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Group: GeneGo - library [79 articles]

Recent papers posted by members of the GeneGo group
  • Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
    Nat Genet, Vol. 29, No. 4. (December 2001), pp. 365-371.
  • Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. e175-e175.
    by Manhong Dai, Pinglang Wang, Andrew D Boyd, Georgi Kostov, Brian Athey, Edward G Jones, William E Bunney, Richard M Myers, Terry P Speed, Huda Akil, Stanley J Watson, Fan Meng
  • 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
  • Systems biology for cancer.
    Curr Opin Oncol, Vol. 17, No. 1. (January 2005), pp. 44-48.
    by IG Khalil, C Hill
    posted to systems_biology network by shikin to the group GeneGo on 2008-05-19 18:11:38 as ** along with 1 person wnpx
  • Computational systems biology.
    Nature, Vol. 420, No. 6912. (14 November 2002), pp. 206-210.
    by H Kitano
  • Noise in Gene Expression: Origins, Consequences, and Control
    Science, Vol. 309, No. 5743. (23 September 2005), pp. 2010-2013.
    by Jonathan M Raser, Erin K O'Shea
  • Network motifs: simple building blocks of complex networks.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 824-827.
  • Computational analysis of microarray data.
    Nat Rev Genet, Vol. 2, No. 6. (June 2001), pp. 418-427.
  • Systems biology and new technologies enable predictive and preventative medicine.
    Science, Vol. 306, No. 5696. (22 October 2004), pp. 640-643.
    by L Hood, JR Heath, ME Phelps, B Lin
    posted to systems_biology hood by shikin to the group GeneGo on 2008-05-04 13:34:48 as ** along with 6 people megraw raiyar AlexanderPico wnpx cconboy maburkitt
  • Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae.
    Molecular & cellular proteomics : MCP, Vol. 1, No. 4. (April 2002), pp. 323-333.
    by TJ Griffin, SP Gygi, T Ideker, B Rist, J Eng, L Hood, R Aebersold
    posted to systems_biology by shikin to the group GeneGo on 2008-05-04 13:30:30 as **
  • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
    Science, Vol. 292, No. 5518. (4 May 2001), pp. 929-934.
  • Global properties of biological networks.
    Drug discovery today, Vol. 10, No. 5. (1 March 2005), pp. 365-372.
    by MG Grigorov
    posted to systems_biology network by shikin to the group GeneGo on 2008-05-04 13:22:48 as ****
  • Systems biology, metabolic modelling and metabolomics in drug discovery and development
    Drug Discovery Today, Vol. 11, No. 23-24. (December 2006), pp. 1085-1092.
    by Douglas B Kell
  • A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism.
    Drug metabolism and disposition: the biological fate of chemicals, Vol. 33, No. 3. (March 2005), pp. 474-481.
    posted to toxicology systems_biology network genego by shikin to the group GeneGo on 2008-05-04 13:19:07 as **
  • Pathway mapping tools for analysis of high content data.
    Methods in molecular biology (Clifton, N.J.), Vol. 356 (2007), pp. 319-350.
  • Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms
    Xenobiotica, Vol. 36, No. 10-11. (8220), pp. 877-901.
    posted to toxicology systems_biology network method genego_articles by shikin to the group GeneGo on 2008-05-04 13:08:06 as **
  • Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
    Genome Biology, Vol. 8, No. 9. (2007)
    by Robert Kleemann, Lars Verschuren, Marjan van Erk, Yuri Nikolsky, Nicole Cnubben, Elwin Verheij, Age Smilde, Henk Hendriks, Susanne Zadelaar, Graham Smith, Valery Kaznacheev, Tatiana Nikolskaya, Anton Melnikov, Eva H Camejo, Jan van der Greef, Ben van Ommen, Teake Kooistra
    posted to systems_biology genego_articles by shikin to the group GeneGo on 2008-05-04 13:04:56 as ** along with 2 people aconesa vinithepooh
  • Modelling microtubule patterns
    Nature Cell Biology, Vol. 8, No. 11., pp. 1204-1211.
    by Eric Karsenti, François Nédélec, Thomas Surrey
  • Data-driven modelling of signal-transduction networks
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 11., pp. 820-828.
    by Kevin A Janes, Michael B Yaffe
  • Physicochemical modelling of cell signalling pathways
    Nature Cell Biology, Vol. 8, No. 11., pp. 1195-1203.
    by Bree B Aldridge, John M Burke, Douglas A Lauffenburger, Peter K Sorger
  • Linking data to models: data regression
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 11. (27 September 2006), pp. 813-819.
    by Khuloud Jaqaman, Gaudenz Danuser
  • Collecting and organizing systematic sets of protein data
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 11., pp. 803-812.
    by John G Albeck, Gavin Macbeath, Forest M White, Peter K Sorger, Douglas A Lauffenburger, Suzanne Gaudet
  • Modelling data across labs, genomes, space and time
    Nature Cell Biology, Vol. 8, No. 11., pp. 1190-1194.
    by Jason R Swedlow, Suzanna E Lewis, Ilya G Goldberg
    posted to systems_biology nature_sysbio_08 by shikin to the group GeneGo on 2008-05-04 12:28:28 as *** along with 4 people jfr glyg MrData scienbox
  • Linking publication, gene and protein data
    Nat Cell Biol, Vol. 8, No. 11. (November 2006), pp. 1183-1189.
    by Paul Kersey, Rolf Apweiler
  • Mapping and sequencing of structural variation from eight human genomes
    Nature, Vol. 453, No. 7191., pp. 56-64.
    by Jeffrey M Kidd, Gregory M Cooper, William F Donahue, Hillary S Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, Alice N Yamada, Peter Tsang, Tera L Newman, Eray Tüzün, Ze Cheng, Heather M Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin Mckernan, Lin Chen, Maika Malig, Joshua D Smith, Joshua M Korn, Steven A Mccarroll, David A Altshuler, Daniel A Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A Nickerson, James C Mullikin, Richard K Wilson, Laurakay Bruhn, Maynard V Olson, Rajinder Kaul, Douglas R Smith, Evan E Eichler
  • How complete are current yeast and human protein-interaction networks?
    Genome Biology, Vol. 7 (01 December 2006), 120.
    by Traver G Hart, Arun K Ramani, Edward M Marcotte
    posted to network ppi systems_biology by shikin to the group GeneGo on 2008-04-17 14:25:58 as ** along with 4 people phoenixzxl carlk eukfn Pao-Yang
  • Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, Vol. 417, No. 6887. (23 May 2002), pp. 399-403.
    by C von Mering, R Krause, B Snel, M Cornell, SG Oliver, S Fields, P Bork
  • Entrez Gene: gene-centered information at NCBI.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by D Maglott, J Ostell, KD Pruitt, T Tatusova
  • notes Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets
    BMC Genomics, Vol. 8 (28 November 2007), 439.
    by Claude Chelala, Stephan A Hahn, Hannah J Whiteman, Sayka Barry, Deepak Hariharan, Tomasz P Radon, Nicholas R Lemoine, Tatjana Crnogorac-Jurcevic
    posted to cancer database gene_expression genomics by shikin to the group GeneGo on 2008-04-15 08:56:39 as *** along with 1 person jfr
  • notes Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases
    BMC Bioinformatics, Vol. 8 (04 October 2007), 372.
    by Seth I Berger, Jeremy M Posner, Avi Ma'ayan
    posted to network systems_biology by shikin to the group GeneGo on 2008-04-15 08:14:04 as read along with 2 people jyuh jfr
  • Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms
    PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e145.
    by Kai Xia, Huiling Xue, Dong Dong, Shanshan Zhu, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen, Jing-Dong J Han
  • Protein-protein interaction networks and biology—what's the connection?
    Nature Biotechnology, Vol. 26, No. 1., pp. 69-72.
    by Luke Hakes, John W Pinney, David L Robertson, Simon C Lovell
  • Integrative analysis of the cancer transcriptome.
    Nat Genet, Vol. 37 Suppl (June 2005)
    by DR Rhodes, AM Chinnaiyan
  • From signatures to models: understanding cancer using microarrays.
    Nat Genet, Vol. 37 Suppl (June 2005)
  • Understanding biological functions through molecular networks
    Cell Res, Vol. 18, No. 2. (0000), pp. 224-237.
    by Jing-Dong J Han
  • Network biology: understanding the cell's functional organization.
    Nat Rev Genet, Vol. 5, No. 2. (February 2004), pp. 101-113.
    by AL Barabási, ZN Oltvai
  • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Journal of Biology, Vol. 5, No. 4. (08 June 2006), 11.
    by Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Ho, David Botstein, Brenda Andrews, Charles Boone, Olga G Troyanskya, Trey Ideker, Kara Dolinski, Nizar N Batada, Mike Tyers
  • Integration of biological networks and gene expression data using Cytoscape.
    Nat Protoc, Vol. 2, No. 10. (2007), pp. 2366-2382.
    posted to ideker network systems_biology by shikin to the group GeneGo on 2008-04-10 14:10:43 as ** along with 5 people AlexanderPico jyuh jfr shung thomaskelder
  • Network-based classification of breast cancer metastasis
    Mol Syst Biol, Vol. 3 (16 October 2007)
    by Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
  • Variations in DNA elucidate molecular networks that cause disease
    Nature (16 March 2008)
    by Yanqing Chen, Jun Zhu, Pek Y Lum, Xia Yang, Shirly Pinto, Douglas J Macneil, Chunsheng Zhang, John Lamb, Stephen Edwards, Solveig K Sieberts, Amy Leonardson, Lawrence W Castellini, Susanna Wang, Marie-France Champy, Bin Zhang, Valur Emilsson, Sudheer Doss, Anatole Ghazalpour, Steve Horvath, Thomas A Drake, Aldons J Lusis, Eric E Schadt
  • Genetics of gene expression and its effect on disease
    Nature (16 March 2008)
    by Valur Emilsson, Gudmar Thorleifsson, Bin Zhang, Amy S Leonardson, Florian Zink, Jun Zhu, Sonia Carlson, Agnar Helgason, Bragi G Walters, Steinunn Gunnarsdottir, Magali Mouy, Valgerdur Steinthorsdottir, Gudrun H Eiriksdottir, Gyda Bjornsdottir, Inga Reynisdottir, Daniel Gudbjartsson, Anna Helgadottir, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Unnur Styrkarsdottir, Solveig Gretarsdottir, Kristinn P Magnusson, Hreinn Stefansson, Ragnheidur Fossdal, Kristleifur Kristjansson, Hjortur G Gislason, Tryggvi Stefansson, Bjorn G Leifsson, Unnur Thorsteinsdottir, John R Lamb, Jeffrey R Gulcher, Marc L Reitman, Augustine Kong, Eric E Schadt, Kari Stefansson
  • Direct multiplexed measurement of gene expression with color-coded probe pairs.
    Nat Biotechnol (17 February 2008)
    by Gary K K Geiss, Roger E E Bumgarner, Brian Birditt, Timothy Dahl, Naeem Dowidar, Dwayne L L Dunaway, H Perry P Fell, Sean Ferree, Renee D D George, Tammy Grogan, Jeffrey J J James, Malini Maysuria, Jeffrey D D Mitton, Paola Oliveri, Jennifer L L Osborn, Tao Peng, Amber L L Ratcliffe, Philippa J J Webster, Eric H H Davidson, Leroy Hood
  • notes False discovery rate, sensitivity and sample size for microarray studies
    Bioinformatics, Vol. 21, No. 13. (July 2005), pp. 3017-3024.
    by Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Statistical significance for genomewide studies.
    Proc Natl Acad Sci U S A, Vol. 100, No. 16. (August 2003), pp. 9440-9445.
    posted to statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    Journal of the Royal Statistical Society. Series B, Methodological, Vol. 57, No. 1. (1995), pp. 289-300.
    posted to statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Estimation and control of multiple testing error rates for microarray studies.
    Brief Bioinform, Vol. 7, No. 1. (March 2006), pp. 25-36.
    by SB Pounds
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Comparison of methods for estimating the number of true null hypotheses in multiplicity testing.
    J Biopharm Stat, Vol. 13, No. 4. (November 2003), pp. 675-689.
    by HM Hsueh, JJ Chen, RL Kodell
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Identifying differentially expressed genes in meta-analysis via Bayesian model-based clustering.
    Biom J, Vol. 48, No. 3. (June 2006), pp. 435-450.
    by YY Jung, MS Oh, DW Shin, SH Kang, HS Oh
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A, Vol. 98, No. 9. (April 2001), pp. 5116-5121.
    by VG Tusher, R Tibshirani, G Chu
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
  • notes Identifying differentially expressed genes using false discovery rate controlling procedures.
    Bioinformatics, Vol. 19, No. 3. (February 2003), pp. 368-375.
    posted to genomics statistics by shikin to the group GeneGo on 2008-02-18 15:58:53 as **
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