Student Publications

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Szpankowski W, Ren W, Szpankowski L. "An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17.
Swamidass JS, Chen J, Bruand J, Phung P, Ralaivola L, Baldi P. "Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity." Bioinformatics. 2005;21 Suppl 1:i359-68.
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12.
Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. "eQED: an efficient method for interpreting eQTL associations using protein networks." Mol. Syst. Biol.. 2008;4:162.
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360.
Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. "Prediction of MicroRNA Precursors Using Parsimonious Feature Sets." Cancer Inform. 2014;13(Suppl 1):95-102.
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.
Smith DM, May SJ, Tweeten S, et al. "A public health model for the molecular surveillance of HIV transmission in San Diego, California." AIDS. 2009;23(2):225-32.
Singh G, Pratt G, Yeo GW, Moore MJ. "The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu. Rev. Biochem.. 2015;84:325-54.
Shokhirev M N, Hoffmann A. "FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses." PLoS ONE. 2013;8(6):e67620.
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.
Shlomi T, Herrgard M, Portnoy V, et al. "Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33.
Shih VF-S, Davis-Turak J, Macal M, et al. "Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways." Nat. Immunol.. 2012;13(12):1162-70.
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.
Shen JPaul, Srivas R, Gross A, et al. "Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69.
Sharan R, Suthram S, Kelley RM, et al. "Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9.
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, He Y, Whitaker JW, et al. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6.
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.
Schmitz RJ, Schultz MD, Lewsey MG, et al. "Transgenerational epigenetic instability is a source of novel methylation variants." Science. 2011;334(6054):369-73.
Schmitz RJ, Schultz MD, Urich MA, et al. "Patterns of population epigenomic diversity." Nature. 2013;495(7440):193-8.
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.

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