MARK DOUGLAS contact YANDELL

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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 Grants

  1. Software for the creation and quality control of genome annotations
    MARK DOUGLAS YANDELL; Fiscal Year: 2010
  2. Whole genome screen for novel regulators of tissue homeostasis and regeneration
    MARK DOUGLAS contact YANDELL; Fiscal Year: 2010

Collaborators

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

Detail Information

Publications10

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

  1. Software for the creation and quality control of genome annotations
    MARK DOUGLAS YANDELL; Fiscal Year: 2010
    ....
  2. Whole genome screen for novel regulators of tissue homeostasis and regeneration
    MARK DOUGLAS contact YANDELL; Fiscal Year: 2010
    ....