Student Publications

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Gross AM, Orosco RK, Shen JP, et al. "Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat. Genet.. 2014;46(9):939-43.
Hu M, Deng K, Qin Z, et al. "Bayesian inference of spatial organizations of chromosomes." PLoS Comput. Biol.. 2013;9(1):e1002893.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. "COBRApy: COnstraints-Based Reconstruction and Analysis for Python." BMC Syst Biol. 2013;7:74.
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.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Kim D, Hong J S-J, Qiu Y, et al. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet.. 2012;8(8):e1002867.
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44.
Orth JD, Conrad TM, Na J, et al. "A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol. Syst. Biol.. 2011;7:535.
Xu X, Nagarajan H, Lewis NE, et al. "The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line." Nat. Biotechnol.. 2011;29(8):735-41.
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86.
Lewis NE, Hixson KK, Conrad TM, et al. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol. Syst. Biol.. 2010;6:390.
Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62.
Hsiao A, Kuo MD. "High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96.
Valas RE, Yang S, Bourne PE. "Nothing about protein structure classification makes sense except in the light of evolution." Curr. Opin. Struct. Biol.. 2009;19(3):329-34.
Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42.
Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30.
Kim T H, Barrera LO, Ren B. "ChIP-chip for genome-wide analysis of protein binding in mammalian cells." Curr Protoc Mol Biol. 2007;Chapter 21:Unit 21.13.
Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73.
Heintzman ND, Stuart RK, Hon G, et al. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat. Genet.. 2007;39(3):311-8.
Birney E, Stamatoyannopoulos JA, Dutta A, et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007;447(7146):799-816.
Cline MS, Smoot M, Cerami E, et al. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82.
Zaitlen N, Kang H M, Eskin E, Halperin E. "Leveraging the HapMap correlation structure in association studies." Am. J. Hum. Genet.. 2007;80(4):683-91.
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.
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.