Student Publications

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Papin JA, Palsson BO. "The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis." Biophys. J.. 2004;87(1):37-46.
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.
Papin JA, Price ND, Palsson BØ. "Extreme pathway lengths and reaction participation in genome-scale metabolic networks." Genome Res.. 2002;12(12):1889-900.
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.
Papin JA, Price ND, Edwards JS, Palsson B BØ. "The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy." J. Theor. Biol.. 2002;215(1):67-82.
Papin JA, Palsson BO. "Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk." J. Theor. Biol.. 2004;227(2):283-97.
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. "Comparison of network-based pathway analysis methods." Trends Biotechnol.. 2004;22(8):400-5.
Panopoulos AD, Yanes O, Ruiz S, et al. "The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming." Cell Res.. 2012;22(1):168-77.
Palsson BO, Price ND, Papin JA. "Development of network-based pathway definitions: the need to analyze real metabolic networks." Trends Biotechnol.. 2003;21(5):195-8.
Pacold M, Smith D, Little S, et al. "Comparison of methods to detect HIV dual infection." AIDS Res. Hum. Retroviruses. 2010;26(12):1291-8.
Pacold M, Soto P. "Retroviruses and opportunistic infections - 15th annual conference." IDrugs. 2008;11(4):233-5.
Pacold ME, Pond S KL, Wagner GA, et al. "Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men." AIDS. 2012;26(2):157-65.
Pacold M. "Retroviruses and opportunistic infections--16th annual conference. Characteristics and prevention of HIV transmission. 8-11 February 2009, Montréal, QC, Canada." IDrugs. 2009;12(4):204-6.
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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.
Orth JD, Conrad TM, Na J, et al. "A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011." Mol. Syst. Biol.. 2011;7:535.
Ogawa S, Lozach J, Benner C, et al. "Molecular determinants of crosstalk between nuclear receptors and toll-like receptors." Cell. 2005;122(5):707-21.
O'Dea EL, Barken D, Peralta RQ, et al. "A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity." Mol. Syst. Biol.. 2007;3:111.
O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-87.
O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr. Opin. Biotechnol.. 2015;34:125-34.
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. "Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction." Mol. Syst. Biol.. 2013;9:693.
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Nguyen D D, Wu C-H, Moree WJ, et al. "MS/MS networking guided analysis of molecule and gene cluster families." Proc. Natl. Acad. Sci. U.S.A.. 2013;110(28):E2611-20.
Ng J, Pevzner PA. "Algorithm for identification of fusion proteins via mass spectrometry." J. Proteome Res.. 2008;7(1):89-95.
Ng J, Bandeira N, Liu W-T, et al. "Dereplication and de novo sequencing of nonribosomal peptides." Nat. Methods. 2009;6(8):596-9.
Nam H, Lewis NE, Lerman JA, et al. "Network context and selection in the evolution to enzyme specificity." Science. 2012;337(6098):1101-4.
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431.

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