Student Publications

Export 400 results:
Suthram S, Sittler T, Ideker T. "The Plasmodium protein network diverges from those of other eukaryotes." Nature. 2005;438(7064):108-12.
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.
Werner SL, Barken D, Hoffmann A. "Stimulus specificity of gene expression programs determined by temporal control of IKK activity." Science. 2005;309(5742):1857-61.
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.
Kelley R, Ideker T. "Systematic interpretation of genetic interactions using protein networks." Nat. Biotechnol.. 2005;23(5):561-6.
Herrgård MJ, Palsson BØ. "Untangling the web of functional and physical interactions in yeast." J. Biol.. 2005;4(2):5.
Hsiao A, Ideker T, Olefsky JM, Subramaniam S. "VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data." Nucleic Acids Res.. 2005;33(Web Server issue):W627-32.
Zhu X, Hart R, Chang M S, et al. "Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands." J. Immunol.. 2004;173(12):7141-9.
Chandonia J-M, Hon G, Walker NS, et al. "The ASTRAL Compendium in 2004." Nucleic Acids Res.. 2004;32(Database issue):D189-92.
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.