Student Publications

Export 400 results:
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.
Bandyopadhyay S, Cookson MR. "Evolutionary and functional relationships within the DJ1 superfamily." BMC Evol. Biol.. 2004;4:6.
Herrgård MJ, Palsson BØ. "Flagellar biosynthesis in silico: building quantitative models of regulatory networks." Cell. 2004;117(6):689-90.
Chaisson M, Pevzner P, Tang H. "Fragment assembly with short reads." Bioinformatics. 2004;20(13):2067-74.
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.
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004;429(6987):92-6.
Haugen AC, Kelley R, Collins JB, et al. "Integrating phenotypic and expression profiles to map arsenic-response networks." Genome Biol.. 2004;5(12):R95.
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.
Barrera L, Benner C, Tao Y-C, Winzeler E, Zhou Y. "Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays." BMC Bioinformatics. 2004;5:42.
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ. "Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space." J. Theor. Biol.. 2004;228(4):437-47.
Raphael B, Zhi D, Tang H, Pevzner P. "A novel method for multiple alignment of sequences with repeated and shuffled elements." Genome Res.. 2004;14(11):2336-46.
Canet-Avilés RM, Wilson MA, Miller DW, et al. "The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization." Proc. Natl. Acad. Sci. U.S.A.. 2004;101(24):9103-8.
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.
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.
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.
Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. "Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes." Bioinformatics. 2004;20(17):3108-27.
Crooks GE, Hon G, Chandonia J-M, Brenner SE. "WebLogo: a sequence logo generator." Genome Res.. 2004;14(6):1188-90.
Covert MW, Leung TH, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-kappaB activation." Science. 2005;309(5742):1854-7.
Tompa M, Li N, Bailey TL, et al. "Assessing computational tools for the discovery of transcription factor binding sites." Nat. Biotechnol.. 2005;23(1):137-44.
Thiele I, Price ND, Vo TD, Palsson BØ. "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet." J. Biol. Chem.. 2005;280(12):11683-95.
Chen J, Swamidass JS, Dou Y, Bruand J, Baldi P. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics. 2005;21(22):4133-9.
Devaraj NK, Miller GP, Ebina W, et al. "Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers." J. Am. Chem. Soc.. 2005;127(24):8600-1.
Barken D, Wang C J, Kearns J, Cheong R, Hoffmann A, Levchenko A. "Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression"." Science. 2005;308(5718):52; author reply 52.
Sharan R, Suthram S, Kelley RM, et al. "Conserved patterns of protein interaction in multiple species." Proc. Natl. Acad. Sci. U.S.A.. 2005;102(6):1974-9.