Student Publications

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Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Prlic A, Bliven S, Rose PW, et al. "Pre-calculated protein structure alignments at the RCSB PDB website." Bioinformatics. 2010;26(23):2983-5.
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.
Price ND, Famili I, Beard DA, Palsson BØ. "Extreme pathways and Kirchhoff's second law." Biophys. J.. 2002;83(5):2879-82.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. "Network-based analysis of metabolic regulation in the human red blood cell." J. Theor. Biol.. 2003;225(2):185-94.
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.
Price ND, Schellenberger J, Palsson BO. "Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies." Biophys. J.. 2004;87(4):2172-86.
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.
Price ND, Reed JL, Papin JA, Famili I, Palsson BO. "Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices." Biophys. J.. 2003;84(2 Pt 1):794-804.
Price ND, Papin JA, Palsson BØ. "Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis." Genome Res.. 2002;12(5):760-9.
Portnoy VA, Herrgård MJ, Palsson BØ. "Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain." Appl. Environ. Microbiol.. 2008;74(24):7561-9.
Polymenidou M, Lagier-Tourenne C, Hutt KR, et al. "Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43." Nat. Neurosci.. 2011;14(4):459-68.
Pevzner PA, Kim S, Ng J. "Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"." Science. 2008;321(5892):1040; author reply 1040.
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. "Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis." J. Proteome Res.. 2008;7(8):3373-81.
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.
Payne SH. "Metabolic pathways." In: Loomis WF, Kuspa A, eds. Dictyostelium Genomics, pp. 41-57. Far Hills, N.J.: Horizon Press; 2005.
Parrish JR, Yu J, Liu G, et al. "A proteome-wide protein interaction map for Campylobacter jejuni." Genome Biol.. 2007;8(7):R130.
Papin JA, Reed JL, Palsson BO. "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks." Trends Biochem. Sci.. 2004;29(12):641-7.