Student Publications

Cheng CS, Johnson TL, Hoffmann A. "Epigenetic control: slow and global, nimble and local." Genes Dev. 2008;22(9):1110-4. PubMed PMC DOI

Covert MW, Xiao N, Chen TJ, Karr JR. "Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli." Bioinformatics. 2008;24(18):2044-50. PubMed DOI

Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. "QNet: a tool for querying protein interaction networks." J Comput Biol. 2008;15(7):913-25. PubMed DOI

Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. "Clustering millions of tandem mass spectra." J Proteome Res. 2008;7(1):113-22. PubMed PMC DOI

Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res. 2008;18(7):1133-42. PubMed PMC DOI

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol. 2008;26(10):1155-60. PubMed PMC DOI

Hon G, Ren B, Wang W. "ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput Biol. 2008;4(10):e1000201. PubMed PMC DOI

Hsiao A, Subramaniam S. "Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data." Syst Synth Biol. 2008;2(3-4):95-104. PubMed PMC DOI

Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol Biol. 2008;416:433-57. PubMed DOI

Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23. PubMed PMC DOI

Kelley R, Feizi H, Ideker T. "Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood." Bioinformatics. 2008;24(1):71-7. PubMed PMC DOI

Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J Proteome Res. 2008;7(8):3354-63. PubMed PMC DOI

König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. "Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60. PubMed PMC DOI

Lee E, Chuang HY, Kim JW, Ideker T, Lee D. "Inferring pathway activity toward precise disease classification." PLoS Comput Biol. 2008;4(11):e1000217. PubMed PMC DOI

Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. "Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res. 2008;36(20):e136. PubMed PMC DOI

Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J Proteome Res. 2008;7(1):89-95. PubMed DOI

Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5. PubMed

Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. "Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J Proteome Res. 2008;7(8):3373-81. PubMed PMC DOI

Pevzner PA, Kim S, Ng J. "Comment on 'Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry'." Science. 2008;321(5892):1040; author reply 1040. PubMed DOI

Portnoy VA, Herrgård MJ, Palsson BØ. "Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain." Appl Environ Microbiol. 2008;74(24):7561-9. PubMed PMC DOI

Rao F, Zhang L, Wessel J, Zhang K, Wen G, Kennedy BP, Rana BK, Das M, Rodriguez-Flores JL, Smith DW, Cadman PE, Salem RM, Mahata SK, Schork NJ, Taupenot L, Ziegler MG, O'Connor DT. "Adrenergic polymorphism and the human stress response." Ann N Y Acad Sci. 2008;1148:282-96. PubMed PMC DOI

Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol. 2008;9(3):R59. PubMed PMC DOI

Rodriguez J, Gupta N, Smith RD, Pevzner PA. "Does trypsin cut before proline?." J Proteome Res. 2008;7(1):300-5. PubMed DOI

Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ. "Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science. 2008;322(5900):405-10. PubMed PMC DOI

Rosen RF, Farberg AS, Gearing M, Dooyema J, Long PM, Anderson DC, Davis-Turak J, Coppola G, Geschwind DH, Paré JF, Duong TQ, Hopkins WD, Preuss TM, Walker LC. "Tauopathy with paired helical filaments in an aged chimpanzee." J Comp Neurol. 2008;509(3):259-70. PubMed PMC DOI