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GustavoLacerda's genefinding [56 articles]

Recent papers added to GustavoLacerda's library classified by the tag genefinding. You can also see everyone's genefinding.
  • Genome Annotation in Plants and Fungi: EuGene as a Model Platform
    Current Bioinformatics, Vol. 3, No. 2. (May 2008), pp. 87-97.
    by Foissac, Sylvain, Gouzy, Jerome, Rombauts, Stephane, Mathe, Catherine, Amselem, Joelle, Sterck, Lieven, De Peer, V Yves, Rouze, Pierre, Schiex, Thomas
    posted to genefinding by GustavoLacerda on 2008-07-14 17:01:32 as ** along with 1 person jamselem
  • 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 genefinding by GustavoLacerda on 2008-07-14 15:44:31 as ** along with 7 people alexl jyuh dchughes jermth wenhan renatomilani drbal
  • Heuristic approach to deriving models for gene finding.
    Nucleic Acids Res, Vol. 27, No. 19. (1 October 1999), pp. 3911-3920.
    by J Besemer, M Borodovsky
    posted to genefinding by GustavoLacerda on 2008-07-09 04:27:04 as ** along with 4 people and 2 groups alexl azazello indigoviolet wenhan MBLAB EisenLab
  • Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
    BMC Bioinformatics, Vol. 9 (13 June 2008), 278.
    by Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack
    posted to genomics genefinding by GustavoLacerda on 2008-06-13 21:23:47 as ** along with 1 person tharris
  • Comparative analysis of sequence features involved in the recognition of tandem splice sites
    BMC Genomics, Vol. 9 (30 April 2008), 202.
    by Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster, Dirk Holste
    posted to splicing genefinding by GustavoLacerda on 2008-05-05 17:59:25 as **
  • Mitochondrial introns: a critical view
    Trends in Genetics, Vol. 23, No. 3. (March 2007), pp. 119-125.
    by Franz B Lang, Marie-Josee Laforest, Gertraud Burger
    posted to fungi genefinding intron mitochondria by GustavoLacerda on 2008-03-18 19:25:34 as **
  • prot4EST: Translating Expressed Sequence Tags from neglected genomes
    BMC Bioinformatics, Vol. 5, No. 1. (2004)
    by James Wasmuth, Mark Blaxter
    posted to est genefinding by GustavoLacerda on 2008-03-18 17:41:40 as **
  • Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    Genome Biology, Vol. 9, No. 2. (2008)
    by Tobias Warnecke, Joanna Parmley, Laurence Hurst
    posted to genefinding splicing by GustavoLacerda on 2008-03-04 14:05:49 as ** along with 1 person biomcgary
  • A practical guide to the art of RNA gene prediction
    Brief Bioinform (4 May 2007), bbm011.
    by Irmtraud M Meyer
    posted to genefinding by GustavoLacerda on 2008-01-25 17:05:59 as ** along with 5 people tharris xingxu penka wenhan xili03
  • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by J Besemer, M Borodovsky
    posted to genefinding by GustavoLacerda on 2008-01-23 23:23:35 as ** along with 2 people jmeppley wenhan
  • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    Genome Res. (19 November 2007), gr.6743907.
    by Brandi L Cantarel, Ian Korf, Sofia M Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Sanchez, Mark Yandell
    posted to genefinding by GustavoLacerda on 2008-01-23 23:22:03 as ** along with 5 people jamselem tharris timflutre stajich urgi
  • Improving gene recognition accuracy by combining predictions from two gene-finding programs
    Bioinformatics, Vol. 18, No. 8. (1 August 2002), pp. 1034-1045.
    by Sanja Rogic, Francis BF Ouellette, Alan K Mackworth
    posted to genefinding by GustavoLacerda on 2008-01-22 18:25:41 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to genefinding graphical_models by GustavoLacerda on 2008-01-22 17:36:25 as ** along with 12 people and 1 group jfr jyuh balicea AbnerCYH stajich cjeans GeeSharpMinor sobolevnrm cabbagezs nklee biehl softsimu baker-group
  • Advancing the State of the Art in Computational Gene Prediction
    Knowledge Discovery and Emergent Complexity in Bioinformatics (2007), pp. 81-106.
    by William Majoros, Uwe Ohler
    posted to genefinding by GustavoLacerda on 2008-01-21 12:40:23 as **
  • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Genome Biology, Vol. 9 (11 January 2008), R7.
    by Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen R White, Robin C Buell, Jennifer R Wortman
    posted to genefinding by GustavoLacerda on 2008-01-18 19:10:27 as ** along with 2 people and 1 group stajich mclarenv Berkeley Mycology
  • CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    Genome Biology, Vol. 8 (20 December 2007), R269.
    by Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou
    posted to genefinding by GustavoLacerda on 2008-01-07 14:51:24 as ** along with 2 people and 2 groups stajich renatomilani EisenLab Berkeley Mycology
  • FlyBase: genes and gene models.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by RA Drysdale, MA Crosby,
    posted to genefinding genome by GustavoLacerda on 2007-11-19 18:48:56 as ** along with 2 people dragonrez nuke2005
  • Conrad: Gene prediction using conditional random fields
    posted to genefinding by GustavoLacerda on 2007-10-27 06:35:01 as **
  • EuSplice: A unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes.
    Bioinformatics (7 March 2007)
    by Ashwini Bhasi, Ram Vinay V Pandey, Suriya Prabha P Utharasamy, Periannan Senapathy
    posted to genefinding splicing by GustavoLacerda on 2007-10-27 05:48:11 as ** along with 1 person jyuh
  • Characterization and prediction of alternative splice sites
    Gene, Vol. 366, No. 2. (1 February 2006), pp. 219-227.
    by Magnus Wang, Antonio Marin
    posted to genefinding splicing by GustavoLacerda on 2007-10-27 05:42:38 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Coevolution of genomic intron number and splice sites.
    Trends Genet, Vol. 23, No. 7. (July 2007), pp. 321-325.
    by M Irimia, D Penny, SW Roy
    posted to genefinding by GustavoLacerda on 2007-10-27 05:21:21 as ** along with 4 people and 1 group dpollard stajich Manchester seitentaisei EisenLab
  • Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome
    posted to genefinding by GustavoLacerda on 2007-09-17 02:47:04 as **
  • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1061-1067.
    by Genis Parra, Keith Bradnam, Ian Korf
    posted to genefinding by GustavoLacerda on 2007-08-21 22:46:03 as ** along with 3 people and 2 groups indigoviolet stajich wenhan EisenLab Berkeley Mycology
  • 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 genefinding by GustavoLacerda on 2007-08-18 05:46:22 as ** along with 1 person and 1 group dpollard EisenLab
  • PALMA: mRNA to genome alignments using large margin algorithms
    Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1892-1900.
    by Uta Schulze, Bettina Hepp, Cheng S Ong, Gunnar Ratsch
    posted to est2genome genefinding by GustavoLacerda on 2007-08-17 17:45:20 as ** along with 1 person cjeans
  • Intron length distributions and gene prediction
    Nucl. Acids Res. (7 July 2007), gkm281.
    by Scott W Roy, David Penny
    posted to genefinding splicing by GustavoLacerda on 2007-08-03 20:21:48 as ** along with 2 people cabbagezs Jporci
  • Positive selection for unpreferred codon usage in eukaryotic genomes
    BMC Evolutionary Biology, Vol. 7 (18 July 2007), 119.
    by Daniel E Neafsey, James E Galagan
    posted to genefinding genomics by GustavoLacerda on 2007-07-27 20:12:37 as ** along with 1 person Ema
  • Homology search for genes
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i97-103.
    by Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, Ming Li
    posted to genefinding by GustavoLacerda on 2007-07-25 17:52:17 as ** along with 1 person jyuh
  • Computational Inference of Homologous Gene Structures in the Human Genome
    Genome Res., Vol. 11, No. 5. (1 May 2001), pp. 803-816.
    by Ru-Fang Yeh, Lee P Lim, Christopher B Burge
    posted to genefinding by GustavoLacerda on 2007-07-19 01:39:50 as ** along with 1 person and 1 group indigoviolet EisenLab
  • ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA.
    J Bioinform Comput Biol, Vol. 4, No. 3. (June 2006), pp. 649-664.
    by K Shimizu, J Adachi, Y Muraoka
    posted to est genefinding by GustavoLacerda on 2007-07-18 21:30:50 as **
  • Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
    Bioinformatics (5 May 2007)
    by Avril Coghlan, Richard Durbin
    posted to genefinding by GustavoLacerda on 2007-06-20 19:58:30 as ** along with 3 people and 2 groups indigoviolet stajich dmc EisenLab Durbin group
  • Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by ME Sparks, V Brendel
    posted to genefinding splicing by GustavoLacerda on 2007-06-12 02:03:38 as **
  • Contemporary Progress in Gene Structure Prediction
    Current Genomics, Vol. 7, No. 5. (August 2006), pp. 283-292.
    by Churbanov, Alexander
    posted to genefinding by GustavoLacerda on 2007-06-12 01:58:42 as **
  • Prediction of splice sites with dependency graphs and their expanded bayesian networks
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 471-482.
    by Te-Ming Chen, Chung-Chin Lu, Wen-Hsiung Li
    posted to genefinding splicing by GustavoLacerda on 2007-06-08 15:32:47 as **
  • The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: implications for automated gene prediction
    Genomics, Vol. 87, No. 3. (March 2006), pp. 338-347.
    by Martijn Rep, Roselinde G Duyvesteijn, Liane Gale, Thomas Usgaard, Ben J Cornelissen, Li-Jun Ma, Todd J Ward
    posted to fungi genefinding splicing by GustavoLacerda on 2007-06-06 19:38:56 as **
  • Hypothesis testing approaches to the exon prediction problem
    Bioinformatics, Vol. 22, No. 24. (15 December 2006), pp. 3003-3008.
    by Vilardell, Mireia, Sanchez-Pla, Alex
    posted to genefinding by GustavoLacerda on 2007-05-09 21:26:42 as **
  • Predicting essential genes in fungal genomes
    Genome Res., Vol. 16, No. 9. (1 September 2006), pp. 1126-1135.
    by Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder, Mark Gerstein
    posted to genefinding by GustavoLacerda on 2007-05-09 21:24:48 as ** along with 4 people balicea saket olympos dbenn
  • Automatic generation of gene finders for eukaryotic species
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Kasper Munch, Anders Krogh
    posted to genefinding by GustavoLacerda on 2007-05-09 21:22:32 as ** along with 2 people and 1 group alexl kaspermunch Bioinformatics
  • Current methods of gene prediction, their strengths and weaknesses.
    Nucleic Acids Res, Vol. 30, No. 19. (1 October 2002), pp. 4103-4117.
    by C Mathé, MF Sagot, T Schiex, P Rouzé
    posted to genefinding by GustavoLacerda on 2007-05-09 20:51:59 as ** along with 3 people wenhan ep161302 arcticrasta
  • 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 genefinding by GustavoLacerda on 2007-05-09 20:44:14 as ** along with 1 person wenhan
  • Gene prediction and verification in a compact genome with numerous small introns
    Genome Res., Vol. 14, No. 11. (1 November 2004), pp. 2330-2335.
    by Aaron E Tenney, Randall H Brown, Charles Vaske, Jennifer K Lodge, Tamara L Doering, Michael R Brent
    posted to fungi genefinding by GustavoLacerda on 2007-05-09 20:06:47 as **
  • An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
    Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. 317-324.
    by Knapp, Keith, Chen, Yi-Ping Phoebe
    posted to genefinding by GustavoLacerda on 2007-05-08 17:02:59 as ** along with 2 people and 1 group indigoviolet wenhan EisenLab
  • An analysis of gene-finding programs for Neurospora crassa
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 901-912.
    by Eileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold
    posted to genefinding by GustavoLacerda on 2007-05-04 20:38:50 as **
  • Introns and splicing elements of five diverse fungi.
    Eukaryot Cell, Vol. 3, No. 5. (October 2004), pp. 1088-1100.
    by DM Kupfer, SD Drabenstot, KL Buchanan, H Lai, H Zhu, DW Dyer, BA Roe, JW Murphy
    posted to fungi genefinding splicing by GustavoLacerda on 2007-05-04 18:50:04 as ** along with 5 people and 2 groups penka jwestbrook alexl angieju seitentaisei Nie King_Lab
  • GFF3
    by Lincoln Stein
    posted to genefinding by GustavoLacerda on 2007-05-02 20:07:53 as **
  • Gene finding in novel genomes.
    BMC Bioinformatics, Vol. 5 (14 May 2004)
    by I Korf
    posted to genefinding by GustavoLacerda on 2007-05-02 19:45:06 as ** along with 5 people and 1 group alexl LeightonP indigoviolet wenhan cmzmasek EisenLab
  • Computational Gene Recognition
    by Wentian Li
    posted to genefinding by GustavoLacerda on 2007-05-02 19:43:25 as **
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2878-2879.
    by WH Majoros, M Pertea, SL Salzberg
    posted to genefinding by GustavoLacerda on 2007-05-02 19:37:51 as ** along with 2 people and 1 group alexl indigoviolet EisenLab
  • Gene identification in novel eukaryotic genomes by self-training algorithm
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. 6494-6506.
    by Alexandre Lomsadze, Vardges Ter-Hovhannisyan, Yury O Chernoff, Mark Borodovsky
    posted to genefinding by GustavoLacerda on 2007-05-02 19:35:25 as ** along with 1 person wenhan
  • A generalized hidden Markov model for the recognition of human genes in DNA.
    ISMB-96 (1996), pp. 134-141.
    by D Kulp, D Haussler, MG Reese, FH Eeckman
    posted to genefinding by GustavoLacerda on 2007-05-02 19:33:37 as ** along with 1 person wenhan
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