Research Topics
Species | Brian J HaasSummaryAffiliation: The Institute for Genomic Research Country: USA Publications
| Collaborators
|
Detail Information
Publications
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final releaseBrian 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...- Improving the Arabidopsis genome annotation using maximal transcript alignment assembliesBrian 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... - DAGchainer: a tool for mining segmental genome duplications and syntenyBrian 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... - Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidyChristopher 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... - Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in ArabidopsisMulu 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... - Comparative genomics of mutualistic viruses of Glyptapanteles parasitic waspsChristopher A Desjardins
J Craig Venter Institute, Rockville, MD 20850, USA
Genome Biol 9:R183. 2008.... - Characterization of paralogous protein families in riceHaining 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... - Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variantsYong 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... - Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technologyFoo Cheung
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
BMC Genomics 7:272. 2006.... - Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closureRobert S Coyne
J Craig Venter Institute formerly The Institute for Genomic Research, 9704 Medical Center Dr, Rockville, MD, USA
BMC Genomics 9:562. 2008.... - Draft genome sequence of the oilseed species Ricinus communisAgnes 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... - Annotation of the Arabidopsis genomeJennifer R Wortman
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Plant Physiol 132:461-8. 2003 - Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsBrian 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... - Computational discovery of internal micro-exonsNatalia 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... - Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genomeH Stanley Kim
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Plant J 41:212-20. 2005.... - Identification and characterization of lineage-specific genes within the PoaceaeMatthew 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... - Full-length messenger RNA sequences greatly improve genome annotationBrian 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... - Comprehensive analysis of alternative splicing in rice and comparative analyses with ArabidopsisMatthew 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... - Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryoteJonathan 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... - Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirusChristopher 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... - Development and evaluation of an Arabidopsis whole genome Affymetrix probe arrayJulia 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... - The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformansBrendan 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... - Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalisJane 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... - Comparative genomics of trypanosomatid parasitic protozoaNajib 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... - Schistosoma mansoni genome: closing in on a final gene setBrian 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... - Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyleEwen 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... - Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoaKelly 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... - Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatusNatalie D Fedorova
The J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS Genet 4:e1000046. 2008.... - Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylationYingjia 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... - Insights into the Musa genome: syntenic relationships to rice and between Musa speciesMagali 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... - Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structuresJohnny 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... - Proteome map of the chloroplast lumen of Arabidopsis thalianaMaria 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...