Student Publications

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

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat Biotechnol. 2008;26(9):1003-10. PubMed DOI

Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. "eQED: an efficient method for interpreting eQTL associations using protein networks." Mol Syst Biol. 2008;4:162. PubMed PMC DOI

Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. "Accurate annotation of peptide modifications through unrestrictive database search." J Proteome Res. 2008;7(1):170-81. PubMed DOI

Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J Mol Evol. 2008;66(5):494-504. PubMed PMC DOI

Walsh CT, Radeff-Huang J, Matteo R, Hsiao A, Subramaniam S, Stupack D, Brown JH. "Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J. 2008;22(11):4011-21. PubMed PMC DOI

Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. "A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing." Mol Cell. 2008;32(5):735-46. PubMed PMC DOI

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70. PubMed PMC DOI

Aktulga HM, Kontoyiannis I, Lyznik LA, Szpankowski L, Grama AY, Szpankowski W. "Identifying statistical dependence in genomic sequences via mutual information estimates." EURASIP J Bioinform Syst Biol. 2007:14741. PubMed PMC DOI

Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res. 2007;17(2):219-30. PubMed PMC DOI

Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. "Optimization of primer design for the detection of variable genomic lesions in cancer." Bioinformatics. 2007;23(21):2807-15. PubMed DOI

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ. "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc. 2007;2(3):727-38. PubMed DOI

Berry RE, Shokhireva TKh, Filippov I, Shokhirev MN, Zhang H, Walker FA. "Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus." Biochemistry. 2007;46(23):6830-43. PubMed PMC DOI

Beyer A, Bandyopadhyay S, Ideker T. "Integrating physical and genetic maps: from genomes to interaction networks." Nat Rev Genet. 2007;8(9):699-710. PubMed PMC DOI