Student Publications

2006

Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56. PubMed DOI
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360. PubMed PMC DOI
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72. PubMed DOI
Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol Cell Proteomics. 2006;5(5):923-34. PubMed DOI
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?." J Proteome Res. 2006;5(10):2554-66. PubMed PMC DOI
Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, Smith RD, Aebersold R. "UniPep--a database for human N-linked glycosites: a resource for biomarker discovery." Genome Biol. 2006;7(8):R73. PubMed PMC DOI
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460. PubMed PMC DOI
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. "Identifying repeat domains in large genomes." Genome Biol. 2006;7(1):R7. PubMed PMC DOI

2005

Barken D, Wang CJ, 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. PubMed PMC DOI
Bashir A, Ye C, Price AL, Bafna V. "Orthologous repeats and mammalian phylogenetic inference." Genome Res. 2005;15(7):998-1006. PubMed PMC DOI
Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9. PubMed DOI
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7. PubMed DOI
Devaraj NK, Miller GP, Ebina W, Kakaradov B, Collman JP, Kool ET, Chidsey CE. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J Am Chem Soc. 2005;127(24):8600-1. PubMed PMC DOI
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. PubMed PMC DOI
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. PubMed PMC DOI
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat Chem Biol. 2005;1(4):191-2. PubMed DOI
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. PubMed DOI
Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J Biol. 2005;4(2):5. PubMed PMC DOI
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