Student Publications

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Chan JE, Kolodner RD. "A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements." PLoS Genet.. 2011;7(5):e1002089.
Wilmes GM, Bergkessel M, Bandyopadhyay S, et al. "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.
Baker CW, Miller CR, Thaweethai T, et al. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55.
Murrell B, Weaver S, Smith MD, et al. "Gene-wide identification of episodic selection." Mol. Biol. Evol.. 2015;32(5):1365-71.
Latif H, Lerman JA, Portnoy VA, et al. "The genome organization of Thermotoga maritima reflects its lifestyle." PLoS Genet.. 2013;9(4):e1003485.
Allen TE, Herrgård MJ, Liu M, et al. "Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets." J. Bacteriol.. 2003;185(21):6392-9.
Papin JA, Price ND, Edwards JS, Palsson B BØ. "The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy." J. Theor. Biol.. 2002;215(1):67-82.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. "Genome-scale metabolic model of Helicobacter pylori 26695." J. Bacteriol.. 2002;184(16):4582-93.
Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-97.
Feist AM, Henry CS, Reed JL, et al. "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol. Syst. Biol.. 2007;3:121.
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. "Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol. Syst. Biol.. 2013;9:693.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network." Genome Res.. 2003;13(2):244-53.
Shen L, Wu H, Diep D, et al. "Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics." Cell. 2013;153(3):692-706.
Barrera LO, Li Z, Smith AD, et al. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59.
Diep D, Zhang K. "Genome-wide mapping of the sixth base." Genome Biol.. 2011;12(6):116.
Lewis NE, Liu X, Li Y, et al. "Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome." Nat. Biotechnol.. 2013;31(8):759-65.
Bechtel JM, Wittenschlaeger T, Dwyer T, et al. "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284.
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.
Huelga SC, Yeo GW. "Genomics of Alternative Splicing in Stem Cells.". In: Computational Biology of Embryonic Stem Cells (Ming Zhan, Ed.), pp. 147-160. Oak Park, IL: Bentham Science Publishers; 2012.
König R, Zhou Y, Elleder D, et al. "Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication." Cell. 2008;135(1):49-60.
Lister R, Mukamel EA, Nery JR, et al. "Global epigenomic reconfiguration during mammalian brain development." Science. 2013;341(6146):1237905.
Utrilla J, O'Brien EJ, Chen K, et al. "Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution." Cell Syst. 2016;2(4):260-71.
Duarte NC, Becker SA, Jamshidi N, et al. "Global reconstruction of the human metabolic network based on genomic and bibliomic data." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(6):1777-82.