Student Publications

2005

Hsiao A, Ideker T, Olefsky JM, Subramaniam S. "VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data." Nucleic Acids Res. 2005;33(Web Server issue):W627-32. PubMed PMC DOI
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat Biotechnol. 2005;23(5):561-6. PubMed PMC DOI
Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. "Direct isolation and identification of promoters in the human genome." Genome Res. 2005;15(6):830-9. PubMed PMC DOI
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. "A high-resolution map of active promoters in the human genome." Nature. 2005;436(7052):876-80. PubMed PMC DOI
Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. "Molecular determinants of crosstalk between nuclear receptors and toll-like receptors." Cell. 2005;122(5):707-21. PubMed PMC DOI
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes." Nucleic Acids Res. 2005;33(17):5691-702. PubMed PMC DOI
Papin JA, Hunter T, Palsson BO, Subramaniam S. "Reconstruction of cellular signalling networks and analysis of their properties." Nat Rev Mol Cell Biol. 2005;6(2):99-111. PubMed DOI
Payne SH. "Metabolic Pathways." Dictyostelium Genomics. 2005:41-57. ISBN
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. "Conserved patterns of protein interaction in multiple species." Proc Natl Acad Sci U S A. 2005;102(6):1974-9. PubMed PMC DOI
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12. PubMed PMC DOI
Swamidass SJ, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. "Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity." Bioinformatics. 2005;21 Suppl 1:i359-68. PubMed DOI
Szpankowski W, Ren W, Szpankowski L. "An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17. PubMed DOI
Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. "InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal Chem. 2005;77(14):4626-39. PubMed DOI
Thiele I, Price ND, Vo TD, Palsson BØ. "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J Biol Chem. 2005;280(12):11683-95. PubMed DOI
Thiele I, Vo TD, Price ND, Palsson BØ. "Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants." J Bacteriol. 2005;187(16):5818-30. PubMed PMC DOI
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. "Assessing computational tools for the discovery of transcription factor binding sites." Nat Biotechnol. 2005;23(1):137-44. PubMed DOI
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat Biotechnol. 2005;23(12):1562-7. PubMed DOI
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66. PubMed
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61. PubMed DOI
Zaitlen NA, Kang HM, Feolo ML, Sherry ST, Halperin E, Eskin E. "Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP." Genome Res. 2005;15(11):1594-600. PubMed PMC DOI

2004

Bandyopadhyay S, Cookson MR. "Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol Biol. 2004;4:6. PubMed PMC DOI
Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y. "Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays." BMC Bioinformatics. 2004;5:42. PubMed PMC DOI
Canet-Avilés RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization." Proc Natl Acad Sci U S A. 2004;101(24):9103-8. PubMed PMC DOI
Chaisson M, Pevzner P, Tang H. "Fragment assembly with short reads." Bioinformatics. 2004;20(13):2067-74. PubMed DOI
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. "The ASTRAL Compendium in 2004." Nucleic Acids Res. 2004;32(Database issue):D189-92. PubMed PMC DOI