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wenhan's library [218 articles]

Recent papers added to wenhan's library.
  • 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 rdp by wenhan on 2008-04-09 17:16:03 as ** along with 1 person balajis
  • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
    Applied and environmental microbiology, Vol. 73, No. 16. (August 2007), pp. 5261-5267.
    by Q Wang, GM Garrity, JM Tiedje, JR Cole
    posted to rdp by wenhan on 2008-04-09 17:11:26 as ** along with 1 person Olaf_Ilzins
  • Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.
    Proc Natl Acad Sci U S A, Vol. 101, No. 39. (28 September 2004), pp. 14240-14245.
    by MT Holden, RW Titball, SJ Peacock, AM Cerdeño-Tárraga, T Atkins, LC Crossman, T Pitt, C Churcher, K Mungall, SD Bentley, M Sebaihia, NR Thomson, N Bason, IR Beacham, K Brooks, KA Brown, NF Brown, GL Challis, I Cherevach, T Chillingworth, A Cronin, B Crossett, P Davis, D DeShazer, T Feltwell, A Fraser, Z Hance, H Hauser, S Holroyd, K Jagels, KE Keith, M Maddison, S Moule, C Price, MA Quail, E Rabbinowitsch, K Rutherford, M Sanders, M Simmonds, S Songsivilai, K Stevens, S Tumapa, M Vesaratchavest, S Whitehead, C Yeats, BG Barrell, PC Oyston, J Parkhill
    posted to genome_problematic by wenhan on 2008-03-12 21:31:14 as ** along with 2 people manzanita jenni_p
  • Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.
    Nature, Vol. 407, No. 6800. (7 September 2000), pp. 81-86.
    by S Shigenobu, H Watanabe, M Hattori, Y Sakaki, H Ishikawa
    posted to genome_problematic by wenhan on 2008-03-12 20:00:17 as ** along with 1 person operon
  • 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
  • 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
  • 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 3 people and 2 groups indigoviolet stajich alexl EisenLab Berkeley Mycology
  • Codon preference and its use in identifying protein coding regions in long DNA sequences.
    Nucleic Acids Res, Vol. 10, No. 1. (11 January 1982), pp. 141-156.
    by R Staden, AD McLachlan
    posted to recent_genefinding by wenhan on 2008-02-26 23:11:12 as **
  • Automated generation of heuristics for biological sequence comparison
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Guy Slater, Ewan Birney
    posted to recent_genefinding by wenhan on 2008-02-26 23:09:32 as ** along with 4 people and 1 group indigoviolet massivemayhem hpaces marti EisenLab
  • 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 **
  • 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
  • Comparative gene prediction in human and mouse.
    Genome Res, Vol. 13, No. 1. (January 2003), pp. 108-117.
    by G Parra, P Agarwal, JF Abril, T Wiehe, JW Fickett, R Guigó
    posted to recent_genefinding by wenhan on 2008-02-26 23:03:10 as ** along with 2 people and 2 groups indigoviolet azazello EisenLab MBLAB
  • GeneID in Drosophila
    Genome Res., Vol. 10, No. 4. (1 April 2000), pp. 511-515.
    by Genis Parra, Enrique Blanco, Roderic Guigo
    posted to recent_genefinding by wenhan on 2008-02-26 23:02:03 as ** along with 1 person and 1 group indigoviolet EisenLab
  • 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 **
  • 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 18 people and 3 groups bpb carpi bjorns dayjm jmeppley arve RMGraze JAShapiro balajis cdawson AaronDarling treangen usagi-kirin azazello beatrizfernandez xingxu erbon tpreeprem Microbial-Ecology GIG gatech-compgenomics
  • 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
  • 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 4 people and 1 group LeightonP indigoviolet GustavoLacerda cmzmasek EisenLab
  • 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
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to recent_genefinding by wenhan on 2008-02-26 22:48:59 as ** along with 17 people and 1 group talponer operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans natstreet antonkratz inesdesantiago yoanjacquemin EisenLab
  • 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
  • Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
    Nucleic Acids Res, Vol. 31, No. 19. (1 October 2003), pp. 5654-5666.
    by BJ Haas, AL Delcher, SM Mount, JR Wortman, RK Smith, LI Hannick, R Maiti, CM Ronning, DB Rusch, CD Town, SL Salzberg, O White
    posted to recent_genefinding by wenhan on 2008-02-26 22:47:00 as ** along with 1 person jwortman
  • 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 1 person antonkratz
  • 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 recent_genefinding by wenhan on 2008-02-26 22:44:07 as ** along with 8 people and 2 groups nklee pcahan1 indigoviolet kaspermunch dullhunk dquest GustavoLacerda nicholso Bioinformatics EisenLab
  • 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 5 people jyuh dchughes jermth renatomilani drbal
  • 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 **
  • 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 3 people and 2 groups 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 39 people and 5 groups 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
  • 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
  • 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 1 person and 1 group indigoviolet EisenLab
  • AceView: a comprehensive cDNA-supported gene and transcripts annotation.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by D Thierry-Mieg, J Thierry-Mieg
    posted to recent_genefinding by wenhan on 2008-02-25 23:40:53 as ** along with 2 people and 1 group jyuh jandot Bioinformatics
  • AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by M Stanke, A Tzvetkova, B Morgenstern
    posted to recent_genefinding by wenhan on 2008-02-25 23:26:50 as ** along with 1 group Bioinformatics
  • AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by M Stanke, B Morgenstern
    posted to recent_genefinding by wenhan on 2008-02-25 23:25:00 as **
  • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Mario Stanke, Oliver Schoffmann, Burkhard Morgenstern, Stephan Waack
    posted to recent_genefinding by wenhan on 2008-02-25 23:24:03 as ** along with 2 people and 1 group azazello GustavoLacerda MBLAB
  • AUGUSTUS: ab initio prediction of alternative transcripts.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by M Stanke, O Keller, I Gunduz, A Hayes, S Waack, B Morgenstern
    posted to recent_genefinding by wenhan on 2008-02-25 23:23:11 as **
  • 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 **
  • 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
  • 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
  • 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
  • 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
  • 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 **
  • 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
  • Evaluation of five ab initio gene prediction programs for the discovery of maize genes.
    Plant Mol Biol, Vol. 57, No. 3. (February 2005), pp. 445-460.
    by H Yao, L Guo, Y Fu, LA Borsuk, TJ Wen, DS Skibbe, X Cui, BE Scheffler, J Cao, SJ Emrich, DA Ashlock, PS Schnable
    posted to recent_genefinding by wenhan on 2008-02-25 21:42:58 as **
  • Using ESTs to improve the accuracy of de novogene prediction
    BMC Bioinformatics, Vol. 7 (03 July 2006), 327.
    by Chaochun Wei, Michael R Brent
    posted to recent_genefinding by wenhan on 2008-02-25 21:40:28 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
  • 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 **
  • Integrating information from existing databases for enhanced function annotation of genes, genomes and networks
    Bioinformation, Vol. 2, No. 4. (2007), pp. 132-134.
    by Bioinformation L Tripathi
    posted to recent_genefinding by wenhan on 2008-02-25 21:36:12 as **
  • Improving gene annotation using peptide mass spectrometry
    Genome Res., Vol. 17, No. 2. (1 February 2007), pp. 231-239.
    by Stephen Tanner, Zhouxin Shen, Julio Ng, Liliana Florea, Roderic Guigo, Steven P Briggs, Vineet Bafna
    posted to recent_genefinding by wenhan on 2008-02-25 21:26:49 as ** along with 2 people and 1 group brant nedwards EisenLab
  • 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 **
  • 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
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