Student Publications

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

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

Papin JA, Palsson BO. "The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis." Biophys J. 2004;87(1):37-46. PubMed PMC DOI

Papin JA, Palsson BO. "Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk." J Theor Biol. 2004;227(2):283-97. PubMed DOI

Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem Sci. 2004;29(12):641-7. PubMed DOI

Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. "Comparison of network-based pathway analysis methods." Trends Biotechnol. 2004;22(8):400-5. PubMed DOI

Price ND, Schellenberger J, Palsson BO. "Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys J. 2004;87(4):2172-86. PubMed PMC DOI