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Tag recent_genefinding [101 articles]

Recent papers classified by the tag recent_genefinding.
  • 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 200806_prop recent_genefinding by wenhan on 2008-02-25 20:35:52 as ** along with 1 person GustavoLacerda
  • Applying negative rule mining to improve genome annotation
    BMC Bioinformatics, Vol. 8 (21 July 2007), 261.
    by Irena I Artamonova, Goar Frishman, Dmitrij Frishman
    posted to recent_genefinding by wenhan on 2008-02-25 17:53:26 as ** along with 1 person sgoetz
  • 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 **
  • 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
  • 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
  • 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 recent_genefinding by wenhan on 2008-02-26 22:52:39 as ** along with 1 person GustavoLacerda
  • GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
    Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 497-499.
    by Tiziana Castrignano, Paolo D De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano G Talamo, Graziano Pesole
    posted to recent_genefinding by wenhan on 2008-02-25 19:37:44 as **
  • Identification of Rat Genes by TWINSCAN Gene Prediction, RT-PCR, and Direct Sequencing
    Genome Res., Vol. 14, No. 4. (1 April 2004), pp. 665-671.
    by Jia Q Wu, David Shteynberg, Manimozhiyan Arumugam, Richard A Gibbs, Michael R Brent
    posted to recent_genefinding by wenhan on 2008-02-25 20:25:16 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
  • 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 **
  • 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 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 LeightonP indigoviolet GustavoLacerda cmzmasek alexl EisenLab
  • 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
  • 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
  • A semantic analysis of the annotations of the human genome.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3416-3421.
    by P Khatri, B Done, A Rao, A Done, S Draghici
    posted to recent_genefinding by wenhan on 2008-02-25 20:32:22 as **
  • GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by AG Jegga, J Chen, S Gowrisankar, MA Deshmukh, R Gudivada, S Kong, V Kaimal, BJ Aronow
    posted to recent_genefinding by wenhan on 2008-02-25 20:26:59 as ** along with 2 people and 1 group guhjy bootsy Bioinformatics
  • Simultaneous alignment and annotation of cis-regulatory regions
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e44-e49.
    by Bais, Abha Singh, Grossmann, Steffen, Vingron, Martin
    posted to recent_genefinding by wenhan on 2008-02-25 17:54:41 as **
  • 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 2 people heliopais guhjy
  • A computer program for aligning a cDNA sequence with a genomic DNA sequence.
    Genome Res, Vol. 8, No. 9. (September 1998), pp. 967-974.
    by L Florea, G Hartzell, Z Zhang, GM Rubin, W Miller
    posted to recent_genefinding by wenhan on 2008-02-26 22:45:25 as ** along with 2 people isimpson antonkratz
  • cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome
    BMC Genomics, Vol. 8 (27 July 2007), 255.
    by Fangli Lu, Hongying Jiang, Jinhui Ding, Jianbing Mu, Jesus G Valenzuela, Jose MC Ribeiro, Xin-Zhuan Su
    posted to recent_genefinding by wenhan on 2008-02-25 20:36:46 as ** along with 1 person shung
  • 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
  • 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 11 people and 4 groups druvus guhjy jfr balajis eweaver dchughes cmm raiyar massivemayhem zwang lylu FAB-lab G4ID steinmetzlab Genetics-of-Gambling
  • 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 **
  • Identifying clusters of functionally related genes in genomes.
    Bioinformatics (19 January 2007)
    by Gangman Yi, Sing-Hoi H Sze, Michael R R Thon
    posted to recent_genefinding by wenhan on 2008-02-25 21:44:06 as ** along with 3 people and 1 group grahamc macavity1g zwang ParkinsonLab_at_MaRS
  • SPACER: identification of cis-regulatory elements with non-contiguous critical residues
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031.
    by Chakravarty, Arijit, Carlson, M Jonathan, Khetani, S Radhika, Deziel, E Charles, Gross, H Robert
    posted to recent_genefinding by wenhan on 2008-02-25 19:38:20 as ** along with 1 person csdhwang
  • Reliable prediction of Drosha processing sites improves microRNA gene prediction
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. 142-149.
    by Helvik, A Snorre, Snove, Ola, Saetrom, Pal
    posted to recent_genefinding by wenhan on 2008-02-25 20:24:20 as **
  • A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs.
    PLoS Biol, Vol. 3, No. 5. (19 April 2005)
    by Kyoungha Han, Gene Yeo, Ping An, Christopher B B Burge, Paula J J Grabowski
    posted to recent_genefinding by wenhan on 2008-02-25 20:22:53 as ** along with 1 person setar
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to 200806_prop recent_genefinding by wenhan on 2008-02-26 22:48:59 as ** along with 23 people and 1 group daforerog pwais umit mmartin paszkows operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans natstreet antonkratz yoanjacquemin talponer bozdagd gpappas EisenLab
  • Annotating Noncoding RNA Genes.
    Annu Rev Genomics Hum Genet (21 May 2007)
    by Sam Griffiths-Jones
    posted to recent_genefinding by wenhan on 2008-02-25 20:10:25 as ** along with 1 person guhjy
  • Distributions of exons and introns in the human genome.
    In Silico Biol, Vol. 4, No. 4. (2004), pp. 387-393.
    by MK Sakharkar, VT Chow, P Kangueane
    posted to recent_genefinding by wenhan on 2008-02-26 23:07:05 as **
  • 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 guhjy indigoviolet dchughes zwang cabbagezs nklee ale EisenLab G4ID Genetics-of-Gambling
  • 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
  • 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 **
  • The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
    Bioinformatics, Vol. 23, No. 5. (March 2007), pp. 545-554.
    by Keibler, Evan, Arumugam, Manimozhiyan, Brent, R Michael
    posted to recent_genefinding by wenhan on 2008-02-25 20:28:40 as ** along with 1 person berthoums
  • 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 **
  • A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae
    BMC Biology, Vol. 5 (10 July 2007), 28.
    by Hisayoshi Nozaki, Hiroyoshi Takano, Osami Misumi, Kimihiro Terasawa, Motomichi Matuzaki, Shinichiro Maruyama, Keiji Nishida, Fumi Yagisawa, Yamato Yoshida, Takayuki Fujiwara, Susumu Takio, Katsunori Tamura, Sung J Chung, Soichi Nakamura, Haruko Kuroiwa, Kan Tanaka, Naoki Sato, Tsuneyoshi Kuroiwa
    posted to recent_genefinding by wenhan on 2008-02-26 22:58:25 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 **
  • 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 **
  • Genome sequencing in microfabricated high-density picolitre reactors
    Nature (31 July 2005)
    by Marcel Margulies, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B Dewell, Lei Du, Joseph M Fierro, Xavier V Gomes, Brian C Godwin, Wen He, Scott Helgesen, Chun H Ho, Gerard P Irzyk, Szilveszter C Jando, Maria LI Alenquer, Thomas P Jarvie, Kshama B Jirage, Jong-Bum Kim, James R Knight, Janna R Lanza, John H Leamon, Steven M Lefkowitz, Ming Lei, Jing Li, Kenton L Lohman, Hong Lu, Vinod B Makhijani, Keith E Mcdade, Michael P Mckenna, Eugene W Myers, Elizabeth Nickerson, John R Nobile, Ramona Plant, Bernard P Puc, Michael T Ronan, George T Roth, Gary J Sarkis, Jan F Simons, John W Simpson, Maithreyan Srinivasan, Karrie R Tartaro, Alexander Tomasz, Kari A Vogt, Greg A Volkmer, Shally H Wang, Yong Wang, Michael P Weiner, Pengguang Yu, Richard F Begley, Jonathan M Rothberg
    posted to recent_genefinding by wenhan on 2008-02-26 22:53:59 as ** along with 24 people and 5 groups leechuck bjorns dayjm jmeppley arve RMGraze JAShapiro balajis cdawson AaronDarling treangen usagi-kirin azazello beatrizfernandez xingxu erbon tpreeprem farhat carpi bpb mcox GustavoLacerda jlgreen kieran101 Microbial-Ecology GIG gatech-compgenomics Green Lab iSEEM
  • Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence.
    J Theor Biol, Vol. 247, No. 4. (21 August 2007), pp. 687-694.
    by C Yin, SS Yau
    posted to recent_genefinding by wenhan on 2008-02-25 21:46:02 as **
  • GENCODE: producing a reference annotation for ENCODE
    Genome Biology, Vol. 7, No. Suppl 1. (2006)
    by Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao K Chen, Jacqueline Chrast, Julien Lagarde, James Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos Antonarakis, Roderic Guigo
    posted to recent_genefinding by wenhan on 2008-02-25 20:23:49 as ** along with 1 person olympos
  • 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 **
  • A compression-based approach for coding sequences identification. I. Application to prokaryotic genomes.
    J Comput Biol, Vol. 13, No. 8. (October 2006), pp. 1477-1488.
    by G Menconi, R Marangoni
    posted to recent_genefinding by wenhan on 2008-02-25 20:41:30 as **
  • Gene prediction with a hidden Markov model and a new intron submodel.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by M Stanke, S Waack
    posted to recent_genefinding by wenhan on 2008-02-26 23:15:01 as ** along with 4 people and 2 groups GustavoLacerda indigoviolet stajich alexl EisenLab Berkeley Mycology
  • Reference based annotation with GeneMapper.
    Genome Biol, Vol. 7, No. 4. (5 April 2006)
    by Sourav Chatterji, Lior Pachter
    posted to recent_genefinding by wenhan on 2008-02-25 19:40:01 as ** along with 4 people and 2 groups indigoviolet dpollard penka skumagai EisenLab Nie
  • 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 recent_genefinding by wenhan on 2008-02-26 23:04:12 as ** along with 3 people and 2 groups indigoviolet stajich GustavoLacerda EisenLab Berkeley Mycology
  • Prediction of complete gene structures in human genomic DNA.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 78-94.
    by C Burge, S Karlin
    posted to 200806_prop recent_genefinding by wenhan on 2008-02-26 22:44:07 as ** along with 10 people and 2 groups Ayest pcahan1 indigoviolet kaspermunch dullhunk dquest GustavoLacerda nicholso nklee bandrewfox Bioinformatics EisenLab
  • Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes
    Nucleic Acids Research, Vol. 33, No. 6. (2005), pp. 1935-1939.
    by Robert Castelo, Alexandre Reymond, Carine Wyss, Francisco Camara, Genis Parra, Stylianos E Antonarakis, Roderic Guigo, Eduardo Eyras
    posted to recent_genefinding by wenhan on 2008-02-25 19:36:55 as **
  • 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
  • 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
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