MARK DOUGLAS contact YANDELL

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. pmc An improved genome release (version Mt4.0) for the model legume Medicago truncatula
    Haibao Tang
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
    BMC Genomics 15:312. 2014
  2. pmc VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix
    Hao Hu
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas, USA
    Genet Epidemiol 37:622-34. 2013
  3. pmc Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct
    Hao Hu
    Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA
    BMC Genomics 13:284. 2012
  4. ncbi request reprint A beginner's guide to eukaryotic genome annotation
    Mark Yandell
    Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah 84112 5330, USA
    Nat Rev Genet 13:329-42. 2012
  5. pmc MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
    Carson Holt
    Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
    BMC Bioinformatics 12:491. 2011
  6. pmc A standard variation file format for human genome sequences
    Martin G Reese
    Omicia, 2200 Powell Street, Suite 525, Emeryville, CA 94608, USA
    Genome Biol 11:R88. 2010
  7. pmc Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    C André Lévesque
    Agriculture and Agri Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
    Genome Biol 11:R73. 2010
  8. pmc Characterization of the Conus bullatus genome and its venom-duct transcriptome
    Hao Hu
    Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA
    BMC Genomics 12:60. 2011
  9. pmc The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
    Allen Kovach
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    BMC Genomics 11:420. 2010
  10. pmc Quantitative measures for the management and comparison of annotated genomes
    Karen Eilbeck
    Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA
    BMC Bioinformatics 10:67. 2009

Collaborators

  • Barry Moore
  • Jinchuan Xing
  • Chad D Huff
  • Chris Mungall
  • Karen Eilbeck
  • Pradip K Bandyopadhyay
  • B M Olivera
  • Hao Hu
  • Carson Holt
  • Martin G Reese
  • Haibao Tang
  • C André Lévesque
  • Allen Kovach
  • Vivek Krishnakumar
  • Heidrun Gundlach
  • Shelby Bidwell
  • David C Schwartz
  • Christopher D Town
  • Benjamin Rosen
  • Klaus F X Mayer
  • Kevin L Childs
  • Agnes Chan
  • Shiguo Zhou
  • Laurent Gentzbittel
  • Steven Flygare
  • Paul D Thomas
  • Laura Grenville-Briggs
  • Sucheta Tripathy
  • Fidel Salas
  • James Hartigan
  • Gordon W Beakes
  • Neil Horner
  • Elodie Gaulin
  • Liliana Cano
  • Pedro M Coutinho
  • Steve Ferriera
  • Lincoln Stein
  • Ned Tisserat
  • Susan I Fuerstenberg
  • Pieter van West
  • Paul Flicek
  • Marco Thines
  • Ian Korf
  • Colin Batchelor
  • Jyoti Shetty
  • Vipaporn Phuntmart
  • John P Hamilton
  • Jason E Stajich
  • Brett R Whitty
  • Edgar Huitema
  • Francine Govers
  • Frank Martin
  • Sophien Kamoun
  • Theerapong Krajaejun
  • Claire M M Gachon
  • Justin Johnson
  • Ronald P de Vries
  • Jill L Wegrzyn
  • Jessica Hostetler
  • Paul Morris
  • Jeffrey L Boore
  • Gregg P Robideau
  • Fiona Cunningham
  • Marcelo M Zerillo
  • Gabor T Marth
  • Bernard Dumas
  • Stephan Wawra
  • Harold J G Meijer
  • Charles H Langley
  • David B Neale
  • Carol A Loopstra
  • Sylvain Raffaele
  • Joe Win
  • Dana Busam
  • Daniela Puiu
  • George E Bruening
  • Henk Brouwer
  • C Robin Buell
  • Rays H Y Jiang
  • Brett M Tyler
  • Genis Parra
  • Haining Lin
  • Bernard Henrissat

Detail Information

Publications12

  1. pmc An improved genome release (version Mt4.0) for the model legume Medicago truncatula
    Haibao Tang
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
    BMC Genomics 15:312. 2014
    ..The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011...
  2. pmc VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix
    Hao Hu
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas, USA
    Genet Epidemiol 37:622-34. 2013
    ..The latter, despite their popularity, have suboptimal performance especially with the increasing case sample size. ..
  3. pmc Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct
    Hao Hu
    Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA
    BMC Genomics 13:284. 2012
    ....
  4. ncbi request reprint A beginner's guide to eukaryotic genome annotation
    Mark Yandell
    Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah 84112 5330, USA
    Nat Rev Genet 13:329-42. 2012
    ..Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches...
  5. pmc MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
    Carson Holt
    Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
    BMC Bioinformatics 12:491. 2011
    ..Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies...
  6. pmc A standard variation file format for human genome sequences
    Martin G Reese
    Omicia, 2200 Powell Street, Suite 525, Emeryville, CA 94608, USA
    Genome Biol 11:R88. 2010
    ....
  7. pmc Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    C André Lévesque
    Agriculture and Agri Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
    Genome Biol 11:R73. 2010
    ..Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species...
  8. pmc Characterization of the Conus bullatus genome and its venom-duct transcriptome
    Hao Hu
    Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA
    BMC Genomics 12:60. 2011
    ..Thus the genomics analyses presented here provide the first step toward a better understanding the enigmatic Textilia clade...
  9. pmc The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
    Allen Kovach
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    BMC Genomics 11:420. 2010
    ..The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda...
  10. pmc Quantitative measures for the management and comparison of annotated genomes
    Karen Eilbeck
    Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA
    BMC Bioinformatics 10:67. 2009
    ....
  11. pmc A probabilistic disease-gene finder for personal genomes
    Mark Yandell
    Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT 84112, USA
    Genome Res 21:1529-42. 2011
    ..Here we demonstrate its ability to identify damaged genes using small cohorts (n = 3) of unrelated individuals, wherein no two share the same deleterious variants, and for common, multigenic diseases using as few as 150 cases...
  12. pmc Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins
    Mark Yandell
    Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, United States of America
    PLoS Comput Biol 4:e1000218. 2008
    ....