Student Publications

Export 400 results:
Young JA, Johnson JR, Benner C, et al. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70.
Lee E, Chuang H-Y, Kim J-W, Ideker T, Lee D. "Inferring pathway activity toward precise disease classification." PLoS Comput. Biol.. 2008;4(11):e1000217.
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.
Chen CY-C, Chen G-W, Chen WY-C. "Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." Journal of the Chinese Chemical Society. 2008;55:297-302.
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol. Cell Proteomics. 2008;7(7):1389-96.
Chen Y, Rao F, Rodriguez-Flores JL, et al. "Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion." J. Am. Coll. Cardiol.. 2008;52(18):1468-81.
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.
Chen OY-C, Chen G-W, Chen WY-C. "A novel strategy for the structure-based drug design of heat shock protein 90 inhibitors.". In: Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on.; 2008.
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.
Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Lee K, Chuang H-Y, Beyer A, et al. "Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species." Nucleic Acids Res.. 2008;36(20):e136.
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.
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504.
Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5.
Raphael BJ, Volik S, Yu P, et al. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30.
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.
Rosen RF, Farberg AS, Gearing M, et al. "Tauopathy with paired helical filaments in an aged chimpanzee." J. Comp. Neurol.. 2008;509(3):259-70.
Walsh CT, Radeff-Huang J, Matteo R, et al. "Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J.. 2008;22(11):4011-21.
Wang H, Kakaradov B, Collins SR, et al. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81.
Mo ML, Palsson BO, Herrgård MJ. "Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37.
Chaisson MJ, Brinza D, Pevzner PA. "De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res.. 2009;19(2):336-46.
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30.
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9.
Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566.