Institution
J. Craig Venter Institute
Nonprofit•La Jolla, California, United States•
About: J. Craig Venter Institute is a nonprofit organization based out in La Jolla, California, United States. It is known for research contribution in the topics: Genome & Gene. The organization has 1268 authors who have published 2300 publications receiving 304083 citations. The organization is also known as: JCVI & The Institute for Genomic Research.
Topics: Genome, Gene, Genomics, Population, Microbiome
Papers published on a yearly basis
Papers
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TL;DR: Comparisons at both genomic and protein levels indicated that PRCV-ISU-1 had a closer relationship with TGEV Miller strains than Purdue strains and that T GEV strains as a group share a common ancestor with PRCV.
58 citations
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J. Craig Venter Institute1, Pontifical Catholic University of Chile2, University of California, San Diego3, Millennium Institute4, Brigham Young University5, University of Pittsburgh6, National Center for Immunization and Respiratory Diseases7, Icahn School of Medicine at Mount Sinai8, University of Geneva9
TL;DR: The authors compare the dynamics of the UTR microbiome in IAV-infected ferrets and humans, finding similar trends at the ecosystem and individual taxon level in both hosts.
Abstract: Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.
58 citations
10 Aug 2016
TL;DR: The authors compared whole-blood RNA-seq profiles at pre-and post-infection time points from Malian adults who were either asymptomatic or febrile during their first seasonal PCR-positive P. falciparum infection with those from malaria-naive Dutch adults after a single controlled human malaria infection.
Abstract: Identifying molecular predictors and mechanisms of malaria disease is important for understanding how Plasmodium falciparum malaria is controlled. Transcriptomic studies in humans have so far been limited to retrospective analysis of blood samples from clinical cases. In this prospective, proof-of-principle study, we compared whole-blood RNA-seq profiles at pre-and post-infection time points from Malian adults who were either asymptomatic (n = 5) or febrile (n = 3) during their first seasonal PCR-positive P. falciparum infection with those from malaria-naive Dutch adults after a single controlled human malaria infection (n = 5). Our data show a graded activation of pathways downstream of pro-inflammatory cytokines, with the highest activation in malaria-naive Dutch individuals and significantly reduced activation in malaria-experienced Malians. Newly febrile and asymptomatic infections in Malians were statistically indistinguishable except for genes activated by pro-inflammatory cytokines. The combined data provide a molecular basis for the development of a pyrogenic threshold as individuals acquire immunity to clinical malaria.
58 citations
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TL;DR: The Sincell R package implements a methodological toolbox allowing flexible workflows under a general framework and contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq.
Abstract: Summary: Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data can be formalized under a general framework composed of (i) a metric to assess cell-to-cell similarities (with or without a dimensionality reduction step) and (ii) a graph-building algorithm (optionally making use of a cell clustering step). The Sincell R package implements a methodological toolbox allowing flexible workflows under such a framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies. The functionalities of Sincell are illustrated in a real case study, which demonstrates its ability to discriminate noisy from stable cell-state hierarchies.
Availability and implementation: Sincell is an open-source R/Bioconductor package available at http://bioconductor.org/packages/sincell. A detailed manual and a vignette are provided with the package.
Contact: hc.bis-bsi@llesuar.oinotna
Supplementary information: Supplementary data are available at Bioinformatics online.
58 citations
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TL;DR: The high fertility in a relatively short period, combined with a high degree of virulence and a high recombination frequency, demonstrates that the mating pair AFB62 and AFIR928 provides an excellent tool for genetic studies of A. fumigatus.
Abstract: The mating efficiency of 50 Aspergillus fumigatus isolates from both clinical and environmental sources was analyzed. Forty isolates completed the sexual cycle in 4 weeks with variable levels of fertility designated high, medium, or low. Two opposite-mating-type strains exhibiting the highest fertility, AFB62 ( MAT1-1 ), isolated from a case of invasive aspergillosis, and AFIR928 ( MAT1-2 ), isolated from the environment, were chosen as the supermater pair. Single cleistothecia obtained from a cross of the two strains harbored a minimum of 1 × 10 4 ascospores. The viability of ascospores increased with the age of the fruiting body, 17% at 4 weeks and reaching 95% at 20 weeks. AFB62 and AFIR928 were equally virulent in two different murine models, despite differences in their sources. High recombination frequencies were observed when the closely linked genes alb1 (AFUA_2G17600) and abr2 (AFUA_2G17530) were used as genetic markers. Comparative genome hybridization analyses revealed that only 86 genes (ca. 0.86% of the genome) are significantly diverged between AFB62 and AFIR928. The high fertility in a relatively short period, combined with a high degree of virulence and a high recombination frequency, demonstrates that the mating pair AFB62 and AFIR928 provides an excellent tool for genetic studies of A. fumigatus. IMPORTANCE Aspergillus fumigatus is a heterothallic fungal pathogen that causes life-threatening infections in immunocompromised hosts. Although heterothallism facilitates genetic study via recombinational analysis, previous work showed that a 6-month incubation period is required for the completion of sexual reproduction in this species. Such a long incubation period impedes progress in genetic research. To discover a highly fertile (supermater) pair that can complete the sexual cycle in a considerably shorter period, we screened 50 strains collected from various geographic regions for mating efficiency. We identified a highly virulent pair of supermaters that can be an invaluable tool for genetic study.
58 citations
Authors
Showing all 1274 results
Name | H-index | Papers | Citations |
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John R. Yates | 177 | 1036 | 129029 |
Anders M. Dale | 156 | 823 | 133891 |
Ronald W. Davis | 155 | 644 | 151276 |
Steven L. Salzberg | 147 | 407 | 231756 |
Mark Raymond Adams | 147 | 1187 | 135038 |
Nicholas J. Schork | 125 | 587 | 62131 |
William R. Jacobs | 118 | 490 | 48638 |
Ian T. Paulsen | 112 | 354 | 69460 |
Michael B. Brenner | 111 | 393 | 44771 |
Kenneth H. Nealson | 108 | 483 | 51100 |
Claire M. Fraser | 108 | 352 | 76292 |
Stephen L. Hoffman | 104 | 458 | 38597 |
Michael J. Brownstein | 102 | 274 | 47929 |
Amalio Telenti | 102 | 421 | 40509 |
John Quackenbush | 99 | 427 | 67029 |