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タグ: recent_genefinding [101 articles]

Recent papers classified by the tag recent_genefinding.
  • Inference of splicing regulatory activities by sequence neighborhood analysis.
    PLoS Genet, Vol. 2, No. 11. (24 November 2006)
    by MB Stadler, N Shomron, GW Yeo, A Schneider, X Xiao, CB Burge
    posted to recent_genefinding by wenhan on 2008-02-25 21:24:45 as **
  • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    Nat Rev Genet, Vol. 9, No. 1. (January 2008), pp. 62-73.
    by Michael R Brent
    posted to recent_genefinding by wenhan on 2008-02-26 22:39:30 as ** along with 7 people GustavoLacerda alexl jyuh dchughes jermth renatomilani drbal
  • Engineering a software tool for gene structure prediction in higher organisms
    Information and Software Technology, Vol. 47, No. 15. (December 2005), pp. 965-978.
    by Gordon Gremme, Volker Brendel, Michael E Sparks, Stefan Kurtz
    posted to recent_genefinding by wenhan on 2008-02-25 20:08:25 as ** along with 1 person GustavoLacerda
  • Recent advances in gene structure prediction.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 264-272.
    by MR Brent, R Guigó
    posted to recent_genefinding by wenhan on 2008-02-26 22:37:45 as **
  • Conrad: Gene prediction using conditional random fields
    Genome Res., Vol. 17, No. 9. (1 September 2007), pp. 1389-1398.
    by David Decaprio, Jade P Vinson, Matthew D Pearson, Philip Montgomery, Matthew Doherty, James E Galagan
    posted to recent_genefinding by wenhan on 2008-02-26 16:12:54 as ** along with 2 people and 1 group alexl indigoviolet EisenLab
  • Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
    BMC Bioinformatics, Vol. 8 (28 June 2007), 225.
    by Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa
    posted to recent_genefinding by wenhan on 2008-02-25 20:06:49 as ** along with 2 people Cortel rsandie
  • Targeted discovery of novel human exons by comparative genomics
    Genome Res. (7 November 2007), gr.7128207.
    by Adam Siepel, Mark Diekhans, Brona Brejova, Laura Langton, Michael Stevens, Charles L Comstock, Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung-Chun Yu, Jianfeng Li, Bruce A Roe, Phil Green, Daniela S Gerhard, Gary Temple, David Haussler, Michael R Brent
    posted to recent_genefinding by wenhan on 2008-02-25 21:19:22 as ** along with 2 people dchughes stajich
  • EGASP: the human ENCODE Genome Annotation Assessment Project.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by R Guigó, P Flicek, JF Abril, A Reymond, J Lagarde, F Denoeud, S Antonarakis, M Ashburner, VB Bajic, E Birney, R Castelo, E Eyras, C Ucla, TR Gingeras, J Harrow, T Hubbard, SE Lewis, MG Reese
    posted to recent_genefinding by wenhan on 2008-02-25 22:32:55 as ** along with 3 people and 2 groups jfr indigoviolet timhubbard Bioinformatics EisenLab
  • Gene prediction: compare and CONTRAST
    Genome Biology, Vol. 8, No. 12. (2007)
    by Paul Flicek
    posted to recent_genefinding by wenhan on 2008-02-25 20:05:55 as ** along with 4 people Borelli alexl dewaldron yoanjacquemin
  • GeneWise and Genomewise
    Genome Res., Vol. 14, No. 5. (1 May 2004), pp. 988-995.
    by Ewan Birney, Michele Clamp, Richard Durbin
    posted to recent_genefinding by wenhan on 2008-02-26 22:34:18 as ** along with 4 people and 2 groups indigoviolet azazello alexl Stew EisenLab MBLAB
  • Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54.
    by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira
    posted to recent_genefinding by wenhan on 2008-02-26 22:32:58 as ** along with 4 people and 2 groups alexl dpollard zwang acarbo Bioinformatics EisenLab
  • Basic local alignment search tool.
    J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to recent_genefinding by wenhan on 2008-02-26 22:30:57 as ** along with 41 people and 5 groups granujilla benwei ashaytan camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti hervelequere dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by P Flicek, MR Brent
    posted to recent_genefinding by wenhan on 2008-02-25 20:04:42 as ** along with 1 person and 1 group eoghanharr Bioinformatics
  • JIGSAW: integration of multiple sources of evidence for gene prediction
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3596-3603.
    by Jonathan E Allen, Steven L Salzberg
    posted to recent_genefinding by wenhan on 2008-02-26 22:28:45 as ** along with 2 people and 1 group indigoviolet stajich EisenLab
  • PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by V Ferretti, C Poitras, D Bergeron, B Coulombe, F Robert, M Blanchette
    posted to recent_genefinding by wenhan on 2008-02-25 20:03:59 as ** along with 1 person jyuh
  • In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
    Bioinformatics, Vol. 23, No. 4. (15 February 2007), pp. 414-420.
    by Saeys, Yvan, Rouze, Pierre, Van de Peer, Yves
    posted to recent_genefinding by wenhan on 2008-02-25 21:15:05 as ** along with 1 person GustavoLacerda
  • Gene finding in the chicken genome
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline Bye, Francisco Camara, Paul Flicek, Elizabeth Huckle, Genis Parra, David Shteynberg, Carine Wyss, Jane Rogers, Stylianos Antonarakis, Ewan Birney, Roderic Guigo, Michael Brent
    posted to recent_genefinding by wenhan on 2008-02-25 20:02:15 as **
  • FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1161-1163.
    by Evert-Jan Blom, Dinne W Bosman, Sacha A van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B Roerdink, Oscar P Kuipers
    posted to recent_genefinding by wenhan on 2008-02-25 20:01:05 as **
  • Detection of broadly expressed neuronal genes in C. elegans.
    Dev Biol, Vol. 302, No. 2. (15 February 2007), pp. 617-626.
    by I Ruvinsky, U Ohler, CB Burge, G Ruvkun
    posted to recent_genefinding by wenhan on 2008-02-25 21:13:57 as **
  • EGASP: Introduction.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by MG Reese, R Guigó
    posted to recent_genefinding by wenhan on 2008-02-25 21:12:21 as **
  • Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Francois Enault, Karsten Suhre, Jean M Claverie
    posted to recent_genefinding by wenhan on 2008-02-25 20:00:06 as **
  • Towards multidimensional genome annotation
    Nature Reviews Genetics, Vol. 7, No. 2., pp. 130-141.
    by Jennifer L Reed, Iman Famili, Ines Thiele, Bernhard O Palsson
    posted to recent_genefinding by wenhan on 2008-02-25 21:10:36 as ** along with 10 people and 4 groups jyuh jfr balajis eweaver dchughes cmm raiyar massivemayhem zwang lylu FAB-lab G4ID steinmetzlab Genetics-of-Gambling
  • BASys: a web server for automated bacterial genome annotation.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by GH Van Domselaar, P Stothard, S Shrivastava, JA Cruz, A Guo, X Dong, P Lu, D Szafron, R Greiner, DS Wishart
    posted to recent_genefinding by wenhan on 2008-02-25 19:58:34 as **
  • Improving the Caenorhabditis elegans genome annotation using machine learning.
    PLoS Comput Biol, Vol. 3, No. 2. (23 February 2007)
    by G Rätsch, S Sonnenburg, J Srinivasan, H Witte, KR Müller, RJ Sommer, B Schölkopf
    posted to recent_genefinding by wenhan on 2008-02-25 21:09:30 as ** along with 2 people balajis alexl
  • On gene ontology and function annotation.
    Bioinformation, Vol. 1, No. 3. (2006), pp. 97-98.
    by D Pal
    posted to recent_genefinding by wenhan on 2008-02-25 21:08:08 as **
  • Features generated for computational splice-site prediction correspond to functional elements
    BMC Bioinformatics, Vol. 8 (24 October 2007), 410.
    by Rezarta I Dogan, Lise Getoor, John W Wilbur, Stephen M Mount
    posted to recent_genefinding by wenhan on 2008-02-25 19:52:17 as ** along with 1 person mcglam
  • Genome annotation past, present, and future: how to define an ORF at each locus.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1777-1786.
    by MR Brent
    posted to recent_genefinding by wenhan on 2008-02-25 19:18:03 as ** along with 3 people and 1 group textoris Ayest indigoviolet EisenLab
  • Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 150-155.
    by Dixon, J Richard, Eperon, C Ian, Samani, J Nilesh
    posted to recent_genefinding by wenhan on 2008-02-25 19:49:36 as **
  • Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions.
    Genome Res, Vol. 15, No. 4. (April 2005), pp. 577-582.
    by C Wei, P Lamesch, M Arumugam, J Rosenberg, P Hu, M Vidal, MR Brent
    posted to recent_genefinding by wenhan on 2008-02-25 21:38:11 as ** along with 1 person tmmurali
  • Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
    Bioinformatics (24 January 2008)
    by Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler
    posted to recent_genefinding by wenhan on 2008-02-25 23:19:56 as **
  • Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
    Bioinformatics, Vol. 21, No. 3. (01 February 2005), 293.
    by Daniel H Haft, Jeremy D Selengut, Nikhat Zafar, Owen White
    posted to recent_genefinding by wenhan on 2008-02-25 20:20:57 as **
  • Recognition of unknown conserved alternatively spliced exons.
    PLoS Comput Biol, Vol. 1, No. 2. (July 2005), pp. 113-122.
    by U Ohler, N Shomron, CB Burge
    posted to recent_genefinding by wenhan on 2008-02-25 21:01:14 as **
  • Iterative gene prediction and pseudogene removal improves genome annotation.
    Genome Res, Vol. 16, No. 5. (May 2006), pp. 678-685.
    by MJ van Baren, MR Brent
    posted to recent_genefinding by wenhan on 2008-02-25 21:37:08 as **
  • ENCODE: More genomic empowerment.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 667-668.
    by GM Weinstock
    posted to recent_genefinding by wenhan on 2008-02-25 23:17:42 as ** along with 4 people and 4 groups dchughes ghattem maximilianh blobbybirdman Bioinformatics G4ID Genetics-of-Gambling UH - Computational Biology
  • Gene finding in novel genomes.
    BMC Bioinformatics, Vol. 5 (14 May 2004)
    by I Korf
    posted to recent_genefinding by wenhan on 2008-02-26 22:51:11 as ** along with 5 people and 1 group alexl LeightonP indigoviolet GustavoLacerda cmzmasek EisenLab
  • SpliceMachine: predicting splice sites from high-dimensional local context representations
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1332-1338.
    by Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouze, Yves Van de Peer
    posted to recent_genefinding by wenhan on 2008-02-25 19:47:52 as ** along with 1 person alexl
  • Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans
    Genome Res., Vol. 17, No. 4. (1 April 2007), pp. 492-502.
    by Quinn M Mitrovich, Brian B Tuch, Christine Guthrie, Alexander D Johnson
    posted to recent_genefinding by wenhan on 2008-02-25 20:59:33 as ** along with 1 person stajich
  • Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by VB Bajic, MR Brent, RH Brown, A Frankish, J Harrow, U Ohler, VV Solovyev, SL Tan
    posted to recent_genefinding by wenhan on 2008-02-25 23:17:26 as ** along with 1 group Bioinformatics
  • Improving genome annotations using phylogenetic profile anomaly detection.
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 464-470.
    by TS Mikkelsen, JE Galagan, JP Mesirov
    posted to recent_genefinding by wenhan on 2008-02-25 20:58:12 as ** along with 1 person jwortman
  • How does eukaryotic gene prediction work?
    Nature Biotechnology, Vol. 25, No. 8., pp. 883-885.
    by Michael R Brent
    posted to recent_genefinding by wenhan on 2008-02-25 19:15:15 as ** along with 7 people and 3 groups jyuh indigoviolet dchughes zwang cabbagezs nklee ale EisenLab G4ID Genetics-of-Gambling
  • Integrating genomic homology into gene structure prediction.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by I Korf, P Flicek, D Duan, MR Brent
    posted to recent_genefinding by wenhan on 2008-02-26 22:50:04 as ** along with 2 people and 1 group indigoviolet dullhunk EisenLab
  • EGASP: collaboration through competition to find human genes
    Nature Methods, Vol. 2, No. 8., pp. 575-577.
    by Roderic Guigó, Martin G Reese
    posted to recent_genefinding by wenhan on 2008-02-25 20:16:23 as **
  • DIG-a system for gene annotation and functional discovery
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2957-2959.
    by Mark Delong, Guang Yao, Quanli Wang, Adrian Dobra, Esther P Black, Jeffrey T Chang, Andrea Bild, Mike West, Joseph R Nevins, Holly Dressman
    posted to recent_genefinding by wenhan on 2008-02-25 19:46:15 as **
  • Automatic annotation of eukaryotic genes, pseudogenes and promoters
    Genome Biology, Vol. 7, No. Suppl 1. (2006)
    by Victor Solovyev, Peter Kosarev, Igor Seledsov, Denis Vorobyev
    posted to recent_genefinding by wenhan on 2008-02-25 23:05:47 as ** along with 1 person operon
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to recent_genefinding 200806_prop by wenhan on 2008-02-26 22:48:59 as ** along with 18 people and 1 group bozdagd gpappas talponer operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans natstreet antonkratz yoanjacquemin EisenLab
  • Identifying bacterial genes and endosymbiont DNA with Glimmer
    Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 673-679.
    by Delcher, L Arthur, Bratke, A Kirsten, Powers, C Edwin, Salzberg, L Steven
    posted to recent_genefinding by wenhan on 2008-02-25 19:43:59 as **
  • The UCSC Known Genes
    Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1036-1046.
    by Fan Hsu, James W Kent, Hiram Clawson, Robert M Kuhn, Mark Diekhans, David Haussler
    posted to recent_genefinding by wenhan on 2008-02-26 22:48:03 as ** along with 3 people kmdaily antonkratz rschulz
  • Genomewide comparative analysis of alternative splicing in plants.
    Proc Natl Acad Sci U S A, Vol. 103, No. 18. (2 May 2006), pp. 7175-7180.
    by BB Wang, V Brendel
    posted to recent_genefinding by wenhan on 2008-02-26 23:16:59 as ** along with 3 people and 1 group saru jwestbrook byy King_Lab
  • Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation
    BMC Bioinformatics, Vol. 8 (08 August 2007), 295.
    by Marija Cvijovic, Daniel Dalevi, Elizabeth Bilsland, Graham JL Kemp, Per Sunnerhagen
    posted to recent_genefinding by wenhan on 2008-02-25 19:43:01 as ** along with 1 person stajich
  • An unsupervised classification scheme for improving predictions of prokaryotic TIS.
    BMC Bioinformatics, Vol. 7, No. 1. (9 March 2006)
    by Maike Tech, Peter Meinicke
    posted to recent_genefinding by wenhan on 2008-02-26 23:16:31 as ** along with 1 person eckart_bindewald
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