Student Publications

2009

Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. "Dereplication and de novo sequencing of nonribosomal peptides." Nat Methods. 2009;6(8):596-9. PubMed PMC DOI
Pacold M. "Retroviruses and opportunistic infections--16th annual conference. Characteristics and prevention of HIV transmission. 8-11 February 2009, Montréal, QC, Canada." IDrugs. 2009;12(4):204-6. PubMed
Sears DD, Hsiao G, Hsiao A, Yu JG, Courtney CH, Ofrecio JM, Chapman J, Subramaniam S. "Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization." Proc Natl Acad Sci U S A. 2009;106(44):18745-50. PubMed PMC DOI
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. PubMed PMC DOI
Smith DM, May SJ, Pérez-Santiago J, Strain MC, Ignacio CC, Haubrich RH, Richman DD, Benson CA, Little SJ. "The use of pooled viral load testing to identify antiretroviral treatment failure." AIDS. 2009;23(16):2151-8. PubMed PMC DOI
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

2008

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