Student Publications

Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. "A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide." Sci Signal. 2009;2(93):ra65. PubMed PMC DOI

Li F, Thiele I, Jamshidi N, Palsson BØ. "Identification of potential pathway mediation targets in Toll-like receptor signaling." PLoS Comput Biol. 2009;5(2):e1000292. PubMed PMC DOI

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. "Human DNA methylomes at base resolution show widespread epigenomic differences." Nature. 2009;462(7271):315-22. PubMed PMC DOI

Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. "Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides." Anal Chem. 2009;81(11):4200-9. PubMed PMC DOI

Loriaux P, Hoffmann A. "Of elections and cell-death decisions." Mol Cell. 2009;34(3):257-8. PubMed PMC DOI

Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA. "Metabolic network analysis integrated with transcript verification for sequenced genomes." Nat Methods. 2009;6(8):589-92. PubMed PMC DOI

Mo ML, Palsson BO, Herrgård MJ. "Connecting extracellular metabolomic measurements to intracellular flux states in yeast." BMC Syst Biol. 2009;3:37. PubMed PMC DOI

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

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