Student Publications

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Lagier-Tourenne C, Polymenidou M, Hutt KR, et al. "Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs." Nat. Neurosci.. 2012;15(11):1488-97.
Rodriguez J, Gupta N, Smith RD, Pevzner PA. "Does trypsin cut before proline?" J. Proteome Res.. 2008;7(1):300-5.
Abdulla M-H, Ruelas DS, Wolff B, et al. "Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening." PLoS Negl Trop Dis. 2009;3(7):e478.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. "Drug off-target effects predicted using structural analysis in the context of a metabolic network model." PLoS Comput. Biol.. 2010;6(9):e1000938.
Hawkins DR, Hon GC, Yang C, et al. "Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency." Cell Res.. 2011;21(10):1393-409.
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.
Behar M, Barken D, Werner SL, Hoffmann A. "The dynamics of signaling as a pharmacological target." Cell. 2013;155(2):448-61.
Chaillon A, Wagner GA, Hepler LN, et al. "Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection." J. Virol.. 2013;87(23):12737-44.
Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. "DyNAVacS: an integrative tool for optimized DNA vaccine design." Nucleic Acids Res.. 2006;34(Web Server issue):W264-6.
Mukund K, Subramaniam S. "Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis." BMC Res Notes. 2015;8:182.
Horler RSP, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH. "EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations." Bioinformatics. 2009;25(2):163-6.
Fong SS, Joyce AR, Palsson BØ. "The econometrics of evolution." Nat. Chem. Biol.. 2005;1(4):191-2.
Berry RE, Shokhirev MN, Ho AYW, et al. "Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes." J. Am. Chem. Soc.. 2009;131(6):2313-27.
Heinz S, Romanoski CE, Benner C, et al. "Effect of natural genetic variation on enhancer selection and function." Nature. 2013.
Berry RE, Shokhireva T K, Filippov I, Shokhirev MN, Zhang H, Walker AF. "Effect of the N-terminus on heme cavity structure, ligand equilibrium, rate constants, and reduction potentials of nitrophorin 2 from Rhodnius prolixus." Biochemistry. 2007;46(23):6830-43.
Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. "The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool." J. Virol. Methods. 2009;162(1-2):280-3.
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23.
Chang MW, Belew RK, Carroll KS, Olson AJ, Goodsell DS. "Empirical entropic contributions in computational docking: evaluation in APS reductase complexes." J Comput Chem. 2008;29(11):1753-61.
Hawkins T, Luban S, Kihara D. "Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci.. 2006;15(6):1550-6.
Conway AE, Van Nostrand EL, Pratt GA, et al. "Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival." Cell Rep. 2016;15(3):666-79.
Cheng CS, Johnson TL, Hoffmann A. "Epigenetic control: slow and global, nimble and local." Genes Dev.. 2008;22(9):1110-4.
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.
Xie W, Schultz MD, Lister R, et al. "Epigenomic analysis of multilineage differentiation of human embryonic stem cells." Cell. 2013;153(5):1134-48.
Hua Z, Pool JE, Schmitz RJ, et al. "Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(42):16927-32.
Cohen T, G Whitfield K, Schvaneveldt RW, Mukund K, Rindflesch T. "EpiphaNet: An Interactive Tool to Support Biomedical Discoveries." J Biomed Discov Collab. 2010;5:21-49.