Student Publications

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. PubMed PMC DOI

Chaisson MJ, Brinza D, Pevzner PA. "De novo fragment assembly with short mate-paired reads: Does the read length matter?." Genome Res. 2009;19(2):336-46. PubMed PMC DOI

DeBlasio D, Bruand J, Zhang S. "PMFastR: A New Approach to Multiple RNA Structure Alignment." Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science. 2009;5724:49-61. DOI

Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. "Reconstruction of biochemical networks in microorganisms." Nat Rev Microbiol. 2009;7(2):129-43. PubMed PMC DOI

Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. "Evolutionarily conserved herpesviral protein interaction networks." PLoS Pathog. 2009;5(9):e1000570. PubMed PMC DOI

Gupta N, Pevzner PA. "False discovery rates of protein identifications: a strike against the two-peptide rule." J Proteome Res. 2009;8(9):4173-81. PubMed PMC DOI

Hawkins T, Chitale M, Luban S, Kihara D. "PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data." Proteins. 2009;74(3):566-82. PubMed DOI

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B. "Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature. 2009;459(7243):108-12. PubMed PMC DOI

Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput Biol. 2009;5(11):e1000566. PubMed PMC DOI

Hon GC, Hawkins RD, Ren B. "Predictive chromatin signatures in the mammalian genome." Hum Mol Genet. 2009;18(R2):R195-201. PubMed PMC DOI

Horler RS, 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. PubMed DOI

Hsiao A, Kuo MD. "High-throughput biology in the postgenomic era." J Vasc Interv Radiol. 2009;20(7 Suppl):S488-96. PubMed DOI

Kim S, Gupta N, Bandeira N, Pevzner PA. "Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra." Mol Cell Proteomics. 2009;8(1):53-69. PubMed PMC DOI

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