Student Publications

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Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO. "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage." PLoS ONE. 2012;7(9):e45635.
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, 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.
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.
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, 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.
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.
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, Herrgard M, Portnoy V, et al. "Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33.
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.
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.