Student Publications

2005

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
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6. PubMed DOI
Crooks GE, Hon G, Chandonia JM, Brenner SE. "WebLogo: a sequence logo generator." Genome Res. 2004;14(6):1188-90. PubMed PMC DOI
Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res. 2004;14(7):1298-309. PubMed PMC DOI
Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol. 2004;5(12):R95. PubMed PMC DOI
Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr Opin Biotechnol. 2004;15(1):70-7. PubMed DOI
Herrgård MJ, Palsson BØ. "Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90. PubMed DOI
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27. PubMed DOI