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kollers library [129 articles]

Nye artikler sendt til kollers bibliotek i prioritert rekkefølge .
  • 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
  • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.
    Nat Genet, Vol. 34, No. 2. (June 2003), pp. 166-176.
  • Towards an integrated protein-protein interaction network: a relational markov network approach.
    J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 145-164.
  • 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
  • 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
  • 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
  • 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
  • Global analysis of protein phosphorylation in yeast
    Nature, Vol. 438, No. 7068., pp. 679-684.
    by Jason Ptacek, Geeta Devgan, Gregory Michaud, Heng Zhu, Xiaowei Zhu, Joseph Fasolo, Hong Guo, Ghil Jona, Ashton Breitkreutz, Richelle Sopko, Rhonda R Mccartney, Martin C Schmidt, Najma Rachidi, Soo-Jung Lee, Angie S Mah, Lihao Meng, Michael JR Stark, David F Stern, Claudio De Virgilio, Mike Tyers, Brenda Andrews, Mark Gerstein, Barry Schweitzer, Paul F Predki, Michael Snyder
  • Transcriptional networks: reverse-engineering gene regulation on a global scale.
    Curr Opin Microbiol, Vol. 7, No. 6. (December 2004), pp. 638-646.
    by G Chua, MD Robinson, Q Morris, TR Hughes
  • Global Mapping of the Yeast Genetic Interaction Network
    Science, Vol. 303, No. 5659. (06 February 2004), pp. 808-813.
    by Amy HY Tong, Guillaume Lesage, Gary D Bader, Huiming Ding, Hong Xu, Xiaofeng Xin, James Young, Gabriel F Berriz, Renee L Brost, Michael Chang, Yiqun Chen, Xin Cheng, Gordon Chua, Helena Friesen, Debra S Goldberg, Jennifer Haynes, Christine Humphries, Grace He, Shamiza Hussein, Lizhu Ke, Nevan Krogan, Zhijian Li, Joshua N Levinson, Hong Lu, Patrice Menard, Christella Munyana, Ainslie B Parsons, Owen Ryan, Raffi Tonikian, Tania Roberts, Anne-Marie Sdicu, Jesse Shapiro, Bilal Sheikh, Bernhard Suter, Sharyl L Wong, Lan V Zhang, Hongwei Zhu, Christopher G Burd, Sean Munro, Chris Sander, Jasper Rine, Jack Greenblatt, Matthias Peter, Anthony Bretscher, Graham Bell, Frederick P Roth, Grant W Brown, Brenda Andrews, Howard Bussey, Charles Boone
  • A quantitative protein interaction network for the ErbB receptors using protein microarrays
    Nature (06 November 2005)
    by Richard B Jones, Andrew Gordus, Jordan A Krall, Gavin Macbeath
  • Dynamic complex formation during the yeast cell cycle.
    Science, Vol. 307, No. 5710. (4 February 2005), pp. 724-727.
  • Proteome survey reveals modularity of the yeast cell machinery
    Nature (22 January 2006)
    by Anne-Claude Gavin, Patrick Aloy, Paola Grandi, Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars J Jensen, Sonja Bastuck, Birgit Dümpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M Rick, Bernhard Kuster, Peer Bork, Robert B Russell, Giulio Superti-Furga
  • Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?
    Genetics, Vol. 172, No. 2. (February 2006), pp. 1363-1367.
    by X He, J Zhang
    posted to evolution network network_motif regulatory transcription by koller on 2006-08-25 23:29:56 as ****
  • The regulatory utilization of genetic redundancy through responsive backup circuits.
    Proc Natl Acad Sci U S A (21 July 2006)
    by Ran Kafri, Melissa Levy, Yitzhak Pilpel
  • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.
    Nat Biotechnol, Vol. 22, No. 1. (January 2004), pp. 86-92.
    by J Ihmels, R Levy, N Barkai
  • A global view of the selection forces in the evolution of yeast cis-regulation.
    Genome Res, Vol. 14, No. 5. (May 2004), pp. 829-834.
    by A Tanay, I Gat-Viks, R Shamir
    posted to cis-regulation evolution network by koller on 2006-08-25 21:25:12 as **** along with 2 people briann carlk
  • Making sense of high-throughput protein-protein interaction data.
    Stat Appl Genet Mol Biol, Vol. 3, No. 1. (2004)
    posted to bayesian network p2p reconstruction by koller on 2006-08-25 21:05:14 as ****
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
  • From the Cover: Conserved patterns of protein interaction in multiple species.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1974-1979.
    by R Sharan, S Suthram, RM Kelley, T Kuhn, S McCuine, P Uetz, T Sittler, RM Karp, T Ideker
  • Systematic interpretation of genetic interactions using protein networks
    Nature Biotechnology, Vol. 23, No. 5. (05 May 2005), pp. 561-566.
    by Ryan Kelley, Trey Ideker
  • A Systems Approach to Mapping DNA Damage Response Pathways
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1054-1059.
    by Christopher T Workman, Craig H Mak, Scott Mccuine, Jean-Bosco Tagne, Maya Agarwal, Owen Ozier, Thomas J Begley, Leona D Samson, Trey Ideker
  • Integrated assessment and prediction of transcription factor binding.
    PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006)
  • Inferring cellular networks using probabilistic graphical models.
    Science, Vol. 303, No. 5659. (6 February 2004), pp. 799-805.
  • 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
  • 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
  • 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
  • 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
  • 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 ***
  • 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
  • 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
  • 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
  • Target hub proteins serve as master regulators of development in yeast.
    Genes Dev, Vol. 20, No. 4. (15 February 2006), pp. 435-448.
  • The regulatory software of cellular metabolism.
    Trends Biotechnol, Vol. 22, No. 6. (June 2004), pp. 261-265.
    by D Segrè
    posted to expression metabolic network regulatory by koller on 2006-08-31 01:12:11 as ***
  • Analysis of optimality in natural and perturbed metabolic networks.
    Proc Natl Acad Sci U S A, Vol. 99, No. 23. (12 November 2002), pp. 15112-15117.
    by D Segrè, D Vitkup, GM Church
  • PathBLAST: a tool for alignment of protein interaction networks.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by BP Kelley, B Yuan, F Lewitter, R Sharan, BR Stockwell, T Ideker
  • Evolution and topology in the yeast protein interaction network.
    Genome Res, Vol. 14, No. 7. (July 2004), pp. 1310-1314.
    by S Wuchty
    posted to evolution network p2p by koller on 2006-08-29 17:30:46 as *** along with 2 people carlk friendpine
  • Integration of gene expression data into genome-scale metabolic models.
    Metab Eng, Vol. 6, No. 4. (October 2004), pp. 285-293.
    posted to expression metabolic network reconstruction regulatory by koller on 2006-08-29 17:20:49 as ***
  • Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.
    by TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph, GK Gerber, NM Hannett, CT Harbison, CM Thompson, I Simon, J Zeitlinger, EG Jennings, HL Murray, DB Gordon, B Ren, JJ Wyrick, JB Tagne, TL Volkert, E Fraenkel, DK Gifford, RA Young
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