Student Publications

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O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
Lovci MT, Ghanem D, Marr H, et al. "Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges." Nat. Struct. Mol. Biol.. 2013;20(12):1434-42.
Bliven S, Prlić A. "Circular permutation in proteins." PLoS Comput. Biol.. 2012;8(3):e1002445.
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44.
Hon G, Wang W, Ren B. "Discovery and annotation of functional chromatin signatures in the human genome." PLoS Comput. Biol.. 2009;5(11):e1000566.
Manichaikul A, Ghamsari L, Hom EFY, et al. "Metabolic network analysis integrated with transcript verification for sequenced genomes." Nat. Methods. 2009;6(8):589-92.
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.
Hon G, Ren B, Wang W. "ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome." PLoS Comput. Biol.. 2008;4(10):e1000201.
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. "Discovery and revision of Arabidopsis genes by proteogenomics." Proc. Natl. Acad. Sci. U.S.A.. 2008;105(52):21034-8.
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23.
Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. "eQED: an efficient method for interpreting eQTL associations using protein networks." Mol. Syst. Biol.. 2008;4:162.
Young JA, Johnson JR, Benner C, et al. "In silico discovery of transcription regulatory elements in Plasmodium falciparum." BMC Genomics. 2008;9:70.
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. "Network-based prediction of human tissue-specific metabolism." Nat. Biotechnol.. 2008;26(9):1003-10.
Joyce AR, Palsson BØ. "Predicting gene essentiality using genome-scale in silico models." Methods Mol. Biol.. 2008;416:433-57.
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504.
Zheng M, Barrera LO, Ren B, Wu Y. "ChIP-chip: data, model, and analysis." Biometrics. 2007;63(3):787-96.
Luban S, Kihara D. "Comparative genomics of small RNAs in bacterial genomes." OMICS. 2007;11(1):58-73.
Heintzman ND, Stuart RK, Hon G, et al. "Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome." Nat. Genet.. 2007;39(3):311-8.
Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30.
Zaitlen N, Kang H M, Eskin E, Halperin E. "Leveraging the HapMap correlation structure in association studies." Am. J. Hum. Genet.. 2007;80(4):683-91.
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.
Herrgård MJ, Lee B-S, 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.
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.
Thiele I, Vo TD, Price ND, Palsson BØ. "Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants." J. Bacteriol.. 2005;187(16):5818-30.
Szpankowski W, Ren W, Szpankowski L. "An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17.