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SARS-CoV-2 Mutation Tracking
The Bacterial Viral Bioinformatic Resource Center (BV-BRC) is proud to introduce a new resource with the goal of providing live tracking of SARS-CoV-2 mutations. This real-time resource will provide regular reports focused on “Variants and Lineages of Concern” (VoCs/LoCs), and will serve as an early warning system for variants that are increasing in frequency in specific geographical locations.
It's all relative: ranking the diversity of aquatic bacterial communities.
The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and...
Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library.
A directional size-selected cDNA library constructed from Schistosoma mansoni (Sm) adult worm RNA was used for the generation of expressed sequence tags (EST). From one or both ends of 429 distinct cDNA clones 607 EST were obtained. Of these, only 16% were previously known Sm genes. More than 22% of the clones had matches with entries for other organisms in the databases. These new Sm genes constituted a broad range of transcripts distributed among cytoplasmic structural and regulatory...
Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q.
Several publicly funded large-scale sequencing efforts have been initiated with the goal of completing the first reference human genome sequence by the year 2005. Here we present the results of analysis of 11.8 Mb of genomic sequence from chromosome 16. The apparent gene density varies throughout the region, but the number of genes predicted (84) suggests that this is a gene-poor region. This result may also suggest that the total number of human genes is likely to be at the lower end of...
Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing.
Neisseria meningitidis is a major cause of bacterial septicemia and meningitis. Sequence variation of surface-exposed proteins and cross-reactivity of the serogroup B capsular polysaccharide with human tissues have hampered efforts to develop a successful vaccine. To overcome these obstacles, the entire genome sequence of a virulent serogroup B strain (MC58) was used to identify vaccine candidates. A total of 350 candidate antigens were expressed in Escherichia coli, purified, and used to...
Paternally inherited cis-regulatory structural variants are associated with autism.
The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families,...
Genomics Scholars Program
Overview The Genomics Scholars Program (GSP) is a long-term internship designed to help community college students with a science focus transition to four-year colleges. GSP began in 2014 and is scheduled to end with the last cohort in the summer of 2018. Interns enrolled in the 15-month program had exposure to: Two, 10-week summer research experiences (40 hours/week) One, 12-months semester research experience (10 hours/week) Mentoring by JCVI...
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.
Genetic factors modifying the blood metabolome have been investigated through genome-wide association studies (GWAS) of common genetic variants and through exome sequencing. We conducted a whole-genome sequencing study of common, low-frequency and rare variants to associate genetic variations with blood metabolite levels using comprehensive metabolite profiling in 1,960 adults. We focused the analysis on 644 metabolites with consistent levels across three longitudinal data collections....
Careers
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Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas.
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey mutational changes in cancer in a high-throughput and comprehensive manner. Here we report on the sequence analysis of members of the receptor tyrosine kinase (RTK) gene family in the genomes of glioblastoma brain tumors. Previous studies have identified a number of molecular alterations in glioblastoma,...