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	Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes [My Copy] Brief Bioinform, Vol. 10, No. 6. (1 November 2009), pp. 654-663. by Carol Soderlund posted to genefinding genefamilies fungi comparative_genomics by GustavoLacerda on 2009-12-21 13:14:51 as along with 2 people tmmurali kshameer
	JIGSAW: integration of multiple sources of evidence for gene prediction. [My Copy] Bioinformatics (Oxford, England), Vol. 21, No. 18. (15 September 2005), pp. 3596-3603. by Jonathan E. Allen, Steven L. Salzberg posted to genefinding by GustavoLacerda on 2009-10-14 18:35:30 as along with 6 people and 1 group rshe azazello jmartin49 indigoviolet stajich wenhan EisenLab
	Conserved introns reveal novel transcripts in Drosophila melanogaster. [My Copy] Genome research, Vol. 19, No. 7. (20 July 2009), pp. 1289-1300. by Michael Hiller, Sven Findeiss, Sandro Lein, et al.Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter, Peter F. Stadler posted to est2genome genefinding by GustavoLacerda on 2009-08-04 17:56:21 as along with 5 people and 3 groups bpcusack daveGerrard megraw stajich ppgardne BergmanLab Mycology Journal picks
	Integrating alternative splicing detection into gene prediction. [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (10 February 2005) by S. Foissac, T. Schiex posted to genefinding by azazello on 2009-01-30 19:58:27 as along with 2 people choede setar
	Evigan: A Hidden Variable Model for Integrating Gene Evidence for Eukaryotic Gene Prediction. [My Copy] Bioinformatics (10 January 2008) by Qian Liu, Aaron J J. Mackey, David S S. Roos, Fernando C N C. Pereira posted to genefinding by azazello on 2009-01-27 01:45:53 as along with 7 people and 2 groups bourby GustavoLacerda druvus stajich mingzhi gongScience alexl EisenLab Mycology
	Combined use of sequence similarity and codon bias for coding region identification. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 1, No. 1. (1994), pp. 39-50. by D. J. States, W. Gish posted to genefinding by azazello on 2008-12-15 20:51:55 as along with 2 people VGreiff wenhan
	Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000176. by Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, John S. Mattick posted to est genefinding by GustavoLacerda on 2008-12-04 01:24:11 as along with 10 people and 1 group rschulz Zephyrus hpaces reyez dswan agustinarce gfliustu cmn eskay GeeSharpMinor Roswell Cancer Crosstalk
	Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins. [My Copy] Mycological research (30 August 2008) by Gustavo Zaparoli, Odalys García G. Cabrera, Francisco Javier J. Medrano, Ricardo Tiburcio, Gustavo Lacerda, Gonçalo Guimarães G. Pereira posted to lge genefinding genefamilies fungi cerato by GustavoLacerda on 2008-11-30 23:24:49 as
	Conrad: Gene prediction using conditional random fields [My Copy] 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 fungi genefinding by GustavoLacerda on 2008-11-28 15:29:37 as along with 3 people and 1 group indigoviolet wenhan alexl EisenLab
	Using native and syntenically mapped cDNA alignments to improve de novo gene finding [My Copy] Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 637-644. by Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler posted to est2genome genefinding by GustavoLacerda on 2008-11-20 21:06:35 as along with 4 people druvus natstreet orzenil cdiwadkar
	GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming [My Copy] Genome Res., Vol. 12, No. 9. (1 September 2002), pp. 1418-1427. by Kevin L. Howe, Tom Chothia, Richard Durbin posted to genefinding by GustavoLacerda on 2008-11-20 20:55:20 as along with 5 people and 2 groups thegoose2 tharris druvus indigoviolet stajich C. elegans / WormBase EisenLab
	Gene finding with a hidden Markov model of genome structure and evolution [My Copy] Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 219-227. by Jakob S. Pedersen, Jotun Hein posted to genefinding by GustavoLacerda on 2008-11-20 20:55:17 as along with 6 people and 2 groups gjuggler jmartin49 indigoviolet redelings stajich azazello EisenLab MBLAB
	Gene prediction with a hidden Markov model and a new intron submodel. [My Copy] Bioinformatics (Oxford, England), Vol. 19 Suppl 2 (October 2003) by Mario Stanke, Stephan Waack posted to genefinding by GustavoLacerda on 2008-11-20 20:53:26 as along with 6 people and 2 groups rshe jmartin49 indigoviolet stajich alexl wenhan EisenLab Mycology
	Mining Genes in DNA Using GeneScout [My Copy] by Michael M. Yin, Jason T. L. Wang posted to genefinding by GustavoLacerda on 2008-11-20 03:47:08 as along with 1 person wenhan
	Applications of generalized pair hidden Markov models to alignment and gene finding problems. [My Copy] J Comput Biol, Vol. 9, No. 2. (2002), pp. 389-399. by L. Pachter, M. Alexandersson, S. Cawley posted to genefinding by GustavoLacerda on 2008-11-20 03:46:20 as along with 2 people and 1 group azazello wenhan MBLAB
	A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao [My Copy] BMC Genomics, Vol. 9, No. 1. (2008) by Jorge Mondego, Marcelo Carazzolle, Gustavo Costa, et al.Eduardo Formighieri, Lucas Parizzi, Johana Rincones, Carolina Cotomacci, Dirce Carraro, Anderson Cunha, Helaine Carrer, Ramon Vidal, Raissa Estrela, Odalys Garcia, Daniela Thomazella, Bruno de Oliveira, Acassia Pires, Maria C. Rio, Marcos R. Araujo, Marcos de Moraes, Luis Castro, Karina Gramacho, Marilda Goncalves, Jose M. Neto, Aristoteles G. Neto, Luciana Barbosa, Mark Guiltinan, Bryan Bailey, Lyndel Meinhardt, Julio Cascardo, Goncalo Pereira posted to lge genomics genome genefinding genefamilies fungi bioinformatics by GustavoLacerda on 2008-11-18 21:16:02 as along with 1 person and 1 group stajich Mycology
	Longer First Introns Are a General Property of Eukaryotic Gene Structure [My Copy] PLoS ONE, Vol. 3, No. 8. (2008), e3093. by Keith R. Bradnam, Ian Korf posted to genefinding by GustavoLacerda on 2008-11-12 03:15:29 as along with 2 people and 1 group stajich bpcusack Mycology
	Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. [My Copy] Genome research (29 August 2008) by Vardges Ter-Hovhannisyan, Alexandre Lomsadze, Yury O O. Chernoff, Mark Borodovsky posted to genefinding by GustavoLacerda on 2008-11-12 03:15:04 as along with 5 people and 1 group kiekyon jmartin49 orzenil stajich bcondon Mycology
	BLogo: A tool for visualization of bias in biological sequences [My Copy] Bioinformatics (4 August 2008), btn407. by Wencheng Li, Bo Yang, Shaoguang Liang, et al.Yonghua Wang, Chris Whiteley, Yicheng Cao, Xiaoning Wang posted to compositionalbias genefinding weblogo by GustavoLacerda on 2008-08-07 17:33:20 as along with 3 people treangen jmeppley grahamc
	Sequences downstream of the start codon and their relations to G + C content and optimal growth temperature in prokaryotic genomes [My Copy] Antonie van Leeuwenhoek, Vol. 92, No. 4. (26 November 2007), pp. 417-427. by Wencheng Li, Huan Zou, Meifeng Tao posted to codon_usage compositionalbias genefinding by GustavoLacerda on 2008-08-07 16:59:07 as
	Genome Annotation in Plants and Fungi: EuGene as a Model Platform [My Copy] Current Bioinformatics, Vol. 3, No. 2. (May 2008), pp. 87-97. by Foissac, Sylvain, Gouzy, et al. 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 3 people and 1 group timflutre jamselem orzenil Centre de Recherches Interdisciplinaires
	Steady progress and recent breakthroughs in the accuracy of automated genome annotation [My Copy] 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 10 people bcondon timflutre druvus guhjy dchughes jermth wenhan renatomilani drbal alexl
	Heuristic approach to deriving models for gene finding. [My Copy] 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 indigoviolet wenhan azazello alexl EisenLab MBLAB
	A practical guide to the art of RNA gene prediction. [My Copy] Briefings in bioinformatics, Vol. 8, No. 6. (4 November 2007), pp. 396-414. by Irmtraud M. Meyer posted to genefinding geneprediction methods rna by tharris on 2008-06-20 17:01:02 as along with 9 people operon NicholasErho thegoose2 zanexu penka wenhan GustavoLacerda xili03 xingxu
	Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. [My Copy] BMC bioinformatics, Vol. 9 (13 June 2008), 278. by O. Keller, F. Odronitz, M. Stanke, M. Kollmar, S. Waack posted to genefinding geneprediction genomics by tharris on 2008-06-20 16:53:40 as along with 5 people thegoose2 natstreet druvus guhjy GustavoLacerda
	Comparative analysis of sequence features involved in the recognition of tandem splice sites [My Copy] BMC Genomics, Vol. 9 (30 April 2008), 202. by Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster, Dirk Holste posted to genefinding splicing by GustavoLacerda on 2008-05-05 17:59:25 as
	Mitochondrial introns: a critical view [My Copy] 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 [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (2004), 187. by James Wasmuth, Mark Blaxter posted to est genefinding by GustavoLacerda on 2008-03-18 17:41:40 as along with 2 people sficklin jameswasmuth
	Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron exon structure [My Copy] Bioinformatics, Vol. 23, No. 12. (15 June 2007), pp. 1468-1475. by Avril Coghlan, Richard Durbin posted to durbingrouppub genefinding by dmc to the group Durbin group on 2008-03-07 13:57:39 as along with 8 people and 2 groups operon thegoose2 jmartin49 tharris druvus indigoviolet stajich GustavoLacerda C. elegans / WormBase EisenLab
	Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. [My Copy] Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050. by A. Siepel, G. Bejerano, J. S. Pedersen, et al.A. S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. W. Hillier, S. Richards, G. M. Weinstock, R. K. Wilson, R. A. Gibbs, W. J. Kent, W. Miller, D. Haussler posted to genefinding by dmc on 2008-03-07 13:41:41 as along with 20 people and 4 groups thegoose2 farhat skembel alessandroparini tharris bpb aprasad balajis eckart_bindewald indigoviolet brant pradiptaray adepace djkt olympos sujaikumar Stew cisevol elfar AlexanderPico C. elegans / WormBase EisenLab cis-regulatory-evolution ConklinLab
	Vertebrate gene finding from multiple-species alignments using a two-level strategy. [My Copy] Genome Biol, Vol. 7 Suppl 1 (2006) by D. Carter, R. Durbin posted to durbingrouppub genefinding by dmc to the group Durbin group on 2008-03-07 12:47:24 as along with 2 people and 1 group indigoviolet dpollard EisenLab
	Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes [My Copy] 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 2 people biomcgary bpcusack
	GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. [My Copy] 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 3 people min013 jmeppley wenhan
	MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes [My Copy] Genome Research, Vol. 18, No. 1. (19 January 2008), pp. 188-196. by Brandi L. Cantarel, Ian Korf, Sofia M. C. Robb, et al.Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell posted to genefinding by GustavoLacerda on 2008-01-23 23:22:03 as along with 10 people nlapalu thegoose2 natstreet Thaverkamp timflutre stajich urgi tharris jamselem orzenil
	Improving gene recognition accuracy by combining predictions from two gene-finding programs [My Copy] Bioinformatics, Vol. 18, No. 8. (1 August 2002), pp. 1034-1045. by Sanja Rogic, Francis B. F. 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 [My Copy] 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 14 people and 1 group buyske mhamada guhjy balicea AbnerCYH stajich cjeans GeeSharpMinor sobolevnrm cabbagezs nklee biehl softsimu jfr baker-group
	Advancing the State of the Art in Computational Gene Prediction [My Copy] 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 along with 1 person rshe
	Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments [My Copy] Genome Biology, Vol. 9 (11 January 2008), R7. by Brian J. Haas, Steven L. Salzberg, Wei Zhu, et al.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 3 people and 1 group druvus stajich mclarenv Mycology
	CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction [My Copy] Genome Biology, Vol. 8, No. 12. (20 December 2007), R269. by Samuel Gross, Chuong Do, Marina Sirota, Serafim Batzoglou posted to genefinding by GustavoLacerda on 2008-01-07 14:51:24 as along with 5 people and 2 groups seb1 talponer dakelley stajich renatomilani EisenLab Mycology
	FlyBase: genes and gene models. [My Copy] Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005) by R. A. Drysdale, M. A. Crosby, posted to genefinding genome by GustavoLacerda on 2007-11-19 18:48:56 as along with 2 people dragonrez nuke2005
	EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 14. (15 July 2007), pp. 1815-1823. by A. Bhasi, R. V. Pandey, S. P. Utharasamy, P. Senapathy posted to genefinding splicing by GustavoLacerda on 2007-10-27 05:48:11 as along with 2 people malcook guhjy
	Characterization and prediction of alternative splice sites [My Copy] 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. [My Copy] Trends Genet, Vol. 23, No. 7. (July 2007), pp. 321-325. by M. Irimia, D. Penny, S. W. 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
	Finding genes in Plasmodium falciparum. [My Copy] Nature, Vol. 404, No. 6773. (2 March 2000) by M. Pertea, S. L. Salzberg, M. J. Gardner posted to computational falciparum genefinding by mdimon on 2007-10-15 21:25:45 as along with 1 person shung
	Automatic generation of gene finders for eukaryotic species [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006) by Kasper Munch, Anders Krogh posted to genefinding by kaspermunch on 2007-09-11 21:21:25 as along with 3 people and 1 group bertelsen GustavoLacerda alexl Bioinformatics
	CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes [My Copy] 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 6 people and 2 groups operon orzenil guhjy indigoviolet stajich wenhan EisenLab Mycology
	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction [My Copy] 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 [My Copy] 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 6 people and 1 group n00c thegoose2 natstreet druvus tharris cjeans C. elegans / WormBase
	Intron length distributions and gene prediction [My Copy] 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 3 people climb0910 cabbagezs Jporci
	Positive selection for unpreferred codon usage in eukaryotic genomes. [My Copy] 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 3 people cazmantis bpcusack Ema

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