Student Publications

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Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. "A dynamic network of transcription in LPS-treated human subjects." BMC Syst Biol. 2009;3:78.
Selvaraj S, Dixon JR, Bansal V, Ren B. "Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing." Nat. Biotechnol.. 2013.
Sears DD, Hsiao G, Hsiao A, et al. "Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization." Proc. Natl. Acad. Sci. U.S.A.. 2009;106(44):18745-50.
Sears DD, Hsiao A, Ofrecio JM, Chapman J, He W, Olefsky JM. "Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem. Biophys. Res. Commun.. 2007;364(3):515-21.
Schultz MD, Schmitz RJ, Ecker JR. "'Leveling' the playing field for analyses of single-base resolution DNA methylomes." Trends Genet.. 2012;28(12):583-5.
Schultz MD, He Y, Whitaker JW, et al. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6.
Schmitz RJ, He Y, Valdés-López O, et al. "Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population." Genome Res.. 2013;23(10):1663-74.
Schmitz RJ, Schultz MD, Urich MA, et al. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8.
Schmitz RJ, Schultz MD, Lewsey MG, et al. "Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73.
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.
Sauls JT, Buescher JM. "Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014.
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr. Opin. Cell Biol.. 2016;38:38-44.
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Ruiz S, Diep D, Gore A, et al. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(40):16196-201.
Ross MK, Wei W, Ohno-Machado L. ""Big data" and the electronic health record." Yearb Med Inform. 2014;9(1):97-104.
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.
Ronen R, Boucher C, Chitsaz H, Pevzner P. "SEQuel: improving the accuracy of genome assemblies." Bioinformatics. 2012;28(12):i188-96.
Ronen R, Udpa N, Halperin E, Bafna V. "Learning natural selection from the site frequency spectrum." Genetics. 2013;195(1):181-93.
Roguev A, Bandyopadhyay S, Zofall M, et al. "Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science. 2008;322(5900):405-10.
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56.
Rodriguez J, Gupta N, Smith RD, Pevzner PA. "Does trypsin cut before proline?" J. Proteome Res.. 2008;7(1):300-5.
Rentas S, Holzapfel NT, Belew MS, et al. "Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells." Nature. 2016;532(7600):508-11.
Reguly T, Breitkreutz A, Boucher L, et al. "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J. Biol.. 2006;5(4):11.
Reed JL, Famili I, Thiele I, Palsson BO. "Towards multidimensional genome annotation." Nat. Rev. Genet.. 2006;7(2):130-41.
Reed JL, Patel TR, Chen KH, et al. "Systems approach to refining genome annotation." Proc. Natl. Acad. Sci. U.S.A.. 2006;103(46):17480-4.
Raphael B, Zhi D, Tang H, Pevzner P. "A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res.. 2004;14(11):2336-46.

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