Student Publications

2006

Barrera LO, Ren B. "The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding." Curr Opin Cell Biol. 2006;18(3):291-8. PubMed DOI
Chaisson MJ, Raphael BJ, Pevzner PA. "Microinversions in mammalian evolution." Proc Natl Acad Sci U S A. 2006;103(52):19824-9. PubMed PMC DOI
Gianchandani EP, Brautigan DL, Papin JA. "Systems analyses characterize integrated functions of biochemical networks." Trends Biochem Sci. 2006;31(5):284-91. PubMed DOI
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. "Matrix formalism to describe functional states of transcriptional regulatory systems." PLoS Comput Biol. 2006;2(8):e101. PubMed PMC DOI
Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. "DyNAVacS: an integrative tool for optimized DNA vaccine design." Nucleic Acids Res. 2006;34(Web Server issue):W264-6. PubMed PMC DOI
Hawkins T, Luban S, Kihara D. "Enhanced automated function prediction using distantly related sequences and contextual association by PFP." Protein Sci. 2006;15(6):1550-6. PubMed PMC DOI
Herrgård MJ, Fong SS, Palsson BØ. "Identification of genome-scale metabolic network models using experimentally measured flux profiles." PLoS Comput Biol. 2006;2(7):e72. PubMed PMC DOI
Herrgård MJ, Lee BS, Portnoy V, Palsson BØ. "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae." Genome Res. 2006;16(5):627-35. PubMed PMC DOI
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BØ. "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale." Nat Genet. 2006;38(12):1406-12. PubMed DOI
Hirose S, Payne SH, Loomis WF. "cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum." Eukaryot Cell. 2006;5(7):1104-10. PubMed PMC DOI
Hua Q, Joyce AR, Fong SS, Palsson BØ. "Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains." Biotechnol Bioeng. 2006;95(5):992-1002. PubMed DOI
Jones NC, Zhi D, Raphael BJ. "AliWABA: alignment on the web through an A-Bruijn approach." Nucleic Acids Res. 2006;34(Web Server issue):W613-6. PubMed PMC DOI
Joyce AR, Palsson BØ. "The model organism as a system: integrating 'omics' data sets." Nat Rev Mol Cell Biol. 2006;7(3):198-210. PubMed DOI
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S. "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol. 2006;188(23):8259-71. PubMed PMC DOI
Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryot Cell. 2006;5(2):272-6. PubMed PMC DOI
Price ND, Thiele I, Palsson BØ. "Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of 'loop law' thermodynamic constraints." Biophys J. 2006;90(11):3919-28. PubMed PMC DOI
Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC Jr, Ribeiro AA, Murphy RC, Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA. "Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4." J Lipid Res. 2006;47(5):1097-111. PubMed DOI
Reed JL, Famili I, Thiele I, Palsson BO. "Towards multidimensional genome annotation." Nat Rev Genet. 2006;7(2):130-41. PubMed DOI
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. "Systems approach to refining genome annotation." Proc Natl Acad Sci U S A. 2006;103(46):17480-4. PubMed PMC DOI
Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." J Biol. 2006;5(4):11. PubMed PMC DOI
Roepcke S, Zhi D, Vingron M, Arndt PF. "Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters." Gene. 2006;365:48-56. PubMed DOI
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. "A direct comparison of protein interaction confidence assignment schemes." BMC Bioinformatics. 2006;7:360. PubMed PMC DOI
Tanner S, Pevzner PA, Bafna V. "Unrestrictive identification of post-translational modifications through peptide mass spectrometry." Nat Protoc. 2006;1(1):67-72. PubMed DOI
Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL. "O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry." Mol Cell Proteomics. 2006;5(5):923-34. PubMed DOI
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?." J Proteome Res. 2006;5(10):2554-66. PubMed PMC DOI