Student Publications

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2001
Covert MW, Schilling CH, Palsson B. "Regulation of gene expression in flux balance models of metabolism." J. Theor. Biol.. 2001;213(1):73-88.
2003
Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures." Genome Res.. 2003;13(11):2423-34.
2004
Duarte NC, Herrgård MJ, Palsson BØ. "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model." Genome Res.. 2004;14(7):1298-309.
Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks." Curr. Opin. Biotechnol.. 2004;15(1):70-7.
2005
Papin JA, Hunter T, Palsson BO, Subramaniam S. "Reconstruction of cellular signalling networks and analysis of their properties." Nat. Rev. Mol. Cell Biol.. 2005;6(2):99-111.
2006
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. "Representing and comparing protein structures as paths in three-dimensional space." BMC Bioinformatics. 2006;7:460.
Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryotic Cell. 2006;5(2):272-6.
2008
Valas RE, Bourne PE. "Rethinking proteasome evolution: two novel bacterial proteasomes." J. Mol. Evol.. 2008;66(5):494-504.
Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5.
2010
Brinza D, Schultz M, Tesler G, Bafna V. "RAPID detection of gene-gene interactions in genome-wide association studies." Bioinformatics. 2010;26(22):2856-62.
2011
Liu G-H, Barkho BZ, Ruiz S, et al. "Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome." Nature. 2011;472(7342):221-5.
Johnson DBF, Xu J, Shen Z, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nat. Chem. Biol.. 2011;7(11):779-86.
2012
Ho Sui SJ, Lo R, Fernandes AR, et al. "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence." Int. J. Antimicrob. Agents. 2012;40(3):246-51.
Chan JE, Kolodner RD. "Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification." PLoS Genet.. 2012;8(3):e1002539.
Johnson DBF, Wang C, Xu J, et al. "Release factor one is nonessential in Escherichia coli." ACS Chem. Biol.. 2012;7(8):1337-44.
2015
Hung T, Pratt GA, Sundararaman B, et al. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9.
2016
Van Nostrand EL, Pratt GA, Shishkin AA, et al. "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)." Nat. Methods. 2016;13(6):508-14.