Student Publications

Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, Kosakovsky Pond SL, Pesano RL, Lie YS, Richman DD, Frost SD, Woelk CH, Little SJ. "A public health model for the molecular surveillance of HIV transmission in San Diego, California." AIDS. 2009;23(2):225-32. PubMed PMC DOI

Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks." Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):285-297. PubMed DOI

Tsai KC, Teng LW, Shao YM, Chen YC, Lee YC, Li M, Hsiao NW. "The first pharmacophore model for potent NF-kappaB inhibitors." Bioorg Med Chem Lett. 2009;19(19):5665-9. PubMed DOI

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. PubMed PMC DOI

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. PubMed PMC DOI

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. PubMed PMC DOI

Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D. "A complex-based reconstruction of the Saccharomyces cerevisiae interactome." Mol Cell Proteomics. 2009;8(6):1361-81. PubMed PMC DOI

Wang L, Rao F, Zhang K, Mahata M, Rodriguez-Flores JL, Fung MM, Waalen J, Cockburn MG, Hamilton BA, Mahata SK, O'Connor DT. "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. PubMed PMC DOI

Yang S, Valas R, Bourne PE. "Evolution Studied Using Protein Structure." Structural Bioinformatics. 2009:559-571. ISBN

Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol Cell Proteomics. 2008;7(7):1389-96. PubMed PMC DOI

Applebee MK, Herrgård MJ, Palsson BØ. "Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli." J Bacteriol. 2008;190(14):5087-94. PubMed PMC DOI

Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. "Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput Biol. 2008;4(4):e1000065. PubMed PMC DOI

Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res. 2008;18(1):46-59. PubMed PMC DOI

Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. "Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer." PLoS Comput Biol. 2008;4(4):e1000051. PubMed PMC DOI

Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y, Khuder S, Fedorov A. "The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence." BMC Res Notes. 2008;1:3. PubMed PMC DOI

Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y, Khuder S, Fedorov A. "Calculation of splicing potential from the Alternative Splicing Mutation Database." BMC Res Notes. 2008;1:4. PubMed PMC DOI

Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A. "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures." BMC Genomics. 2008;9:284. PubMed PMC DOI

Briedis KM, Starr A, Bourne PE. "Analysis of the human kinome using methods including fold recognition reveals two novel kinases." PLoS One. 2008;3(2):e1597. PubMed PMC DOI

Cachay ER, Frost SD, Poon AF, Looney D, Rostami SM, Pacold ME, Richman DD, Little SJ, Smith DM. "Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels." J Acquir Immune Defic Syndr. 2008;47(5):592-6. PubMed PMC DOI

Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc Natl Acad Sci U S A. 2008;105(52):21034-8. PubMed PMC DOI

Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res. 2008;18(2):324-30. PubMed PMC DOI

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. PubMed PMC DOI

Chen CY-C, Chen G-W, Chen WY-C. "Molecular Simulation of HER2/neu Degradation by HSP90 Inhibitors." J Chin Chem Soc. 2008;55(2):297-302. DOI

Chen Y, Rao F, Rodriguez-Flores JL, Mahapatra NR, Mahata M, Wen G, Salem RM, Shih PA, Das M, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, O'Connor DT. "Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure." Kidney Int. 2008;74(1):115-25. PubMed PMC DOI

Chen Y, Rao F, Rodriguez-Flores JL, Mahata M, Fung MM, Stridsberg M, Vaingankar SM, Wen G, Salem RM, Das M, Cockburn MG, Schork NJ, Ziegler MG, Hamilton BA, Mahata SK, Taupenot L, O'Connor DT. "Naturally occurring human genetic variation in the 3'-untranslated region of the secretory protein chromogranin A is associated with autonomic blood pressure regulation and hypertension in a sex-dependent fashion." J Am Coll Cardiol. 2008;52(18):1468-81. PubMed PMC DOI