Foo Cheung

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
    M A Rouf Mian
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73402, USA
    BMC Plant Biol 8:27. 2008
  2. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
  3. pmc Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    Foo Cheung
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 7:272. 2006
  4. pmc A BAC end view of the Musa acuminata genome
    Foo Cheung
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Plant Biol 7:29. 2007
  5. ncbi request reprint TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
  6. pmc Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
    Christopher D Town
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Cell 18:1348-59. 2006
  7. pmc The institute for genomic research Osa1 rice genome annotation database
    Qiaoping Yuan
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 138:18-26. 2005
  8. pmc The TIGR Plant Transcript Assemblies database
    Kevin L Childs
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D846-51. 2007
  9. pmc The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
    Qiaoping Yuan
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Nucleic Acids Res 31:229-33. 2003
  10. pmc The TIGR Maize Database
    Agnes P Chan
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 34:D771-6. 2006

Collaborators

Detail Information

Publications24

  1. pmc Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
    M A Rouf Mian
    Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73402, USA
    BMC Plant Biol 8:27. 2008
    ..The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported...
  2. pmc Spotted cotton oligonucleotide microarrays for gene expression analysis
    Joshua A Udall
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA
    BMC Genomics 8:81. 2007
    ..Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species...
  3. pmc Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    Foo Cheung
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Genomics 7:272. 2006
    ....
  4. pmc A BAC end view of the Musa acuminata genome
    Foo Cheung
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Plant Biol 7:29. 2007
    ..Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the Musa acuminata genome in a cost effective and efficient manner...
  5. ncbi request reprint TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  6. pmc Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
    Christopher D Town
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Cell 18:1348-59. 2006
    ..We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes...
  7. pmc The institute for genomic research Osa1 rice genome annotation database
    Qiaoping Yuan
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 138:18-26. 2005
    ..To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org...
  8. pmc The TIGR Plant Transcript Assemblies database
    Kevin L Childs
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D846-51. 2007
    ..Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species...
  9. pmc The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
    Qiaoping Yuan
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Nucleic Acids Res 31:229-33. 2003
    ..All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System...
  10. pmc The TIGR Maize Database
    Agnes P Chan
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 34:D771-6. 2006
    ..All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads...
  11. pmc Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray
    Heenam Kim
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Res 13:327-40. 2003
    ..Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region...
  12. pmc Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence
    Foo Cheung
    The J Craig Venter Institute, Rockville, Maryland 20850, USA
    Plant Cell 21:1912-28. 2009
    ....
  13. pmc Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)
    Yuandan Lee
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 12:493-502. 2002
    ..TOGA provides an important new resource for the analysis of gene function in eukaryotes. In addition, an analysis of the most widely represented sequences can begin to provide insight into eukaryotic biological processes...
  14. ncbi request reprint Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice
    Jernej Jakse
    Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
    Theor Appl Genet 114:31-9. 2006
    ....
  15. pmc A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales
    Joseph C Kuhl
    Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
    Plant Cell 16:114-25. 2004
    ..The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics...
  16. pmc Sequencing and analysis of the gene-rich space of cowpea
    Michael P Timko
    Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
    BMC Genomics 9:103. 2008
    ..With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing...
  17. pmc Insights into the Musa genome: syntenic relationships to rice and between Musa species
    Magali Lescot
    French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40 03, FR 34398, Montpellier, Cedex 5, France
    BMC Genomics 9:58. 2008
    ..Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome...
  18. pmc Databases and information integration for the Medicago truncatula genome and transcriptome
    Steven B Cannon
    Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA
    Plant Physiol 138:38-46. 2005
    ..ucdavis.edu, and genome viewers at the University of Oklahoma (www.genome.ou.edu), the Institute for Genomic Research (www.tigr.org), and Munich Information for Protein Sequences Center (mips.gsf.de)...
  19. ncbi request reprint Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.)
    Melanie Febrer
    Teagasc, Crops Research Centre, Oak Park, Carlow, Ireland
    Genome 50:412-21. 2007
    ..The results suggest that a large-scale BAC-end sequencing strategy has the potential to anchor a significant proportion of the genome of white clover onto the gene-space sequence of M. truncatula...
  20. ncbi request reprint Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides
    Daren W Brown
    Mycotoxin Research Unit, U S Department of Agriculture ARS, Peoria, IL 61604, USA
    Fungal Genet Biol 42:848-61. 2005
    ..Finally, analysis of an EST that aligns to genomic sequence between FUM12 and FUM13 provided evidence for a previously unidentified gene (FUM20) in the FUM gene cluster...
  21. ncbi request reprint Comparative genomic analyses in Asparagus
    Joseph C Kuhl
    Department of Horticulture, Michigan State University, East Lansing 48824, USA
    Genome 48:1052-60. 2005
    ..officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales...
  22. pmc Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
    Steven B Cannon
    Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 103:14959-64. 2006
    ..Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar)...
  23. ncbi request reprint Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots
    Jinyuan Liu
    Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY14853, USA
    Plant J 50:529-44. 2007
    ..Thus, the symbiosis is accompanied by a complex pattern of local and systemic changes in gene expression, including the induction of a functional defense response...
  24. ncbi request reprint Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton
    S Samuel Yang
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843, USA
    Plant J 47:761-75. 2006
    ..These results suggest general roles for genome-specific, phytohormonal and transcriptional gene regulation during the early stages of fiber cell development in cotton allopolyploids...