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タグ: nsf2007 [29 articles]

Recent papers classified by the tag nsf2007.
  • Detecting conserved interaction patterns in biological networks.
    J Comput Biol, Vol. 13, No. 7. (September 2006), pp. 1299-1322.
    by M Koyutürk, Y Kim, S Subramaniam, W Szpankowski, A Grama
    posted to nsf2007 by balajis on 2007-03-03 22:13:14 as ** along with 2 people and 1 group massivemayhem mirzazadeh Bioinformatics
  • The Biomolecular Interaction Network Database and related tools 2005 update.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by C Alfarano, CE Andrade, K Anthony, N Bahroos, M Bajec, K Bantoft, D Betel, B Bobechko, K Boutilier, E Burgess, K Buzadzija, R Cavero, C D'Abreo, I Donaldson, D Dorairajoo, MJ Dumontier, MR Dumontier, V Earles, R Farrall, H Feldman, E Garderman, Y Gong, R Gonzaga, V Grytsan, E Gryz, V Gu, E Haldorsen, A Halupa, R Haw, A Hrvojic, L Hurrell, R Isserlin, F Jack, F Juma, A Khan, T Kon, S Konopinsky, V Le, E Lee, S Ling, M Magidin, J Moniakis, J Montojo, S Moore, B Muskat, I Ng, JP Paraiso, B Parker, G Pintilie, R Pirone, JJ Salama, S Sgro, T Shan, Y Shu, J Siew, D Skinner, K Snyder, R Stasiuk, D Strumpf, B Tuekam, S Tao, Z Wang, M White, R Willis, C Wolting, S Wong, A Wrong, C Xin, R Yao, B Yates, S Zhang, K Zheng, T Pawson, BF Ouellette, CW Hogue
    posted to nsf2007 by balajis on 2007-03-03 22:24:01 as ** along with 5 people and 3 groups yas zlu frohike dagmar dragonrez T_lab dIEMoSIRIS compneur
  • 'Conserved hypothetical' proteins: prioritization of targets for experimental study.
    Nucleic Acids Res, Vol. 32, No. 18. (2004), pp. 5452-5463.
    by MY Galperin, EV Koonin
    posted to nsf2007 by balajis on 2007-03-05 16:52:32 as ** along with 3 people and 2 groups ana dayjm bakakaj structural_bioinformatics Bioinformatics
  • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 303-305.
    by I Xenarios, L Salwínski, XJ Duan, P Higney, SM Kim, D Eisenberg
    posted to nsf2007 by balajis on 2007-03-03 22:23:40 as ** along with 4 people nuke2005 wnpx gurkanbebek carlk
  • Bergey's Manual of Systematic Bacteriology, Vol. 2 (Parts A, B & C; Three-Volume Set)
    (25 August 2005)
    by G Garrity
    posted to nsf2007 by balajis on 2007-03-03 23:09:25 as **
  • Towards a genome-based taxonomy for prokaryotes.
    J Bacteriol, Vol. 187, No. 18. (September 2005), pp. 6258-6264.
    by KT Konstantinidis, JM Tiedje
    posted to nsf2007 by balajis on 2007-03-03 23:10:40 as ** along with 1 person and 1 group gelack iSEEM
  • SWISS-2DPAGE, ten years later
    PROTEOMICS, Vol. 4, No. 8. (2004), pp. 2352-2356.
    by Christine Hoogland, Khaled Mostaguir, Jean-Charles Sanchez, Denis F Hochstrasser, Ron D Appel
    posted to nsf2007 by balajis on 2007-03-03 20:08:54 as **
  • Creation and implications of a phenome-genome network
    Nature Biotechnology, Vol. 24, No. 1. (10 January 2006), pp. 55-62.
    by Atul J Butte, Isaac S Kohane
    posted to nsf2007 by balajis on 2007-03-05 16:55:28 as ** along with 8 people and 2 groups BioGeek bpb okarsligil wnpx tag elsiatcase eukfn jyuh Bioinformatics metric_embeddings
  • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
    Nucleic Acids Res, Vol. 33, No. 17. (2005), pp. 5691-5702.
    by R Overbeek, T Begley, RM Butler, JV Choudhuri, HY Chuang, M Cohoon, V de Crécy-Lagard, N Diaz, T Disz, R Edwards, M Fonstein, ED Frank, S Gerdes, EM Glass, A Goesmann, A Hanson, D Iwata-Reuyl, R Jensen, N Jamshidi, L Krause, M Kubal, N Larsen, B Linke, AC McHardy, F Meyer, H Neuweger, G Olsen, R Olson, A Osterman, V Portnoy, GD Pusch, DA Rodionov, C Rückert, J Steiner, R Stevens, I Thiele, O Vassieva, Y Ye, O Zagnitko, V Vonstein
    posted to nsf2007 by balajis on 2007-03-03 22:01:09 as ** along with 1 person jwortman
  • STRING 7--recent developments in the integration and prediction of protein interactions.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by C von Mering, LJ Jensen, M Kuhn, S Chaffron, T Doerks, B Krüger, B Snel, P Bork
    posted to nsf2007 by balajis on 2007-03-05 16:50:25 as ** along with 10 people jyuh kuhn fisherp raiyar massivemayhem larsjuhljensen higueruelo renatomilani carlk bicko
  • Integrated Protein Interaction Networks for 11 Microbes
    : Research in Computational Molecular Biology (2006), pp. 1-14.
    by Balaji S Srinivasan, Antal F Novak, Jason A Flannick, Serafim Batzoglou, Harley H Mcadams
    posted to nsf2007 by balajis on 2007-03-03 22:10:26 as ** along with 2 people nedwards carlk
  • Identification and characterization of novel competence genes comA and exbB involved in natural genetic transformation of Pseudomonas stutzeri.
    Res Microbiol, Vol. 152, No. 5. (June 2001), pp. 451-460.
    by S Graupner, W Wackernagel
    posted to nsf2007 by balajis on 2007-03-05 15:57:39 as ** along with 1 person nuke2005
  • IntAct--open source resource for molecular interaction data.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by S Kerrien, Y Alam-Faruque, B Aranda, I Bancarz, A Bridge, C Derow, E Dimmer, M Feuermann, A Friedrichsen, R Huntley, C Kohler, J Khadake, C Leroy, A Liban, C Lieftink, L Montecchi-Palazzi, S Orchard, J Risse, K Robbe, B Roechert, D Thorneycroft, Y Zhang, R Apweiler, H Hermjakob
    posted to nsf2007 by balajis on 2007-03-02 23:30:04 as ** along with 1 person massivemayhem
  • Cell type-specific phosphorylation and proteolysis of a transcriptional regulator controls the G1-to-S transition in a bacterial cell cycle.
    Cell, Vol. 90, No. 3. (8 August 1997), pp. 415-424.
    by IJ Domian, KC Quon, L Shapiro
    posted to nsf2007 by balajis on 2007-03-03 22:22:02 as **
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to nsf2007 thesis by balajis on 2006-04-24 10:28:32 as ** along with 45 people and 4 groups dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • 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
    posted to nsf2007 by balajis on 2007-03-03 23:14:05 as ** along with 23 people and 2 groups dragonrez lfriedl yoh j3xucite kintoki koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes winterschlaefer Evangelia cdeane shung phoenixzxl stefanoallesina ellakat frohike shikin ksiek carlk kdl GeneGo
  • A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes
    Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 109-115.
    by Kam Jim, Kush Parmar, Mona Singh, Saeed Tavazoie
    posted to nsf2007 by balajis on 2007-03-05 16:54:19 as **
  • The ORFanage: an ORFan database.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by N Siew, Y Azaria, D Fischer
    posted to nsf2007 by balajis on 2007-03-03 22:26:54 as **
  • Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
    (2001), pp. 282-289.
    by John Lafferty, Andrew Mccallum, Fernando Pereira
    posted to nsf2007 by balajis on 2007-03-03 22:19:35 as ** along with 20 people and 4 groups davidr halacsy unnonouno buescher76 wcohen sids j3xucite knmnyn student_t dwf bundschu johnkork koji_matsuda mkolar markusd vlachmore kohei-h oyen jmackay idornescu oktave-labs generif_paper Statistical Machine Learning WLV-RGCL
  • A genomic perspective on protein families.
    Science, Vol. 278, No. 5338. (24 October 1997), pp. 631-637.
    by RL Tatusov, EV Koonin, DJ Lipman
    posted to nsf2007 by balajis on 2007-03-03 23:15:32 as ** along with 6 people bjorns nuke2005 AaronDarling ruvido ninch Ema
  • A Bayesian networks approach for predicting protein-protein interactions from genomic data.
    Science, Vol. 302, No. 5644. (17 October 2003), pp. 449-453.
    by R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein
    posted to no-tag nsf2007 by balajis on 2006-12-31 23:29:22 as ** along with 18 people and 2 groups lfriedl opheliav yuval wnpx nickluscombe ruvido raiyar massivemayhem kdang dbgrant nedwards karfunkel Evangelia shung phoenixzxl penpen926 carlk frohike kdl EBI-regulation
  • Cytoscape: a software environment for integrated models of biomolecular interaction networks.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2498-2504.
    by P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, B Schwikowski, T Ideker
    posted to nsf2007 by balajis on 2007-03-05 14:26:26 as ** along with 12 people and 3 groups dragonrez tvdbulck frohike carmaus dagmar natstreet jlh64 Evangelia pmendes yggdrasil carlk Borelli dIEMoSIRIS MoSi-Rostock compneur
  • Estimating the number of clusters in a dataset via the gap statistic
    (2000)
    by R Tibshirani, G Walther, T Hastie
    posted to nsf2007 by balajis on 2007-03-03 22:32:31 as ** along with 5 people archroad aviad_work sugarexpletive ykuoka frohike
  • The UCSC genome browser database: update 2007.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by RM Kuhn, D Karolchik, AS Zweig, H Trumbower, DJ Thomas, A Thakkapallayil, CW Sugnet, M Stanke, KE Smith, A Siepel, KR Rosenbloom, B Rhead, BJ Raney, A Pohl, JS Pedersen, F Hsu, AS Hinrichs, RA Harte, M Diekhans, H Clawson, G Bejerano, GP Barber, R Baertsch, D Haussler, WJ Kent
    posted to nsf2007 by balajis on 2007-03-03 23:15:09 as ** along with 2 people miguel olympos
  • Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales.
    Genome Biol, Vol. 3, No. 12. (2002)
    by B Dombrecht, K Marchal, J Vanderleyden, J Michiels
    posted to nsf2007 by balajis on 2007-03-02 23:20:46 as ** along with 1 person and 1 group adria TNT
  • Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.
    BMC Bioinformatics, Vol. 6 (2005)
    by CJ Wolfe, IS Kohane, AJ Butte
    posted to nsf2007 by balajis on 2007-03-03 22:15:10 as ** along with 3 people maryee srp33 dragonrez
  • The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by JR Cole, B Chai, RJ Farris, Q Wang, AS Kulam-Syed-Mohideen, DM McGarrell, AM Bandela, E Cardenas, GM Garrity, JM Tiedje
    posted to nsf2007 by balajis on 2007-03-03 22:33:48 as ** along with 1 person wenhan
  • An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits
    PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e159.
    by Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark Gerstein, Yves A Lussier
    posted to nsf2007 by balajis on 2007-03-05 16:55:01 as ** along with 2 people aswin totolee
  • The comprehensive updated regulatory network of Escherichia coli K-12.
    BMC Bioinformatics, Vol. 7, No. 1. (6 January 2006)
    by Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martin Peralta-Gil, Monica I Penaloza-Spinola, Agustino Martinez-Antonio, Peter D Karp, Julio Collado-Vides
    posted to nsf2007 by balajis on 2007-03-03 23:16:10 as ** along with 2 people discreteonyxorb dquest
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