Cornish VW.  2009.  Natural amino acids do not require their native tRNAs for efficient selection by the ribosome. Nat Chem Biol. 5(12):947-53. Go to Pubmed
Mugler A, Walczak AM, Wiggins CH.  2009.  Spectral solutions to stochastic models of gene expression with bursts and regulation. Phys Rev E Stat Nonlin Soft Matter Phys. 80(4 Pt 1):041921. Go to Pubmed
Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A.  2009.  Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol. 5(11):e1000559. Go to Pubmed
Chen B-J, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe'er D.  2009.  Harnessing gene expression to identify the genetic basis of drug resistance. Mol Syst Biol. 5:310. Go to Pubmed
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B.  2009.  The role of DNA shape in protein-DNA recognition. Nature. 461(7268):1248-53. Go to Pubmed
Khiabanian H, Trifonov V, Rabadan R.  2009.  Reassortment patterns in Swine influenza viruses. PLoS One. 4(10):e7366. Go to Pubmed
Petrey D, Fischer M, Honig B.  2009.  Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci U S A. 106(41):17377-82. Go to Pubmed
Wang K, Saito M, Bisikirska B, Alvarez M, Lim WKeat, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin A et al.  2009.  Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 27(9):829-39. Go to Pubmed
Khiabanian H, Farrell GM, St George K, Rabadan R.  2009.  Differences in patient age distribution between influenza A subtypes. PLoS One. 4(8):e6832. Go to Pubmed
Zhao X, Arca DD', Lim WKeat, Brahmachary M, Carro MStella, Ludwig T, Cardo CCordon, Guillemot F, Aldape K, Califano A et al.  2009.  The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 17(2):210-21. Go to Pubmed
Katsamba PS, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price SR, Jessell T, Ben-Shaul A et al.  2009.  Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc Natl Acad Sci U S A. 106(28):11594-9. Go to Pubmed
Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A et al.  2009.  BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 106(27):11294-9. Go to Pubmed
Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR et al.  2009.  HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet. 41(7):816-9. Go to Pubmed
Trifonov V, Khiabanian H, Rabadan R.  2009.  Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus. N Engl J Med. 361(2):115-9. Go to Pubmed
Khan AA, Betel D, Miller ML, Sander C, Leslie C, Marks DS.  2009.  Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 27(6):549-55. Go to Pubmed
Prabhu S, Pe'er I.  2009.  Overlapping pools for high-throughput targeted resequencing. Genome Res. 19(7):1254-61. Go to Pubmed
Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen C-Z, Califano A et al.  2009.  Identification of the human mature B cell miRNome. Immunity. 30(5):744-52. Go to Pubmed
Trifonov V, Khiabanian H, Greenbaum B, Rabadan R.  2009.  The origin of the recent swine influenza A(H1N1) virus infecting humans. Euro Surveill. 14(17) Go to Pubmed
Compagno M, Lim WKeat, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A et al.  2009.  Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 459(7247):717-21. Go to Pubmed
Rohs R, West SM, Liu P, Honig B.  2009.  Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol. 19(2):171-7. Go to Pubmed
Walczak AM, Mugler A, Wiggins C.  2009.  A stochastic spectral analysis of transcriptional regulatory cascades. Proc Natl Acad Sci U S A. 106(16):6529-34. Go to Pubmed
Waltz D, Buchanan BG.  2009.  Computer science. Automating science. Science. 324(5923):43-4. Go to Pubmed
Petrey D, Honig B.  2009.  Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol. 19(3):363-8. Go to Pubmed
Nimrod G, Szilágyi A, Leslie C, Ben-Tal N.  2009.  Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol. 387(4):1040-53. Go to Pubmed
Litvin O, Causton HC, Chen B-J, Pe'er D.  2009.  Modularity and interactions in the genetics of gene expression. Proc Natl Acad Sci U S A. 106(16):6441-6. Go to Pubmed
Lim WKeat, Lyashenko E, Califano A.  2009.  Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. :504-15. Go to Pubmed
Wang K, Alvarez M, Bisikirska B, Linding R, Basso K, Dalla-Favera R, Califano A.  2009.  Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput. :264-75. Go to Pubmed
Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier Y.  2009.  PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics. 10 Suppl 2:S8. Go to Pubmed
Liu Y, Sam L, Li J, Lussier Y.  2009.  Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. BMC Bioinformatics. 10 Suppl 2:S11. Go to Pubmed
Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, J Smith G, Ji W et al.  2009.  Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. PLoS Genet. 5(2):e1000365. Go to Pubmed
Sachs K, Itani S, Carlisle J, Nolan GP, Pe'er D, Lauffenburger DA.  2009.  Learning signaling network structures with sparsely distributed data. J Comput Biol. 16(2):201-12. Go to Pubmed
Lee S-I, Dudley AM, Drubin D, Silver PA, Krogan N, Pe'er D, Koller D.  2009.  Learning a prior on regulatory potential from eQTL data. PLoS Genet. 5(1):e1000358. Go to Pubmed
Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T et al.  2009.  Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science. 323(5918):1218-22. Go to Pubmed
Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenoski C, Husain AN, Mitra S, Moreno-Vinasco L, Jacobson JR et al.  2009.  GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling. FASEB J. 23(5):1325-37. Go to Pubmed
Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.  2009.  ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A. 106(1):244-9. Go to Pubmed
Melvin I, Weston J, Leslie C, Noble WStafford.  2009.  RANKPROP: a web server for protein remote homology detection. Bioinformatics. 25(1):121-2. Go to Pubmed
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow J, Friedman JM, Pe'er I.  2009.  Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19(2):318-26. Go to Pubmed