Student Publications

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Thiele I, Vo TD, Price ND, Palsson BØ. "Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants." J. Bacteriol.. 2005;187(16):5818-30.
Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-97.
Tanner S, Shu H, Frank A, et al. "InsPecT: identification of posttranslationally modified peptides from tandem mass spectra." Anal. Chem.. 2005;77(14):4626-39.
Tanner S, Shen Z, Ng J, et al. "Improving gene annotation using peptide mass spectrometry." Genome Res.. 2007;17(2):231-9.
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72.
Tanner S, Payne SH, Dasari S, et al. "Accurate annotation of peptide modifications through unrestrictive database search." J. Proteome Res.. 2008;7(1):170-81.
Tan M, Luo H, Lee S, et al. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification." Cell. 2011;146(6):1016-28.
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42.
Taheri-Araghi S, Bradde S, Sauls JT, et al. "Cell-Size Control and Homeostasis in Bacteria." Curr. Biol.. 2014.
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, 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.
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12.
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, 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.
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.
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.