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Group: MBLAB - library [86 articles]

Recent papers posted by members of the MBLAB group
  • Microbial gene identification using interpolated Markov models.
    Nucleic Acids Res, Vol. 26, No. 2. (15 January 1998), pp. 544-548.
    by SL Salzberg, AL Delcher, S Kasif, O White
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-25 21:28:02 as ** along with 5 people ziquje gg bnchakraborty bluto jguinney
  • Titins in C.elegans with unusual features: coiled-coil domains, novel regulation of kinase activity and two new possible elastic regions.
    Journal of molecular biology, Vol. 323, No. 3. (25 October 2002), pp. 533-549.
    by DB Flaherty, KM Gernert, N Shmeleva, X Tang, KB Mercer, M Borodovsky, GM Benian
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-25 16:20:50 as **
  • The gene identification problem: an overview for developers.
    Computers & chemistry, Vol. 20, No. 1. (March 1996), pp. 103-118.
    by JW Fickett
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:45:39 as **
  • Recognition of protein coding regions in DNA sequences.
    Nucleic acids research, Vol. 10, No. 17. (11 September 1982), pp. 5303-5318.
    by JW Fickett
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:45:11 as **
  • Finding genes by computer: the state of the art.
    Trends Genet, Vol. 12, No. 8. (August 1996), pp. 316-320.
    by JW Fickett
  • Gene structure prediction by linguistic methods.
    Genomics, Vol. 23, No. 3. (October 1994), pp. 540-551.
    by S Dong, DB Searls
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:44:07 as **
  • Maximum Likelihood from Incomplete Data via the EM Algorithm
    by AP Dempster, NM Laird, DB Rubin
  • Alignment of whole genomes.
    Nucleic Acids Res, Vol. 27, No. 11. (1 June 1999), pp. 2369-2376.
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:41:27 as ** along with 3 people bozdagd dragonrez yoanjacquemin
  • Effective large-scale sequence similarity searches.
    Methods in enzymology, Vol. 266 (1996), pp. 212-227.
    by JM Claverie
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:40:50 as **
  • Computational methods for the identification of genes in vertebrate genomic sequences.
    Human molecular genetics, Vol. 6, No. 10. (1997), pp. 1735-1744.
    by JM Claverie
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:39:44 as **
  • Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments.
    Journal of molecular biology, Vol. 223, No. 1. (5 January 1992), pp. 159-170.
    by LR Cardon, GD Stormo
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:38:36 as **
  • HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.
    J Mol Biol, Vol. 301, No. 1. (4 August 2000), pp. 173-190.
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:38:03 as ** along with 4 people wouterboomsma j3xucite dgront rabio
  • Evaluation of gene structure prediction programs.
    Genomics, Vol. 34, No. 3. (15 June 1996), pp. 353-367.
    by M Burset, R Guigó
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:37:22 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Finding the genes in genomic DNA.
    Current opinion in structural biology, Vol. 8, No. 3. (June 1998), pp. 346-354.
    by CB Burge, S Karlin
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:32:52 as **
  • Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.
    Nucleic acids research, Vol. 22, No. 22. (11 November 1994), pp. 4756-4767.
    by M Borodovsky, KE Rudd, EV Koonin
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:29:58 as **
  • Using GeneWise in the Drosophila annotation experiment.
    Genome Res, Vol. 10, No. 4. (April 2000), pp. 547-548.
    by E Birney, R Durbin
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:52:25 as **
  • Heuristic approach to deriving models for gene finding.
    Nucleic Acids Res, Vol. 27, No. 19. (1 October 1999), pp. 3911-3920.
  • Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
    Genome Res., Vol. 10, No. 7. (1 July 2000), pp. 950-958.
    by Serafim Batzoglou, Lior Pachter, Jill P Mesirov, Bonnie Berger, Eric S Lander
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:18:35 as ** along with 3 people and 1 group indigoviolet j3xucite treangen EisenLab
  • On the convergence of a clustering algorithm for protein-coding regions in microbial genomes.
    Bioinformatics, Vol. 16, No. 4. (April 2000), pp. 367-371.
    by P Baldi
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:16:51 as ** along with 1 person bioinfo
  • An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.
    The Journal of steroid biochemistry and molecular biology, Vol. 62, No. 1. (May 1997), pp. 29-44.
    by TL Bailey, ME Baker, CP Elkan
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:16:22 as **
  • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    (1994)
    by T Bailey, C Elkan
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:07:00 as **
  • The conserved exon method for gene finding.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 3-12.
    by V Bafna, DH Huson
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 21:08:18 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Self-identification of protein-coding regions in microbial genomes.
    Proc Natl Acad Sci U S A, Vol. 95, No. 17. (18 August 1998), pp. 10026-10031.
    by S Audic, JM Claverie
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 21:07:22 as ** along with 1 person bioinfo
  • Predicting genes expressed via -1 and +1 frameshifts
    Nucl. Acids Res., Vol. 32, No. 16. (15 September 2004), pp. 4884-4892.
    by Sanghoon Moon, Yanga Byun, Hong-Jin Kim, Sunjoo Jeong, Kyungsook Han
    posted to frameshift by azazello to the group MBLAB on 2007-10-16 22:33:38 as ** along with 1 person weaver
  • Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
    Nature Methods, Vol. 4, No. 3. (11 February 2007), pp. 251-256.
    by Mamie Z Li, Stephen J Elledge
    posted to no-tag by azazello to the group MBLAB on 2007-09-18 19:16:29 as ** along with 7 people austin pansapiens bala jyuh dbikard yeastyboy faion
  • 454 sequencing put to the test using the complex genome of barley
    BMC Genomics, Vol. 7 (26 October 2006), 275.
    by Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J Close, Beat Keller, Nils Stein
  • Predicting functionally important residues from sequence conservation
    Bioinformatics (22 May 2007), btm270.
    by John A Capra, Mona Singh
  • Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
    Genome Biol, Vol. 5, No. 9. (2004)
    by Y Liu, PM Harrison, V Kunin, M Gerstein
    posted to no-tag by azazello to the group MBLAB on 2007-05-23 17:33:03 as ** along with 2 people operon alexl
  • Psi-Phi: Exploring the outer limits of bacterial pseudogenes
    Genome Res., Vol. 14, No. 11. (1 November 2004), pp. 2273-2278.
    by Emmanuelle Lerat, Howard Ochman
    posted to no-tag by azazello to the group MBLAB on 2007-04-25 19:07:52 as ** along with 3 people operon AaronDarling alexl
  • Recognizing the pseudogenes in bacterial genomes.
    Nucleic Acids Res, Vol. 33, No. 10. (2005), pp. 3125-3132.
    by E Lerat, H Ochman
    posted to no-tag by azazello to the group MBLAB on 2007-04-25 18:47:51 as ** along with 2 people manzanita alexl
  • Alignments of DNA and protein sequences containing frameshift errors
    Comput. Appl. Biosci., Vol. 12, No. 1. (1 February 1996), pp. 31-40.
    by Xiaojun Guan, Edward C Uberbacher
    posted to no-tag by azazello to the group MBLAB on 2007-03-13 16:05:27 as **
  • PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames
    Nucl. Acids Res., Vol. 24, No. 14. (15 July 1996), pp. 2730-2739.
    by E Birney, Jd Thompson, Tj Gibson
    posted to no-tag by azazello to the group MBLAB on 2007-03-13 15:31:37 as ** along with 1 person alexl
  • Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?
    Genome Biology, Vol. 8 (12 February 2007), R20.
    by Caroline Deshayes, Emmanuel Perrodou, Sebastien Gallien, Daniel Euphrasie, Christine Schaeffer, Alain Van-Dorsselaer, Olivier Poch, Odile Lecompte, Jean-Marc Reyrat
    posted to no-tag by azazello to the group MBLAB on 2007-03-12 20:55:30 as ** along with 2 people alexl nitiniitk
  • Global variation in copy number in the human genome
    Nature, Vol. 444, No. 7118. (23 November 2006), pp. 444-454.
    by Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, Daniel T Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen, Eun K Cho, Stephanie Dallaire, Jennifer L Freeman, Juan R Gonzalez, Monica Gratacos, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R Macdonald, Christian R Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P Carter, Hiroyuki Aburatani, Charles Lee, Keith W Jones, Stephen W Scherer, Matthew E Hurles
  • The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    posted to no-tag by azazello to the group MBLAB on 2007-03-09 15:44:10 as ** along with 7 people jyuh tvdbulck dragonrez jfr balajis hpiwowar ghattem
  • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
    (1998)
    by Richard Durbin, Sean R Eddy, Anders Krogh, Graeme Mitchison
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 17:01:26 as **
  • Problems and Solutions in Biological Sequence Analysis
    (2006)
    by Mark Borodovsky, Svetlana Ekisheva
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:58:32 as **
  • Codon usage between genomes is constrained by genome-wide mutational processes
    PNAS, Vol. 101, No. 10. (9 March 2004), pp. 3480-3485.
    by Swaine L Chen, William Lee, Alison K Hottes, Lucy Shapiro, Harley H Mcadams
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:48:28 as ** along with 2 people operon wenhan
  • Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract.
    Appl Environ Microbiol, Vol. 73, No. 4. (February 2007), pp. 1388-1392.
    by ES Klaassens, WM de Vos, EE Vaughan
  • ARACHNE: A Whole-Genome Shotgun Assembler
    Genome Res., Vol. 12, No. 1. (1 January 2002), pp. 177-189.
    by Serafim Batzoglou, David B Jaffe, Ken Stanley, Jonathan Butler, Sante Gnerre, Evan Mauceli, Bonnie Berger, Jill P Mesirov, Eric S Lander
  • Heterogeneous genomic molecular clocks in primates
    PLoS Genetics, Vol. preprint, No. 2006. (1 August 2006), e163.eor.
    by Seong-Ho Kim, Navin Elango, Charles Warden, Eric Vigoda, Soojin Yi
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:30:47 as **
  • Heterogeneous Genomic Molecular Clocks in Primates
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:28:49 as **
  • Community structure and metabolism through reconstruction of microbial genomes from the environment
    Nature, Vol. 428, No. 6978. (4 March 2004), pp. 37-43.
    by Gene W Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E Allen, Rachna J Ram, Paul M Richardson, Victor V Solovyev, Edward M Rubin, Daniel S Rokhsar, Jillian F Banfield
  • GISMO--gene identification using a support vector machine for ORF classification.
    Nucleic Acids Res, Vol. 35, No. 2. (2007), pp. 540-549.
    by L Krause, AC McHardy, TW Nattkemper, A Pühler, J Stoye, F Meyer
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:38:36 as ** along with 1 person wenhan
  • Detection of short protein coding regions within the cyanobacterium genome: application of the hidden Markov model.
    DNA Res, Vol. 3, No. 6. (31 December 1996), pp. 355-361.
    by T Yada, M Hirosawa
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:37:33 as ** along with 1 person wenhan
  • YACOP: Enhanced gene prediction obtained by a combination of existing methods.
    In Silico Biol, Vol. 3, No. 4. (2003), pp. 441-451.
    by M Tech, R Merkl
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:36:31 as ** along with 1 person wenhan
  • Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
    BMC Bioinformatics, Vol. 5 (5 March 2004)
    by S Mahony, JO McInerney, TJ Smith, A Golden
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:35:37 as ** along with 1 person wenhan
  • Development of joint application strategies for two microbial gene finders.
    Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1622-1631.
    by AC McHardy, A Goesmann, A Pühler, F Meyer
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:34:42 as ** along with 1 person wenhan
  • Dictionary-driven prokaryotic gene finding.
    Nucleic Acids Res, Vol. 30, No. 12. (15 June 2002), pp. 2710-2725.
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 03:33:21 as ** along with 1 person wenhan
  • Identifying bacterial genes and endosymbiont DNA with Glimmer.
    Bioinformatics (19 January 2007)
    by Arthur L L Delcher, Kirsten A A Bratke, Edwin C C Powers, Steven L L Salzberg
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 00:04:24 as ** along with 1 person wenhan
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