MARK DOUGLAS contact YANDELL

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. 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
  2. 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
  3. doi 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

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
  • C André Lévesque
  • Allen Kovach
  • Steven Flygare
  • Brett R Whitty
  • Dana Busam
  • Gabor T Marth
  • Stephan Wawra
  • Fiona Cunningham
  • Harold J G Meijer
  • James Hartigan
  • Haining Lin
  • Paul Morris
  • Steve Ferriera
  • Claire M M Gachon
  • Gordon W Beakes
  • Jessica Hostetler
  • Bernard Dumas
  • Marcelo M Zerillo
  • Carol A Loopstra
  • Jill L Wegrzyn
  • C Robin Buell
  • Paul Flicek
  • Charles H Langley
  • Elodie Gaulin
  • Pedro M Coutinho
  • Susan I Fuerstenberg
  • Neil Horner
  • Jyoti Shetty
  • Genis Parra
  • Ned Tisserat
  • Frank Martin
  • Ian Korf
  • Jeffrey L Boore
  • David B Neale
  • Fidel Salas
  • Francine Govers
  • Colin Batchelor
  • Liliana Cano
  • Edgar Huitema
  • Paul D Thomas
  • Ronald P de Vries
  • Rays H Y Jiang
  • Daniela Puiu
  • Sylvain Raffaele
  • Laura Grenville-Briggs
  • Marco Thines
  • Justin Johnson
  • Sucheta Tripathy
  • John P Hamilton
  • Sophien Kamoun
  • Gregg P Robideau
  • Bernard Henrissat
  • Pieter van West
  • Lincoln Stein
  • Vipaporn Phuntmart
  • Joe Win
  • Henk Brouwer
  • George E Bruening
  • Jason E Stajich
  • Brett M Tyler
  • Theerapong Krajaejun

Detail Information

Publications11

  1. 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. ..
  2. 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
    ....
  3. doi 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...
  4. 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...
  5. 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
    ....
  6. 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. 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
    ....

Research Grants4