Student Publications

2010

Hughey JJ, Lee TK, Covert MW. "Computational modeling of mammalian signaling networks." Wiley Interdiscip Rev Syst Biol Med. 2010;2(2):194-209. PubMed PMC DOI
Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. "A catalog of reference genomes from the human microbiome." Science. 2010;328(5981):994-9. PubMed PMC DOI
König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK. "Human host factors required for influenza virus replication." Nature. 2010;463(7282):813-7. PubMed PMC DOI
Lerman J, Palsson BO. "Microbiology. Topping off a multiscale balancing act." Science. 2010;330(6007):1058-9. PubMed DOI
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Mol Syst Biol. 2010;6:390. PubMed PMC DOI
Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. "De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads." PLoS One. 2010;5(6):e10922. PubMed PMC DOI
Pacold M, Smith D, Little S, Cheng PM, Jordan P, Ignacio C, Richman D, Pond SK. "Comparison of methods to detect HIV dual infection." AIDS Res Hum Retroviruses. 2010;26(12):1291-8. PubMed PMC DOI
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5. PubMed PMC DOI

2009

Abdulla MH, Ruelas DS, Wolff B, Snedecor J, Lim KC, Xu F, Renslo AR, Williams J, McKerrow JH, Caffrey CR. "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. PubMed PMC DOI
Barrett CL, Herrgard MJ, Palsson B. "Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation." BMC Syst Biol. 2009;3:30. PubMed PMC DOI
Berry RE, Shokhirev MN, Ho AY, Yang F, Shokhireva TK, Zhang H, Weichsel A, Montfort WR, Walker FA. "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. PubMed PMC DOI
Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. "Host cell factors in HIV replication: meta-analysis of genome-wide studies." PLoS Pathog. 2009;5(5):e1000437. PubMed PMC DOI
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