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292 results match your criteria: "The Institute for Genomic Research[Affiliation]"
Nat Genet
July 2020
School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDFCurr Protoc Pharmacol
March 2014
The Institute For Genomic Research, Rockville, Maryland.
Understanding the physiology, pharmacology, and plasticity associated with synaptic function is a key goal of neuroscience research and is fundamental to identifying the processes involved in the development and manifestation of neurological disease. A diverse range of electrophysiological methodologies are used to study synaptic function. Described in this unit is a technique for recording electrical activity from a single component of the central nervous system that is used to investigate pre- and post-synaptic elements of synaptic function.
View Article and Find Full Text PDFMethods Mol Biol
May 2009
The Institute for Genomic Research, Rockville, MD, USA.
Annotation of plant genomic sequences can be separated into structural and functional annotation. Structural annotation is the foundation of all genomics as without accurate gene models understanding gene function or evolution of genes across taxa can be impeded. Structural annotation is dependent on sensitive, specific computational programs and deep experimental evidence to identify gene features within genomic DNA.
View Article and Find Full Text PDFAppl Environ Microbiol
April 2009
The Institute for Genomic Research, Rockville, Maryland 20850, USA.
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi.
View Article and Find Full Text PDFBMC Genomics
December 2008
The Institute for Genomic Research/J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Background: Parasites in the genus Theileria cause lymphoproliferative diseases in cattle, resulting in enormous socio-economic losses. The availability of the genome sequences and annotation for T. parva and T.
View Article and Find Full Text PDFBMC Genomics
November 2008
J. Craig Venter Institute (formerly The Institute for Genomic Research), 9704 Medical Center Dr., Rockville, MD, USA.
Background: Tetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly.
View Article and Find Full Text PDFBiotechnol Bioeng
January 2009
Metabolic Engineering and Systems Biology Laboratory, Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742.
The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures.
View Article and Find Full Text PDFJ Bacteriol
January 2009
The Institute for Genomic Research, Rockville, Maryland 20850, USA.
The pathogenic bacterium Bacillus anthracis has become the subject of intense study as a result of its use in a bioterrorism attack in the United States in September and October 2001. Previous studies suggested that B. anthracis Ames Ancestor, the original Ames fully virulent plasmid-containing isolate, was the ideal reference.
View Article and Find Full Text PDFNature
October 2008
The Institute for Genomic Research/J. Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA.
The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P.
View Article and Find Full Text PDFCurr Protoc Bioinformatics
November 2002
The Institute For Genomic Research, Rockville, Maryland, USA.
GlimmerM is a eukaryotic gene finder that has been used in the annotation of the genomes of Plasmodium falciparum (the malaria parasite), the model plant Arabidopsis thaliana, Oryza sativa (rice), the parasite Theileria parva, and the fungus Aspergillus fumigatus. A unique feature of the system compared to other eukaryotic gene finders is a module that allows users to provide their own data and train GlimmerM for any organism.
View Article and Find Full Text PDFCurr Protoc Bioinformatics
February 2003
The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA.
The MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological sequences. Version 2.1 makes several improvements to the package, including: increased speed and reduced memory requirements; the ability to handle both protein and DNA sequences; the ability to handle multiple sequence fragments; and new algorithms for clustering together basic matches.
View Article and Find Full Text PDFCurr Protoc Bioinformatics
November 2003
The Institute for Genomic Research, Rockville, Maryland, USA.
The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database.
View Article and Find Full Text PDFMethods Mol Biol
June 2008
The Institute for Genomic Research, Rockville, Maryland, USA.
Reproducible procedures for the preparation of protein samples isolated from human urine are essential for meaningful proteomic analyses. Key applications are the discovery of novel proteins or their modifications in the human urine as well as protein biomarker discovery for diseases and drug treatments. The methodology presented here features experimental steps aimed at limiting protein losses because of organic solvent precipitation, effective separation of proteins from other compounds in the human urine and molecular weight-based enrichment of proteins in two distinct fractions.
View Article and Find Full Text PDFMethods Mol Biol
January 2009
The Institute for Genomic Research, Rockville, MD, USA.
With the completion of the genome sequences of the model plants Arabidopsis and rice, and the continuing sequencing efforts of other economically important crop plants, an unprecedented amount of genome sequence data is now available for large-scale genomics studies and analyses, such as the identification and discovery of novel genes, comparative genomics, and functional genomics. Efficient utilization of these large data sets is critically dependent on the ease of access and organization of the data. The plant databases at The Institute for Genomic Research (TIGR) have been set up to maintain various data types including genomic sequence, annotation and analyses, expressed transcript assemblies and analyses, and gene expression profiles from microarray studies.
View Article and Find Full Text PDFBMC Plant Biol
February 2008
The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, MD 20850, USA.
Background: High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. 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.
View Article and Find Full Text PDFGenome Biol
January 2008
J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA.
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
View Article and Find Full Text PDFNucleic Acids Res
January 2008
Pathogen Functional Genomics Resource Center, The Institute for Genomic Research at the J. Craig Venter Institute, Rockville, MD 20850, USA.
DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid high-resolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets.
View Article and Find Full Text PDFBMC Genomics
October 2007
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
Background: Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation.
View Article and Find Full Text PDFPlant Physiol
December 2007
The Institute for Genomic Research and J. Craig Venter Institute, Rockville, Maryland 20850, USA.
Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies.
View Article and Find Full Text PDFMicrobiology (Reading)
October 2007
Department of Microbiology, 203N Morrill Science Center IVN, University of Massachusetts at Amherst, Amherst, MA 01003, USA.
A soluble ferric reductase, SfrAB, which catalysed the NADPH-dependent reduction of chelated Fe(III), was previously purified from the dissimilatory Fe(III)-reducing micro-organism Geobacter sulfurreducens, suggesting that reduction of chelated forms of Fe(III) might be cytoplasmic. However, metabolically active spheroplast suspensions could not catalyse acetate-dependent Fe(III) citrate reduction, indicating that periplasmic and/or outer-membrane components were required for Fe(III) citrate reduction. Furthermore, phenotypic analysis of an SfrAB knockout mutant suggested that SfrAB was involved in acetate metabolism rather than respiration-linked Fe(III) reduction.
View Article and Find Full Text PDFPLoS Genet
August 2007
J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America.
The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci.
View Article and Find Full Text PDFBMC Microbiol
June 2007
The Institute for Genomic Research, J. Craig Venter Institute, Rockville, Maryland, USA.
Background: Bracoviruses (BVs), a group of double-stranded DNA viruses with segmented genomes, are mutualistic endosymbionts of parasitoid wasps. Virus particles are replication deficient and are produced only by female wasps from proviral sequences integrated into the wasp genome. Virus particles are injected along with eggs into caterpillar hosts, where viral gene expression facilitates parasitoid survival and therefore perpetuation of proviral DNA.
View Article and Find Full Text PDFJ Mol Microbiol Biotechnol
September 2007
The Institute for Genomic Research, Rockville, MD 20850, USA.
The recent advancements in genome sequencing make it possible for the comparative analyses of essential cellular processes like transport in organisms across the three domains of life. Membrane transporters play crucial roles in fundamental cellular processes and functions in prokaryotic systems. Between 3 and 16% of open reading frames in prokaryotic genomes were predicted to encode membrane transport proteins, emphasizing the importance of transporters in their lifestyles.
View Article and Find Full Text PDFMicrobiology (Reading)
June 2007
Northern Arizona University, Flagstaff, AZ 86001, USA.
Biofilms, communities of micro-organisms attached to a surface, are responsible for many chronic diseases and are often associated with environmental reservoirs or lifestyles. Bacillus anthracis is a Gram-positive, endospore-forming bacterium and is the aetiological agent of pulmonary, gastrointestinal and cutaneous anthrax. Anthrax infections are part of the natural lifecycle of many ruminants in North America, including cattle and bison, and B.
View Article and Find Full Text PDFNat Biotechnol
May 2007
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe.
View Article and Find Full Text PDF