Brian J Haas

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. ncbi DAGchainer: a tool for mining segmental genome duplications and synteny
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 20:3643-6. 2004
  2. pmc Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
    Brian J Haas
    The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Biol 3:7. 2005
  3. pmc Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:5654-66. 2003
  4. 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
  5. pmc Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants
    Yong Li Xiao
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Plant Physiol 139:1323-37. 2005
  6. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
  7. pmc Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps
    Christopher A Desjardins
    J Craig Venter Institute, Rockville, MD 20850, USA
    Genome Biol 9:R183. 2008
  8. pmc Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
    Mulu Ayele
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:487-95. 2005
  9. pmc Annotation of the Arabidopsis genome
    Jennifer R Wortman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 132:461-8. 2003
  10. pmc Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
    Robert S Coyne
    J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
    BMC Genomics 9:562. 2008

Detail Information

Publications32

  1. ncbi DAGchainer: a tool for mining segmental genome duplications and synteny
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 20:3643-6. 2004
    ..Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer...
  2. pmc Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
    Brian J Haas
    The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Biol 3:7. 2005
    ..However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications...
  3. pmc Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:5654-66. 2003
    ..The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations...
  4. 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...
  5. pmc Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants
    Yong Li Xiao
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Plant Physiol 139:1323-37. 2005
    ..Thus, by using this targeted approach, high-throughput RACE, we revealed numerous transcripts including many uncharacterized variants from these hypothetical genes...
  6. pmc Characterization of paralogous protein families in rice
    Haining Lin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    BMC Plant Biol 8:18. 2008
    ..This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families...
  7. pmc Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps
    Christopher A Desjardins
    J Craig Venter Institute, Rockville, MD 20850, USA
    Genome Biol 9:R183. 2008
    ....
  8. pmc Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
    Mulu Ayele
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:487-95. 2005
    ..Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated...
  9. pmc Annotation of the Arabidopsis genome
    Jennifer R Wortman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 132:461-8. 2003
  10. pmc Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
    Robert S Coyne
    J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
    BMC Genomics 9:562. 2008
    ....
  11. 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
    ....
  12. pmc Draft genome sequence of the oilseed species Ricinus communis
    Agnes P Chan
    J Craig Venter Institute, Rockville, Maryland, USA
    Nat Biotechnol 28:951-6. 2010
    ..Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage...
  13. pmc Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Brian J Haas
    J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Biol 9:R7. 2008
    ..Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation...
  14. pmc Computational discovery of internal micro-exons
    Natalia Volfovsky
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 13:1216-21. 2003
    ..The algorithm also aids in the discovery of micro-exon-skipping events and cross-species micro-exon conservation...
  15. ncbi Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome
    H Stanley Kim
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant J 41:212-20. 2005
    ....
  16. pmc Full-length messenger RNA sequences greatly improve genome annotation
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 3:RESEARCH0029. 2002
    ..We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism...
  17. pmc Identification and characterization of lineage-specific genes within the Poaceae
    Matthew A Campbell
    The Institute for Genomic Research and J Craig Venter Institute, Rockville, Maryland 20850, USA
    Plant Physiol 145:1311-22. 2007
    ..Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae...
  18. pmc Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
    Jane M Carlton
    Institute for Genomic Research, 9712 Medical Research Drive, Rockville, MD 20850, USA
    Science 315:207-12. 2007
    ..The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria...
  19. pmc Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    Matthew A Campbell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    BMC Genomics 7:327. 2006
    ..Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species...
  20. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...
  21. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  22. ncbi Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
    Julia C Redman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant J 38:545-61. 2004
    ..Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes...
  23. pmc Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus
    Christopher A Desjardins
    The Institute for Genomic Research, J Craig Venter Institute, Rockville, Maryland, USA
    BMC Microbiol 7:61. 2007
    ..Here we describe a 223 kbp region of Glyptapanteles indiensis genomic DNA which contains a part of the G. indiensis bracovirus (GiBV) proviral genome...
  24. ncbi Comparative genomics of trypanosomatid parasitic protozoa
    Najib M El-Sayed
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 309:404-9. 2005
    ..Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont...
  25. ncbi Schistosoma mansoni genome: closing in on a final gene set
    Brian J Haas
    The J C Venter Institute, Rockville, MD 20850, USA
    Exp Parasitol 117:225-8. 2007
    ..mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes...
  26. pmc Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
    Ewen F Kirkness
    J Craig Venter Institute, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 107:12168-73. 2010
    ..Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens...
  27. pmc Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation
    Yingjia Shen
    Department of Botany, Miami University, Oxford, OH 45056, USA
    Nucleic Acids Res 36:3150-61. 2008
    ..Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites...
  28. pmc Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
    Natalie D Fedorova
    The J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Genet 4:e1000046. 2008
    ..The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories"...
  29. 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...
  30. pmc Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa
    Kelly A Brayton
    Program in Genomics, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
    PLoS Pathog 3:1401-13. 2007
    ..The genome sequence provides a greater understanding of B. bovis metabolism and potential avenues for drug therapies and vaccine development...
  31. pmc Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures
    Johnny C Loke
    Department of Botany, Miami University, Oxford, Ohio 45056, USA
    Plant Physiol 138:1457-68. 2005
    ..These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3'-ends for gene annotation...
  32. ncbi Proteome map of the chloroplast lumen of Arabidopsis thaliana
    Maria Schubert
    Department of Medical Nutrition, Karolinska Institute, Novum, Huddinge SE 14186, Sweden
    J Biol Chem 277:8354-65. 2002
    ..As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsis genome and estimated that the thylakoid lumen of the chloroplast contains approximately 80 proteins...