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kollers library [129 articles]

Nye artikler sendt til kollers bibliotek.
  • The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
    Science, Vol. 313, No. 5795. (29 September 2006), pp. 1929-1935.
    by J Lamb, ED Crawford, D Peck, JW Modell, IC Blat, MJ Wrobel, J Lerner, JP Brunet, A Subramanian, KN Ross, M Reich, H Hieronymus, G Wei, SA Armstrong, SJ Haggarty, PA Clemons, R Wei, SA Carr, ES Lander, TR Golub
  • Co-evolution of transcriptional and post-translational cell-cycle regulation
    Nature (27 September 2006)
    by Lars J Jensen, Thomas S Jensen, Ulrik de Lichtenberg, Søren Brunak, Peer Bork
  • Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1107-1118.
    by H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein
  • Utilizing logical relationships in genomic data to decipher cellular processes.
    FEBS J, Vol. 272, No. 20. (October 2005), pp. 5110-5118.
    by PM Bowers, BD O'Connor, SJ Cokus, E Sprinzak, TO Yeates, D Eisenberg
  • Genome-wide map of nucleosome acetylation and methylation in yeast.
    Cell, Vol. 122, No. 4. (26 August 2005), pp. 517-527.
    by DK Pokholok, CT Harbison, S Levine, M Cole, NM Hannett, TI Lee, GW Bell, K Walker, PA Rolfe, E Herbolsheimer, J Zeitlinger, F Lewitter, DK Gifford, RA Young
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
  • Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
    Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 392-399.
    by Xiang Guo, Kay Tatsuoka, Rongxiang Liu
  • Core transcriptional regulatory circuitry in human hepatocytes.
    Mol Syst Biol, Vol. 2 (2006)
    by DT Odom, RD Dowell, ES Jacobsen, L Nekludova, PA Rolfe, TW Danford, DK Gifford, E Fraenkel, GI Bell, RA Young
  • Evidence for an instructive mechanism of de novo methylation in cancer cells
    Nature Genetics, Vol. 38, No. 2. (24 January 2006), pp. 149-153.
    by Ilana Keshet, Yeshayahu Schlesinger, Shlomit Farkash, Eyal Rand, Merav Hecht, Eran Segal, Eli Pikarski, Richard A Young, Alain Niveleau, Howard Cedar, Itamar Simon
  • Identification and analysis of evolutionarily cohesive functional modules in protein networks.
    Genome Res (31 January 2006)
    by Mónica Campillos, Christian von Mering, Lars Juhl J Jensen, Peer Bork
  • A metabolic network in the evolutionary context: Multiscale structure and modularity.
    Proc Natl Acad Sci U S A (26 May 2006)
    by Victor Spirin, Mikhail S S Gelfand, Andrey A A Mironov, Leonid A A Mirny
  • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes.
    Mol Biol Evol, Vol. 18, No. 7. (July 2001), pp. 1283-1292.
    by A Wagner
  • Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.
    Proc Natl Acad Sci U S A, Vol. 101, No. 16. (20 April 2004), pp. 5934-5939.
  • Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.
    Nat Biotechnol, Vol. 22, No. 1. (January 2004), pp. 62-69.
    by AB Parsons, RL Brost, H Ding, Z Li, C Zhang, B Sheikh, GW Brown, PM Kane, TR Hughes, C Boone
  • Regulatory on/off minimization of metabolic flux changes after genetic perturbations.
    Proc Natl Acad Sci U S A, Vol. 102, No. 21. (24 May 2005), pp. 7695-7700.
    by T Shlomi, O Berkman, E Ruppin
    posted to metabolic network regulatory by koller on 2006-09-11 06:16:57 as ** along with 1 person roys
  • Structure-based assembly of protein complexes in yeast.
    Science, Vol. 303, No. 5666. (26 March 2004), pp. 2026-2029.
  • Protein interaction networks from yeast to human.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 292-299.
    by P Bork, LJ Jensen, C von Mering, AK Ramani, I Lee, EM Marcotte
  • STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by C von Mering, LJ Jensen, B Snel, SD Hooper, M Krupp, M Foglierini, N Jouffre, MA Huynen, P Bork
  • Structure and evolution of transcriptional regulatory networks.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 283-291.
    by MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann
  • Design principles of molecular networks revealed by global comparisons and composite motifs
    Genome Biology, Vol. 7 (19 July 2006), R55.
    by Haiyuan Yu, Yu Xia, Valery Trifonov, Mark Gerstein
  • Multiple knockout analysis of genetic robustness in the yeast metabolic network
    Nature Genetics, Vol. 38, No. 9. (29 August 2006), pp. 993-998.
    by David Deutscher, Isaac Meilijson, Martin Kupiec, Eytan Ruppin
  • Genetics of gene expression surveyed in maize, mouse and man.
    Nature, Vol. 422, No. 6929. (20 March 2003), pp. 297-302.
    by EE Schadt, SA Monks, TA Drake, AJ Lusis, N Che, V Colinayo, TG Ruff, SB Milligan, JR Lamb, G Cavet, PS Linsley, M Mao, RB Stoughton, SH Friend
  • Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice.
    Mamm Genome, Vol. 17, No. 6. (June 2006), pp. 466-479.
    by TA Drake, EE Schadt, AJ Lusis
  • Mapping determinants of human gene expression by regional and genome-wide association
    Nature, Vol. 437, No. 7063., pp. 1365-1369.
    by Vivian G Cheung, Richard S Spielman, Kathryn G Ewens, Teresa M Weber, Michael Morley, Joshua T Burdick
  • GENOME-WIDE ASSOCIATION STUDIES: THEORETICAL AND PRACTICAL CONCERNS
    Nat Rev Genet, Vol. 6, No. 2. (February 2005), pp. 109-118.
    by William Y Wang, Bryan J Barratt, David G Clayton, John A Todd
  • Cis-acting expression quantitative trait loci in mice.
    Genome Res, Vol. 15, No. 5. (May 2005), pp. 681-691.
    by S Doss, EE Schadt, TA Drake, AJ Lusis
    posted to association cis-regulation network regulatory by koller on 2006-09-06 23:18:42 as ***
  • An integrative genomics approach to infer causal associations between gene expression and disease
    Nature Genetics, Vol. 37, No. 7. (19 June 2005), pp. 710-717.
    by Eric E Schadt, John Lamb, Xia Yang, Jun Zhu, Steve Edwards, Debraj Guhathakurta, Solveig K Sieberts, Stephanie Monks, Marc Reitman, Chunsheng Zhang, Pek Y Lum, Amy Leonardson, Rolf Thieringer, Joseph M Metzger, Liming Yang, John Castle, Haoyuan Zhu, Shera F Kash, Thomas A Drake, Alan Sachs, Aldons J Lusis
  • Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight.
    PLoS Genet, Vol. 2, No. 8. (18 August 2006)
    by Anatole Ghazalpour, Sudheer Doss, Bin Zhang, Susanna Wang, Christopher Plaisier, Ruth Castellanos, Alec Brozell, Eric E E Schadt, Thomas A A Drake, Aldons J J Lusis, Steve Horvath
  • The amino-acid mutational spectrum of human genetic disease.
    Genome Biol, Vol. 4, No. 11. (2003)
    by D Vitkup, C Sander, GM Church
  • Identifying metabolic enzymes with multiple types of association evidence.
    BMC Bioinformatics, Vol. 7 (2006)
    by P Kharchenko, L Chen, Y Freund, D Vitkup, GM Church
  • A global view of pleiotropy and phenotypically derived gene function in yeast
    Molecular Systems Biology, Vol. 1, No. 1. (29 March 2005), pp. msb4100004-E1-msb4100004-E11.
    by Aimée M Dudley, Daniel M Janse, Amos Tanay, Ron Shamir, George M Church
  • Expression dynamics of a cellular metabolic network
    Molecular Systems Biology, Vol. 1, No. 1. (02 August 2005), pp. msb4100023-E1-msb4100023-E6.
    by Peter Kharchenko, George M Church, Dennis Vitkup
  • Identifying regulatory networks by combinatorial analysis of promoter elements.
    Nat Genet, Vol. 29, No. 2. (October 2001), pp. 153-159.
  • Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.
    J Biol, Vol. 4, No. 2. (2005)
    by LV Zhang, OD King, SL Wong, DS Goldberg, AH Tong, G Lesage, B Andrews, H Bussey, C Boone, FP Roth
  • Transcriptional regulation in constraints-based metabolic models of Escherichia coli.
    J Biol Chem, Vol. 277, No. 31. (2 August 2002), pp. 28058-28064.
    by MW Covert, BØ Palsson
    posted to metabolic network reconstruction regulatory by koller on 2006-08-31 06:54:53 as ***
  • Regulation of gene expression in flux balance models of metabolism.
    J Theor Biol, Vol. 213, No. 1. (7 November 2001), pp. 73-88.
    by MW Covert, CH Schilling, B Palsson
  • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
    Proc Natl Acad Sci U S A, Vol. 100, No. 23. (11 November 2003), pp. 13134-13139.
    by I Famili, J Forster, J Nielsen, BO Palsson
  • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
    Genome Res, Vol. 16, No. 5. (May 2006), pp. 627-635.
    by MJ Herrgård, BS Lee, V Portnoy, BØ Palsson
  • Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e72.
    by Markus J Herrgård, Stephen S Fong, Bernhard Palsson
    posted to network reconstruction metabolic by koller on 2006-08-31 06:33:01 as **** along with 1 person aswin
  • Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions
    Genome Res., Vol. 14, No. 2. (1 February 2004), pp. 301-312.
    by Anthony P Burgard, Evgeni V Nikolaev, Christophe H Schilling, Costas D Maranas
  • The Activity Reaction Core and Plasticity of Metabolic Networks.
    PLoS Comput Biol, Vol. 1, No. 7. (16 December 2005)
    by Eivind Almaas, Zoltán N N Oltvai, Albert-László L Barabási
    posted to metabolic network phenotype by koller on 2006-08-31 06:12:11 as **** along with 2 people kentsis tny
  • Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Nature, Vol. aop, No. current. (30 January 2005)
    by Lee P Lim, Nelson C Lau, Philip Garrett-Engele, Andrew Grimson, Janell M Schelter, John Castle, David P Bartel, Peter S Linsley, Jason M Johnson
  • The synthetic genetic interaction spectrum of essential genes
    Nat Genet, Vol. 37, No. 10. (October 2005), pp. 1147-1152.
    by Armaity P Davierwala, Jennifer Haynes, Zhijian Li, Renee L Brost, Mark D Robinson, Lisa Yu, Sanie Mnaimneh, Huiming Ding, Hongwei Zhu, Yiqun Chen, Xin Cheng, Grant W Brown, Charles Boone, Brenda J Andrews, Timothy R Hughes
  • Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.
    PLoS Comput Biol, Vol. 2, No. 8. (4 August 2006)
    by C Haynes, CJ Oldfield, F Ji, N Klitgord, ME Cusick, P Radivojac, VN Uversky, M Vidal, LM Iakoucheva
  • Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
    Nature, Vol. 436, No. 7052., pp. 861-865.
    by Kristin C Gunsalus, Hui Ge, Aaron J Schetter, Debra S Goldberg, Jing-Dong J Han, Tong Hao, Gabriel F Berriz, Nicolas Bertin, Jerry Huang, Ling-Shiang Chuang, Ning Li, Ramamurthy Mani, Anthony A Hyman, Birte Sönnichsen, Christophe J Echeverri, Frederick P Roth, Marc Vidal, Fabio Piano
  • Effect of sampling on topology predictions of protein-protein interaction networks
    Nature Biotechnology, Vol. 23, No. 7. (07 July 2005), pp. 839-844.
    by Jing-Dong J Han, Denis Dupuy, Nicolas Bertin, Michael E Cusick, Marc Vidal
  • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    Nature, Vol. 430, No. 6995. (01 July 2004), pp. 88-93.
    by Jing-Dong J Han, Nicolas Bertin, Tong Hao, Debra S Goldberg, Gabriel F Berriz, Lan V Zhang, Denis Dupuy, Albertha JM Walhout, Michael E Cusick, Frederick P Roth, Marc Vidal
  • Genomic analysis of regulatory network dynamics reveals large topological changes.
    Nature, Vol. 431, No. 7006. (16 September 2004), pp. 308-312.
    by NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein
  • Target hub proteins serve as master regulators of development in yeast.
    Genes Dev, Vol. 20, No. 4. (15 February 2006), pp. 435-448.
  • Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
    Proc Natl Acad Sci U S A (19 June 2006)
    by Su-Wen W Ho, Ghil Jona, Christina T L T Chen, Mark Johnston, Michael Snyder
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