Student Publications

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Wilmarth PA, Tanner S, Dasari S, et al. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?" J. Proteome Res.. 2006;5(10):2554-66.
Wilbert ML, Huelga SC, Kapeli K, et al. "LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance." Mol. Cell. 2012;48(2):195-206.
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ. "Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space." J. Theor. Biol.. 2004;228(4):437-47.
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61.
Wang H, Kakaradov B, Collins SR, et al. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol. Cell Proteomics. 2009;8(6):1361-81.
Wang C-C, Bajikar SS, Jamal L, Atkins KA, Janes KA. "A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies." Nat. Cell Biol.. 2014.
Wang L, Rao F, Zhang K, et al. "Neuropeptide Y(1) Receptor NPY1R discovery of naturally occurring human genetic variants governing gene expression in cella as well as pleiotropic effects on autonomic activity and blood pressure in vivo." J. Am. Coll. Cardiol.. 2009;54(10):944-54.
Walsh CT, Radeff-Huang J, Matteo R, et al. "Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61." FASEB J.. 2008;22(11):4011-21.
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4.
Wagner GA, Pacold ME, Kosakovsky Pond SL, et al. "Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States." J. Infect. Dis.. 2013.
Vosseller K, Trinidad JC, Chalkley RJ, et al. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol. Cell Proteomics. 2006;5(5):923-34.
Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. "Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome." PLoS Comput. Biol.. 2009;5(3):e1000315.
Van Nostrand EL, Pratt GA, Shishkin AA, et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat. Methods. 2016;13(6):508-14.
Valas RE, Bourne PE. "Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life." Biol. Direct. 2009;4:30.
Valas RE, Yang S, Bourne PE. "Nothing about protein structure classification makes sense except in the light of evolution." Curr. Opin. Struct. Biol.. 2009;19(3):329-34.
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications via blind search of mass-spectra." Proc IEEE Comput Syst Bioinform Conf. 2005:157-66.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. "Identification of post-translational modifications by blind search of mass spectra." Nat. Biotechnol.. 2005;23(12):1562-7.
Tsai K-C, Teng L-W, Shao Y-M, et al. "The first pharmacophore model for potent NF-kappaB inhibitors." Bioorg. Med. Chem. Lett.. 2009;19(19):5665-9.
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
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.
Thiele I, Price ND, Vo TD, Palsson BØ. "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J. Biol. Chem.. 2005;280(12):11683-95.