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Meet Richard Scheuermann, Ph.D., JCVI’s Director of Bioinformatics
Richard H. Scheuermann, Ph.D., who joined JCVI in 2012 from the University of Texas Southwestern as the Director of Bioinformatics, is an accomplished researcher and educator. He and his team apply their deep knowledge in molecular immunology and infectious disease to develop novel computational data mining methods and knowledge representation approaches. From an early age, Richard was very interested in science and the living world around him. He was a curious child who...
Cataloguing the Gene Expression Patterns of Dental Plaque Biofilms: A Reference Dental Plaque Transcriptome
The RNA-Seq method has been widely adopted as an alternative to the use of DNA microarrays. In most contexts, the RNA-Seq method is implemented when a single reference organism is being studied. Our project endeavored to establish working methods to enable the generation of cDNA libraries that were depleted of contaminating human mRNA and host/microbiome rRNA sequences that would otherwise represent over 95% of the total sequence reads obtained. We have also made significant efforts to...
The Gene Ontology in 2010: extensions and refinements.
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and...
TIGR Completes Sequencing of 19th AND 20th Genomes and Chromosomes
July 11, 2000 ROCKVILLE, MD - The Institute for Genomic Research (TIGR) this week celebrates the completion of its 19th and 20th genome sequencing projects. The completion of the entire genome sequences of Chlorobium tepidum and Caulobacter crescentus mark a major milestone in TIGR's history. The genome of Chlorobium tepidum is the first from a member of the green sulfur bacteria, an evolutionarily distinct lineage of bacteria that possess a unique mechanism of photosynthesis relative...
Innovative Metagenomics Strategy Used To Study Oral Microbes
December 10, 2004 Rockville, MD - The mouth is awash in microbes, but scientists so far have merely scratched the surface in identifying and studying the hundreds of bacteria that live in biofilm communities that stick to the teeth and gums. In an innovative new project that could help improve the detection and treatment of oral diseases, scientists are now using a metagenomics strategy to analyze the complex and difficult-to-study community of microbes in the oral cavity. The...
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids.
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication, and transposition. Here, we describe the chromosomal positional history of all genes in Arabidopsis thaliana throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their...
Gene synteny and chloroquine resistance in Plasmodium chabaudi.
Chloroquine resistance in the rodent malaria parasite Plasmodium chabaudi has been shown to be caused by a gene on chromosome 11, and is not linked to orthologues of the Plasmodium falciparum chloroquine resistance transporter (pfcrt) or Pgh-1 (pfmdr1) genes. In the current work, the progeny of crosses between chloroquine-resistant and sensitive clones of P. chabaudi have been analysed for the inheritance of 658 AFLP markers. Markers linked to the chloroquine responses of the progeny,...
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis.
Enteroviruses are potentially linked to the emergence of Acute Flaccid Myelitis (AFM), a rare but very serious condition that affects the nervous system. AFM has been associated with coxsackievirus A16, enterovirus A71 (EVA71) and enterovirus D68 (EVD68). Little is known about host-pathogen interactions for these viruses, and whether immune responses may have a protective or immunopathological role in disease presentations. Towards addressing this issue, we used the Immune Epitope Database...
Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans.
The monkeypox virus (MPXV) outbreak confirmed in May 2022 in non-endemic countries is raising concern about the pandemic potential of novel orthopoxviruses. Little is known regarding MPXV immunity in the context of MPXV infection or vaccination with vaccinia-based vaccines (VACV). As with vaccinia, T cells are likely to provide an important contribution to overall immunity to MPXV. Here, we leveraged the epitope information available in the Immune Epitope Database (IEDB) on VACV to predict...
Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.
Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types.