Student Publications

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Famili I, Forster J, Nielsen J, Palsson BO. "Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network." Proc. Natl. Acad. Sci. U.S.A.. 2003;100(23):13134-9.
Sears DD, Hsiao A, Ofrecio JM, Chapman J, He W, Olefsky JM. "Selective modulation of promoter recruitment and transcriptional activity of PPARgamma." Biochem. Biophys. Res. Commun.. 2007;364(3):515-21.
Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. "A sensing array of radically coupled genetic 'biopixels'." Nature. 2012;481(7379):39-44.
Kwon Y-S, Garcia-Bassets I, Hutt KR, et al. "Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters." Proc. Natl. Acad. Sci. U.S.A.. 2007;104(12):4852-7.
Ronen R, Boucher C, Chitsaz H, Pevzner P. "SEQuel: improving the accuracy of genome assemblies." Bioinformatics. 2012;28(12):i188-96.
Raphael BJ, Volik S, Yu P, et al. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. "Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2013.
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42.
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.
Yurkovich JT, Palsson BO. "Solving Puzzles With Missing Pieces: The Power of Systems Biology." Proceedings of the IEEE. 2016;104(1):2-7.
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.
Kim S, Gupta N, Pevzner PA. "Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases." J. Proteome Res.. 2008;7(8):3354-63.
Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, Walker AF. "Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function." Biochemistry. 2007;46(46):13254-68.
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61.
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.
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. "Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli." Science. 2013;340(6137):1220-3.
Overbeek R, Begley T, Butler RM, et al. "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes." Nucleic Acids Res.. 2005;33(17):5691-702.
Kurihara Y, Schmitz RJ, Nery JR, et al. "Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis." G3 (Bethesda). 2012;2(4):487-98.
Shlomi T, Herrgard M, Portnoy V, et al. "Systematic condition-dependent annotation of metabolic genes." Genome Res.. 2007;17(11):1626-33.
Bandyopadhyay S, Sharan R, Ideker T. "Systematic identification of functional orthologs based on protein network comparison." Genome Res.. 2006;16(3):428-35.
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6.
Jung H, Bleazard T, Lee J, Hong D. "Systematic investigation of cancer-associated somatic point mutations in SNP databases." Nat. Biotechnol.. 2013;31(9):787-9.
Famili I, Palsson BO. "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." J. Theor. Biol.. 2003;224(1):87-96.
Gianchandani EP, Brautigan DL, Papin JA. "Systems analyses characterize integrated functions of biochemical networks." Trends Biochem. Sci.. 2006;31(5):284-91.