Student Publications

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Joyce AR, Palsson BO. "Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach." Prog Drug Res. 2007;64:265, 267-309.
Gross AM, Cohen EEW. "Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015;35:28-32.
Reed JL, Famili I, Thiele I, Palsson BO. "Towards multidimensional genome annotation." Nat. Rev. Genet.. 2006;7(2):130-41.
Bernard A, Lubbers LS, Tanis KQ, et al. "Transcriptional architecture of the primate neocortex." Neuron. 2012;73(6):1083-99.
Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli." J. Biol. Chem.. 2002;277(31):28058-64.
Barrera LO, Ren B. "The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr. Opin. Cell Biol.. 2006;18(3):291-8.
DeBoever C, Ghia EM, Shepard PJ, et al. "Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers." PLoS Comput. Biol.. 2015;11(3):e1004105.
Schmitz RJ, Schultz MD, Lewsey MG, et al. "Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73.
Rao F, Zhang L, Wessel J, et al. "Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo." Circulation. 2007;116(9):993-1006.
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Price ND, Schellenberger J, Palsson BO. "Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys. J.. 2004;87(4):2172-86.
Zhang H, Loriaux P, Eng J, et al. "UniPep--a database for human N-linked glycosites: a resource for biomarker discovery." Genome Biol.. 2006;7(8):R73.
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72.
Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J. Biol.. 2005;4(2):5.
Smith DM, May SJ, Pérez-Santiago J, et al. "The use of pooled viral load testing to identify antiretroviral treatment failure." AIDS. 2009;23(16):2151-8.
O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4.
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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.
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27.
Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. "Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res.. 2013.
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Crooks GE, Hon G, Chandonia J-M, Brenner SE. "WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90.
Udpa N, Ronen R, Zhou D, et al. "Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes." Genome Biol.. 2014;15(2):R36.
Gupta N, Tanner S, Jaitly N, et al. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res.. 2007;17(9):1362-77.
DeBoever C, Reid EG, Smith EN, et al. "Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas." PLoS ONE. 2013;8(9):e73956.
Selvaraj S, Dixon JR, Bansal V, Ren B. "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat. Biotechnol.. 2013.
Zhou D, Udpa N, Ronen R, et al. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62.

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