Student Publications

Export 400 results:
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
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.
Chen J, Swamidass JS, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9.
Devaraj NK, Miller GP, Ebina W, et al. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1.
Barken D, Wang C J, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52.
Sharan R, Suthram S, Kelley RM, et al. "Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9.
Kim T H, Barrera LO, Qu C, et al. "Direct isolation and identification of promoters in the human genome." Genome Res.. 2005;15(6):830-9.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
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.
Kim T H, Barrera LO, Zheng M, et al. "A high-resolution map of active promoters in the human genome." Nature. 2005;436(7052):876-80.
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.
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.
Zaitlen NA, Kang H M, 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.
Tanner S, Shu H, Frank A, et al. "InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal. Chem.. 2005;77(14):4626-39.
Famili I, Mahadevan R, Palsson BO. "k-Cone analysis: determining all candidate values for kinetic parameters on a network scale." Biophys. J.. 2005;88(3):1616-25.
Swamidass JS, 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.
Payne SH. "Metabolic pathways." In: Loomis WF, Kuspa A, eds. Dictyostelium Genomics, pp. 41-57. Far Hills, N.J.: Horizon Press; 2005.
Ogawa S, Lozach J, Benner C, et al. "Molecular determinants of crosstalk between nuclear receptors and toll-like receptors." Cell. 2005;122(5):707-21.
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.
Bashir A, Ye C, Price AL, Bafna V. "Orthologous repeats and mammalian phylogenetic inference." Genome Res.. 2005;15(7):998-1006.
Fong SS, Joyce AR, Palsson BØ. "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states." Genome Res.. 2005;15(10):1365-72.
Frank A, Tanner S, Bafna V, Pevzner P. "Peptide sequence tags for fast database search in mass-spectrometry." J. Proteome Res.. 2005;4(4):1287-95.