Doreen Ware

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. ncbi request reprint Comparison of genes among cereals
    Doreen Ware
    Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Curr Opin Plant Biol 6:121-7. 2003
  2. pmc Panzea: an update on new content and features
    Payan Canaran
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D1041-3. 2008
  3. pmc Gramene: a growing plant comparative genomics resource
    Chengzhi Liang
    Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D947-53. 2008
  4. pmc Evidence-based gene predictions in plant genomes
    Chengzhi Liang
    Cold Spring Harbor Laboratory, New York 11724, USA
    Genome Res 19:1912-23. 2009
  5. ncbi request reprint Gramene
    Doreen Ware
    Gramene, Cold Spring Harbor, NY, USA
    Methods Mol Biol 406:315-29. 2007
  6. pmc The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
    Shulamit Avraham
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D449-54. 2008
  7. pmc Gramene database in 2010: updates and extensions
    Ken Youens-Clark
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 39:D1085-94. 2011
  8. pmc Gramene 2013: comparative plant genomics resources
    Marcela K Monaco
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil and Nutrition Laboratory Research Unit, USDA ARS, Ithaca, NY 14853, USA
    Nucleic Acids Res 42:D1193-9. 2014
  9. pmc GrameneMart: the BioMart data portal for the Gramene project
    William Spooner
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Database (Oxford) 2012:bar056. 2012
  10. ncbi request reprint Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
    Payan Canaran
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 22:885-6. 2006

Collaborators

Detail Information

Publications29

  1. ncbi request reprint Comparison of genes among cereals
    Doreen Ware
    Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Curr Opin Plant Biol 6:121-7. 2003
    ..Preliminary evidence from limited comparative analysis of sequenced orthologous genomic segments suggests that local gene amplification and translocation within a plant genome may be linked in some cases...
  2. pmc Panzea: an update on new content and features
    Payan Canaran
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D1041-3. 2008
    ..We have enhanced our existing code base and have made our new tools available. Finally, we have also made available new informational sections as part of our educational and outreach efforts...
  3. pmc Gramene: a growing plant comparative genomics resource
    Chengzhi Liang
    Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D947-53. 2008
    ....
  4. pmc Evidence-based gene predictions in plant genomes
    Chengzhi Liang
    Cold Spring Harbor Laboratory, New York 11724, USA
    Genome Res 19:1912-23. 2009
    ..We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and discuss potential application of the pipeline to other genomes...
  5. ncbi request reprint Gramene
    Doreen Ware
    Gramene, Cold Spring Harbor, NY, USA
    Methods Mol Biol 406:315-29. 2007
    ....
  6. pmc The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
    Shulamit Avraham
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 36:D449-54. 2008
    ..In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement...
  7. pmc Gramene database in 2010: updates and extensions
    Ken Youens-Clark
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 39:D1085-94. 2011
    ..Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data...
  8. pmc Gramene 2013: comparative plant genomics resources
    Marcela K Monaco
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil and Nutrition Laboratory Research Unit, USDA ARS, Ithaca, NY 14853, USA
    Nucleic Acids Res 42:D1193-9. 2014
    ..The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology. ..
  9. pmc GrameneMart: the BioMart data portal for the Gramene project
    William Spooner
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Database (Oxford) 2012:bar056. 2012
    ..DATABASE URL: http://www.gramene.org/biomart/martview...
  10. ncbi request reprint Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
    Payan Canaran
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 22:885-6. 2006
    ..panzea.org/software/alignment_viewer.html). CONTACT: ware@cshl.edu SUPPLEMENTARY INFORMATION: The Supplementary information includes sample lists of multiple sequence alignment software and sample screenshots of the viewer...
  11. pmc Panzea: a database and resource for molecular and functional diversity in the maize genome
    Wei Zhao
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 34:D752-7. 2006
    ....
  12. doi request reprint Maize HapMap2 identifies extant variation from a genome in flux
    Jer Ming Chia
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Genet 44:803-7. 2012
    ..There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize...
  13. pmc Digital gene expression signatures for maize development
    Andrea L Eveland
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Plant Physiol 154:1024-39. 2010
    ..Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene...
  14. pmc CMap 1.01: a comparative mapping application for the Internet
    Ken Youens-Clark
    Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 25:3040-2. 2009
    ..CMap is freely available, can run on a variety of database engines and uses only free and open software components...
  15. pmc A genome-wide characterization of microRNA genes in maize
    Lifang Zhang
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Genet 5:e1000716. 2009
    ..As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes...
  16. pmc Ensembl Genomes 2013: scaling up access to genome-wide data
    Paul Julian Kersey
    The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA and USDA ARS, Cornell University, Ithaca, NY, 14853, USA
    Nucleic Acids Res 42:D546-52. 2014
    ....
  17. pmc Regulatory modules controlling maize inflorescence architecture
    Andrea L Eveland
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 24:431-43. 2014
    ....
  18. pmc Gramene: a resource for comparative grass genomics
    Doreen Ware
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 30:103-5. 2002
    ..This paper describes the initial steps we have taken towards realizing these goals...
  19. pmc Evolution of Arabidopsis microRNA families through duplication events
    Christopher Maher
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 16:510-9. 2006
    ....
  20. ncbi request reprint Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3
    Derrick J Zwickl
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and Robert W Holley Center for Agriculture and Health, United States Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, USA
    Syst Biol 63:645-59. 2014
    ..sativa. [gene trees; multilocus data; Oryza; phylogenomics; phylogeny reconstruction; species trees.]. ..
  21. pmc The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
    Michael Regulski
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 23:1651-62. 2013
    ..The methylation map will provide an invaluable resource for epigenetic studies in maize. ..
  22. pmc Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots
    Sunita Kumari
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS ONE 8:e79011. 2013
    ..This study will be useful for future work related to genome annotation projects and can inspire research efforts aimed to better understand regulatory mechanisms of transcription. ..
  23. pmc Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)
    Cheng Lu
    Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Proc Natl Acad Sci U S A 105:4951-6. 2008
    ..These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes...
  24. ncbi request reprint Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)
    Susan R McCouch
    Plant Breeding Dept, Cornell University, Ithaca, NY 14853 1901, USA
    DNA Res 9:199-207. 2002
    ..In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb...
  25. ncbi request reprint Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement)
    Susan R McCouch
    Plant Breeding Dept, Cornell University, Ithaca, NY 14853 1901, USA
    DNA Res 9:257-79. 2002
  26. ncbi request reprint Maintaining collections of mutants for plant functional genomics
    Randy Scholl
    Department of Plant Biology, The Ohio State University, Columbus, OH, USA
    Methods Mol Biol 236:311-26. 2003
    ..Hence, locating and obtaining materials is rapid and simple. Currently, available genomic resources are described, and references, links for Web data, and ordering information are also included...
  27. pmc Gramene: a bird's eye view of cereal genomes
    Pankaj Jaiswal
    Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
    Nucleic Acids Res 34:D717-23. 2006
    ..Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication...
  28. pmc Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
    Barbara L Hass-Jacobus
    Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
    BMC Genomics 7:199. 2006
    ..Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago...
  29. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran Kim
    Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Genome Biol 9:R45. 2008
    ..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...