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grahamc's library [363 articles]

最近录入 grahamc's 文献库.
  • Analyzing Protein Interaction Networks Using Structural Information
    Annual Review of Biochemistry, Vol. 77, No. 1. (2008)
    by Christina Kiel, Pedro Beltrao, Luis Serrano
    posted to tools review network_biology bioinformatics by grahamc on 2008-05-01 07:24:30 as ** along with 2 people neils Evangelia
  • Protein complexes and functional modules in molecular networks.
    Proc Natl Acad Sci U S A, Vol. 100, No. 21. (14 October 2003), pp. 12123-12128.
    by V Spirin, LA Mirny
    posted to protein-protein interactions function_prediction biological_networks by grahamc on 2008-04-23 17:38:21 as ** along with 9 people and 4 groups biehl camster kentsis ujh tmmurali dragonrez karfunkel joseph_x_zhou Evangelia dbk-lab biophysics HIV_DR bioNetwork_sysBio
  • A new way to explore the world of extracellular protein interactions
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 517-520.
    by Christopher M Sanderson
    posted to protein-protein methods interactions by grahamc on 2008-04-23 17:34:40 as **
  • Flexible web-based integration of distributed large-scale human protein interaction maps
    Journal of Integrative Bioinformatics, Vol. 4, No. 1. (2007), pp. 51-61.
    by Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E Wanker, Matthias E Futschik
    posted to tools protein-protein interactions human data_integration database bioinformatics by grahamc on 2008-04-23 17:13:15 as read
  • UniHI: an entry gate to the human protein interactome.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by G Chaurasia, Y Iqbal, C Hänig, H Herzel, EE Wanker, ME Futschik
    posted to tools protein-protein interactions human data_integration biological_networks bioinformatics by grahamc on 2008-04-23 17:04:53 as read along with 3 people jyuh jfr massivemayhem
  • A tree kernel to analyse phylogenetic profiles.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by JP Vert
    posted to phylogenetic_analysis by grahamc on 2008-04-18 19:02:10 as ** along with 2 people bioinfo girschick
  • Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis
    Mol Biol Evol (12 December 2007), msm274.
    by Ward C Wheeler, Kurt M Pickett
    posted to phylogenetic_analysis by grahamc on 2008-04-18 18:57:10 as ** along with 1 person cjeans
  • Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.
    Genome Biol, Vol. 6, No. 5. (2005)
    by AK Ramani, RC Bunescu, RJ Mooney, EM Marcotte
    posted to data_integration human interactions protein-protein by grahamc on 2008-04-16 18:59:40 as ** along with 16 people and 3 groups setar tmmurali dragonrez okarsligil lfriedl ccots balajis maryee brant opheliav davidandrzej wnpx rlhsiao bundschu mikaelhuss raiyar kdl Bioinformatics generif_paper
  • Towards a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
    Mol Cell Proteomics (2 January 2007)
    by Sean R R Collins, Patrick Kemmeren, Xue-Chu C Zhao, Jack F F Greenblatt, Forrest Spencer, Frank C C Holstege, Jonathan S S Weissman, Nevan J J Krogan
    posted to interactions model_organisms network_biology protein-protein yeast by grahamc on 2008-03-28 21:34:06 as ** along with 2 people and 1 group nickluscombe roys EBI-regulation
  • A probabilistic view of gene function.
    Nat Genet, Vol. 36, No. 6. (June 2004), pp. 559-564.
    by AG Fraser, EM Marcotte
    posted to function_prediction genomics by grahamc on 2008-03-28 20:50:08 as ** along with 9 people and 1 group snuppepuppan ziquje lfriedl opheliav wnpx samal massivemayhem bootsy vietanh0 kdl
  • 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
    posted to interactions network_confidence protein-protein statistics by grahamc on 2008-03-28 20:49:11 as ** along with 18 people and 6 groups camster barry dragonrez bicko lfriedl chad_davis alexg j3xucite bundschu yeastyboy ruvido raiyar iris_2001 cmor shu Evangelia shikin Pao-Yang dbk-lab structural_bioinformatics kdl Bioinformatics generif_paper GeneGo
  • Insights into Protein-Protein Interfaces using a Bayesian Network Prediction Method
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by James R Bradford, Chris J Needham, Andrew J Bulpitt, David R Westhead
    posted to methods network_biology prediction by grahamc on 2008-03-28 20:46:28 as ** along with 6 people and 2 groups marti barry conkymacro ameetsoni massivemayhem phoenixzxl structural_bioinformatics Bioinformatics
  • Computational analysis of human protein interaction networks.
    Proteomics, Vol. 7, No. 15. (August 2007), pp. 2541-2552.
    by F Ramírez, A Schlicker, Y Assenov, T Lengauer, M Albrecht
    posted to data_integration human interactions network_biology protein-protein by grahamc on 2008-03-28 20:45:02 as ** along with 2 people jyuh balicea
  • 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
    posted to interactions model_organisms network_biology protein-protein yeast by grahamc on 2008-03-28 20:43:03 as ** along with 16 people and 3 groups snuppepuppan tmmurali lfriedl balajis wnpx nickluscombe egralla citecat noano koller iris_2001 sgoetz shikin s041629 pmendes mtruksa kdl EBI-regulation GeneGo
  • Discovery of biological networks from diverse functional genomic data.
    Genome Biol, Vol. 6, No. 13. (2005)
    by CL Myers, D Robson, A Wible, MA Hibbs, C Chiriac, CL Theesfeld, K Dolinski, OG Troyanskaya
    posted to function_prediction genomics network_biology by grahamc on 2008-03-28 20:41:42 as **
  • Hierarchical multi-label prediction of gene function.
    Bioinformatics (12 January 2006)
    by Zafer Barutcuoglu, Robert E E Schapire, Olga G G Troyanskaya
    posted to function_prediction statistics by grahamc on 2008-03-28 20:39:59 as ** along with 1 person uknandal
  • Finding function: evaluation methods for functional genomic data
    BMC Genomics, Vol. 7 (25 July 2006), 187.
    by Chad L Myers, Daniel R Barrett, Matthew A Hibbs, Curtis Huttenhower, Olga G Troyanskaya
    posted to function_prediction genomics network_biology network_confidence statistics by grahamc on 2008-03-28 20:39:02 as ** along with 4 people and 2 groups tjimenez jfr smbaxtersf dejori ic4 generif_paper
  • Context-sensitive data integration and prediction of biological networks
    Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2322-2330.
    by Chad L Myers, Olga G Troyanskaya
    posted to data_integration network_biology by grahamc on 2008-03-28 20:37:21 as ** along with 6 people jyuh tmmurali rdiaz iris_2001 nedwards shung
  • 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
    posted to interactions network_biology network_topology protein-protein by grahamc on 2008-03-28 20:30:40 as ** along with 9 people snuppepuppan kuhn rabbat gurkanbebek koller eukfn mikaelhuss cjeans iris_2001
  • Computational systems biology.
    Nature, Vol. 420, No. 6912. (14 November 2002), pp. 206-210.
    by H Kitano
    posted to review systems_biology by grahamc on 2008-03-28 20:29:21 as ** along with 13 people and 4 groups irenas rhem1224 lyongu eweaver wnpx ddahlem shivakumar3_14 os252 dgront mmt livingthingdan agileproteomics maburkitt dbk-lab TCR_Signaling SysbioMPI-TCells livingthing
  • Genomic analysis of essentiality within protein networks.
    Trends Genet, Vol. 20, No. 6. (June 2004), pp. 227-231.
    by H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein
    posted to genomics interactions network_biology protein-protein by grahamc on 2008-03-28 20:28:34 as ** along with 3 people and 1 group shikin niolis nickluscombe EBI-regulation
  • Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
    Curr Opin Microbiol, Vol. 7, No. 5. (October 2004), pp. 535-545.
    by R Jansen, M Gerstein
    posted to function_prediction genomics network_biology network_confidence standards by grahamc on 2008-03-28 20:26:40 as ** along with 4 people and 2 groups okarsligil lfriedl wnpx neils kdl Bioinformatics
  • PROTEOMICS: Enhanced: Integrating Interactomes
    Science, Vol. 295, No. 5553. (11 January 2002), pp. 284-287.
    by Mark Gerstein, Ning Lan, Ronald Jansen
    posted to data_integration interactions by grahamc on 2008-03-28 20:25:16 as ** along with 2 people and 1 group lfriedl balajis kdl
  • Integrating 'omic' information: a bridge between genomics and systems biology.
    Trends Genet, Vol. 19, No. 10. (October 2003), pp. 551-560.
    by H Ge, AJ Walhout, M Vidal
    posted to data_integration genomics network_biology by grahamc on 2008-03-28 20:23:38 as ** along with 4 people and 1 group lfriedl wnpx biosv reidy kdl
  • Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.
    Curr Biol, Vol. 12, No. 22. (19 November 2002), pp. 1952-1958.
    by AJ Walhout, J Reboul, O Shtanko, N Bertin, P Vaglio, H Ge, H Lee, L Doucette-Stamm, KC Gunsalus, AJ Schetter, DG Morton, KJ Kemphues, V Reinke, SK Kim, F Piano, M Vidal
    posted to data_integration interactions network_biology by grahamc on 2008-03-28 20:21:59 as **
  • Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
    Genome Res., Vol. 11, No. 9. (September 2001), pp. 1463-1468.
    by D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein
    posted to data_integration interactions network_biology protein-protein by grahamc on 2008-03-28 20:18:17 as **
  • NETWORK BIOLOGY: UNDERSTANDING THE CELL'S FUNCTIONAL ORGANIZATION
    Nat Rev Genet, Vol. 5, No. 2. (February 2004), pp. 101-113.
    by Albert-Laszlo Barabasi, Zoltan N Oltvai
    posted to evolution function_prediction network_biology protein_evolution by grahamc on 2008-03-28 20:08:04 as ** along with 9 people and 1 group okarsligil bayesian tny mmt mirzazadeh lpfernandes karfunkel vietanh0 nolodie Bioinformatics
  • The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 February 2007), e59.eor.
    by Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifinov, Mark Gerstein
    posted to evolution interactions network_biology network_topology protein-protein by grahamc on 2008-03-28 20:06:47 as ** along with 3 people zwang Pao-Yang taiei688
  • Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context
    Proceedings of the National Academy of Sciences (12 December 2007), 0710183104.
    by Philip M Kim, Jan O Korbel, Mark B Gerstein
    posted to evolution network_biology selection by grahamc on 2008-03-28 20:05:37 as ** along with 6 people wilbur jyuh tmmurali cjeans mingzhi minostro
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to data_integration evolution interactions protein-protein by grahamc on 2008-03-28 20:04:42 as ** along with 14 people and 2 groups bicko lfriedl chad_davis Einat tny choonpeng timflutre ramensky massivemayhem efge lpfernandes cdeane Pao-Yang phoenixzxl structural_bioinformatics kdl
  • Relating whole-genome expression data with protein-protein interactions.
    Genome Res, Vol. 12, No. 1. (January 2002), pp. 37-46.
    by R Jansen, D Greenbaum, M Gerstein
    posted to data_integration expression interactions protein-protein by grahamc on 2008-03-28 20:03:18 as ** along with 6 people nedwards gurkanbebek gespim cjeans iris_2001 kintoki
  • Systems biology: a brief overview.
    Science, Vol. 295, No. 5560. (1 March 2002), pp. 1662-1664.
    by H Kitano
    posted to review systems_biology by grahamc on 2008-03-28 20:00:44 as ** along with 18 people and 6 groups soramame_0518 lenov irenas Yanno Borelli wnpx biosv shivakumar3_14 dgront kehan cconboy mmt margaritis roland_ewald carmaus jdiezperezj maburkitt mertnuhoglu dbk-lab biodiversity_conservation Bioinformatics GrassBase dIEMoSIRIS MoSi-Rostock
  • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.
    Nat Genet, Vol. 29, No. 4. (December 2001), pp. 482-486.
    by H Ge, Z Liu, GM Church, M Vidal
    posted to data_integration interactions model_organisms network_biology translation yeast by grahamc on 2008-03-28 19:59:46 as ** along with 9 people and 1 group roys BioGeek lfriedl wnpx mmt gespim bluto ruvido kintoki kdl
  • Getting connected: analysis and principles of biological networks.
    Genes Dev, Vol. 21, No. 9. (1 May 2007), pp. 1010-1024.
    by X Zhu, M Gerstein, M Snyder
    posted to interactions net network_biology network_statistics protein-protein by grahamc on 2008-03-28 19:57:55 as ** along with 7 people jfr balajis fishtank nedwards naegele Evangelia kristen
  • Understanding Network Concepts in Modules
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Jun Dong, Steve Horvath
    posted to network_biology network_properties network_statistics network_topology by grahamc on 2008-03-28 17:42:09 as ** along with 3 people and 1 group jfr kengg natstreet Bioinformatics
  • What is a gene, post-ENCODE? History and updated definition.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 669-681.
    by MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder
    posted to encode_project evolution genomics by grahamc on 2008-03-28 17:38:16 as ** along with 23 people and 4 groups hpaces jyuh carolh12 eweaver dpollard balicea dchughes dullhunk madhadron cottrell egonw ghattem sujaikumar Garamonfok PunkRock jasonbobe PredictER cabbagezs Jporci kmdaily krokicki antonkratz Minty Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • An encyclopaedia of interactions
    Nat Rev Mol Cell Biol, Vol. 8, No. 7. (July 2007), pp. 512-512.
    by Ekat Kritikou
    posted to interactions review by grahamc on 2008-03-28 17:37:26 as ** along with 1 group Bioinformatics
  • Genome Transplantation in Bacteria: Changing One Species to Another
    Science (28 June 2007), 1144622.
    by Carole Lartigue, John I Glass, Nina Alperovich, Rembert Pieper, Prashanth P Parmar, Hutchison, Hamilton O Smith, Craig J Venter
    posted to synthetic_biology by grahamc on 2008-03-28 17:32:16 as ** along with 8 people and 1 group jyuh operon madhadron yeastyboy zwang cabbagezs gulsacan westoll Bioinformatics
  • Key biology databases go wiki
    Nature, Vol. 445, No. 7129. (14 February 2007), pp. 691-691.
    by Jim Giles
    posted to no-tag by grahamc on 2008-03-28 17:31:16 as ** along with 9 people and 6 groups jyuh marcius eweaver kehan raiyar leechuck PunkRock barriot mircea biodiversity_conservation Bioinformatics BioinfoCIPF SGU-CIPF steinmetzlab GrassBase
  • The human disease network
    PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8685-8690.
    by Kwang-Il Goh, Michael E Cusick, David Valle, Barton Childs, Marc Vidal, Albert-Laszlo Barabasi
    posted to disease human network_biology by grahamc on 2008-03-28 17:21:27 as ** along with 21 people and 8 groups mingzhi Yanno jyuh aalibes cannin kuhn jfr yas balicea neveaire bundschu raiyar joepickrell leSyl henning dejori xingxu winterschlaefer naegele shikin nolodie GomezLab Biostatistics Computational-Genomics Bioinformatics Neuroscience steinmetzlab ic4 generif_paper
  • Genetics of global gene expression
    Nature Reviews Genetics, Vol. 7, No. 11., pp. 862-872.
    by Matthew V Rockman, Leonid Kruglyak
    posted to genomics review by grahamc on 2008-03-28 17:18:28 as ** along with 16 people and 10 groups jyuh dpollard tardigrade balicea dchughes nickluscombe neveaire aswin qfwills ealloza giovanni mlovell lp2 emarker natstreet mimulus_99 Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience G4ID EBI-regulation BioinfoCIPF GeschwindLab Genetics-of-Gambling
  • GOing from functional genomics to biological significance.
    Cytogenet Genome Res, Vol. 117, No. 1-4. (2007), pp. 278-287.
    by FM McCarthy, SM Bridges, SC Burgess
    posted to annotation comparative_genomics gene_ontology model_organisms statistics by grahamc on 2008-03-28 17:16:55 as ** along with 1 person and 1 group sgoetz Bioinformatics
  • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
    J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795.
    by X Li, O Keskin, B Ma, R Nussinov, J Liang
    posted to domains interactions protein-protein by grahamc on 2008-03-28 17:12:28 as ** along with 9 people and 2 groups barry baaden bicko nickolay j3xucite bluvsh1 xz Evangelia ladab structural_bioinformatics Bioinformatics
  • Integrating physical and genetic maps: from genomes to interaction networks
    Nature Reviews Genetics, Vol. 8, No. 9., pp. 699-710.
    by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
    posted to data_integration network_biology by grahamc on 2008-03-28 17:09:51 as ** along with 9 people and 3 groups cdeane jyuh balicea dchughes sebastien_vigneau joepickrell zwang shikin lh1 Bioinformatics G4ID Genetics-of-Gambling
  • Graph-based methods for analysing networks in cell biology.
    Brief Bioinform, Vol. 7, No. 3. (September 2006), pp. 243-255.
    by T Aittokallio, B Schwikowski
    posted to network_biology network_properties network_statistics network_topology review by grahamc on 2008-03-28 17:07:29 as ** along with 5 people and 2 groups iris_2001 barry tmmurali aswin jmarcelino structural_bioinformatics Bioinformatics
  • Current progress in bioinformatics 2007.
    Brief Bioinform (27 August 2007)
    by Russ B B Altman
    posted to bioinformatics review by grahamc on 2008-03-28 17:05:42 as ** along with 1 group Bioinformatics
  • Current progress in network research: toward reference networks for key model organisms.
    Brief Bioinform (29 August 2007)
    by Balaji S S Srinivasan, Nigam H H Shah, Jason A A Flannick, Eduardo Abeliuk, Antal F F Novak, Serafim Batzoglou
    posted to data_integration interactions model_organisms protein-protein by grahamc on 2008-03-28 17:03:57 as ***** along with 3 people and 1 group jyuh nedwards roys Bioinformatics
  • Optimization of specificity in a cellular protein interaction network by negative selection.
    Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680.
    by A Zarrinpar, SH Park, WA Lim
    posted to domains interactions protein_evolution protein-protein by grahamc on 2008-03-28 17:01:55 as ** along with 2 people and 2 groups barry cjeans structural_bioinformatics Bioinformatics
  • A Primer on Learning in Bayesian Networks for Computational Biology
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e129.
    by Chris J Needham, James R Bradford, Andrew J Bulpitt, David R Westhead
    posted to network_properties network_statistics by grahamc on 2008-03-28 16:58:16 as ** along with 10 people and 2 groups jyuh brian jfr balicea zwang bertelsen cabbagezs groepl ppark idonaldson Bioinformatics BergmanLab
  • Fuzzy association rules for biological data analysis: a case study on yeast
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Francisco Lopez, Armando Blanco, Fernando Garcia, Carlos Cano, Antonio Marin
    posted to data_integration fuzzy_logic statistics by grahamc on 2008-03-28 16:51:21 as ** along with 4 people and 1 group laughcry barriot xili03 yoanjacquemin Bioinformatics
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