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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
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:44:42 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • 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
    posted to 200806_prop by wenhan to the group MBLAB on 2008-06-24 23:43:28 as ** along with 43 people and 7 groups iansimon qwermish eegilbert weymouth jake ingo anoopsarkar gangli rpadams wkw hoangmtbk dragonrez Freyr lukec dheena songhaoyuan amirsaemi j3xucite ecome walkking nandan marrtin tvdbulck MichaelDonoser MikeDoni rwilliamson calamar qq987 ichbins81 petrposik ggorjan shiquanwang lcigler ciga kvorg ifejobi DavidSchulz ykuoka singhsh trop_wizz eddymier schulz stkhu Statistics_and_Social_Science tulip LTN Computer_Graphics Computational_Information_Geometry csb_journal_club_public Medical Image Analysis and Visualization @ OSU
  • Alignment of whole genomes.
    Nucleic Acids Res, Vol. 27, No. 11. (1 June 1999), pp. 2369-2376.
    by AL Delcher, S Kasif, RD Fleischmann, J Peterson, O White, SL Salzberg
    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.
    by C Bystroff, V Thorsson, D Baker
    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.
    by J Besemer, M Borodovsky
    posted to metagenomics_0208 200806_prop by wenhan to the group MBLAB on 2008-06-24 22:50:22 as ** along with 4 people and 1 group GustavoLacerda alexl azazello indigoviolet EisenLab
  • 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
    posted to no-tag by azazello to the group MBLAB on 2007-09-13 17:46:17 as ** along with 5 people and 2 groups jmeppley balicea ghattem cisevol tpreeprem BergmanLab gatech-compgenomics
  • Predicting functionally important residues from sequence conservation
    Bioinformatics (22 May 2007), btm270.
    by John A Capra, Mona Singh
    posted to no-tag by azazello to the group MBLAB on 2007-05-24 17:30:13 as ** along with 7 people and 1 group dgront grahamc zwang cabbagezs Jporci niallhaslam santiago ParkinsonLab_at_MaRS
  • 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
    posted to no-tag by azazello to the group MBLAB on 2007-03-09 15:45:39 as ** along with 25 people and 5 groups pradiptaray daed Ema srp33 bpb jfr balajis dpollard mtagaya adepace aswin rdiaz qfwills ealloza vplagnol giovanni jeremymiller frohike vpschulz raiyar ramensky ccr dbgrant colinveal xingxu Bioinformatics EisenLab BioinfoCIPF GeschwindLab steinmetzlab
  • 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)
    by J Demeter, C Beauheim, J Gollub, T Hernandez-Boussard, H Jin, D Maier, JC Matese, M Nitzberg, F Wymore, ZK Zachariah, PO Brown, G Sherlock, CA Ball
    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
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:47:50 as ** along with 6 people and 2 groups mcox dchughes michC wenhan nitiniitk barberan G4ID Genetics-of-Gambling
  • 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
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 16:38:29 as ** along with 10 people and 2 groups pradiptaray Neeperando bpb dayjm balajis indigoviolet balicea ccr wenhan tpreeprem EisenLab gatech-compgenomics
  • 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
    posted to no-tag by azazello to the group MBLAB on 2007-03-08 14:45:59 as ** along with 7 people and 1 group balajis eweaver michC mabedin beatrizfernandez niallhaslam rvgomes Microbial-Ecology
  • 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.
    by T Shibuya, I Rigoutsos
    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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