Institution
Dalhousie University
Education•Halifax, Nova Scotia, Canada•
About: Dalhousie University is a education organization based out in Halifax, Nova Scotia, Canada. It is known for research contribution in the topics: Population & Health care. The organization has 25660 authors who have published 58465 publications receiving 2082403 citations. The organization is also known as: Dalhousie College & The Governors of Dalhousie College and University.
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University of Massachusetts Amherst1, University of Michigan2, University of New Mexico3, University of British Columbia4, Texas A&M University5, University of Minnesota6, University of Warwick7, Dalhousie University8, Colorado School of Mines9, University of Ljubljana10, Graz University of Technology11, Louisiana State University12
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
17,350 citations
University of Toronto1, St. Michael's Hospital2, Northeastern University3, Ottawa Hospital Research Institute4, University of South Australia5, Royal College of Physicians and Surgeons of Canada6, Canadian Agency for Drugs and Technologies in Health7, RAND Corporation8, American University of Beirut9, Agency for Healthcare Research and Quality10, University of Ottawa11, University of York12, University of Alberta13, McMaster University14, South African Medical Research Council15, Queen's University16, Dalhousie University17, World Health Organization18, Cochrane Collaboration19, King's College London20
TL;DR: A PRISMA extension for scoping reviews was needed to provide reporting guidance for this specific type of knowledge synthesis and was developed according to published guidance by the EQUATOR (Enhancing the QUAlity and Transparency of health Research) Network for the development of reporting guidelines.
Abstract: Scoping reviews, a type of knowledge synthesis, follow a systematic approach to map evidence on a topic and identify main concepts, theories, sources, and knowledge gaps. Although more scoping reviews are being done, their methodological and reporting quality need improvement. This document presents the PRISMA-ScR (Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews) checklist and explanation. The checklist was developed by a 24-member expert panel and 2 research leads following published guidance from the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network. The final checklist contains 20 essential reporting items and 2 optional items. The authors provide a rationale and an example of good reporting for each item. The intent of the PRISMA-ScR is to help readers (including researchers, publishers, commissioners, policymakers, health care providers, guideline developers, and patients or consumers) develop a greater understanding of relevant terminology, core concepts, and key items to report for scoping reviews.
11,709 citations
TL;DR: In this paper, the authors estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010.
9,324 citations
Northern Arizona University1, National Institutes of Health2, University of Minnesota3, Woods Hole Oceanographic Institution4, University of California, Davis5, Massachusetts Institute of Technology6, University of Copenhagen7, University of Trento8, Chinese Academy of Sciences9, University of California, San Francisco10, University of Pennsylvania11, Pacific Northwest National Laboratory12, North Carolina State University13, University of California, San Diego14, Institute for Systems Biology15, Dalhousie University16, University of British Columbia17, Statens Serum Institut18, Anschutz Medical Campus19, University of Washington20, Michigan State University21, Stanford University22, Harvard University23, Broad Institute24, Australian National University25, University of Düsseldorf26, University of New South Wales27, Sookmyung Women's University28, San Diego State University29, Howard Hughes Medical Institute30, Cornell University31, Max Planck Society32, Colorado State University33, Google34, Syracuse University35, Webster University36, United States Department of Agriculture37, University of Arkansas for Medical Sciences38, Colorado School of Mines39, National Oceanic and Atmospheric Administration40, University of Southern Mississippi41, University of California, Merced42, Wageningen University and Research Centre43, University of Arizona44, Environment Agency45, University of Florida46, Merck & Co.47
TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Abstract: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.
8,821 citations
TL;DR: The results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
Abstract: Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
6,860 citations
Authors
Showing all 25969 results
| Name | H-index | Papers | Citations |
|---|---|---|---|
| Graciela S. Alarcón | 94 | 641 | 43254 |
| Philip J. Devereaux | 94 | 443 | 110428 |
| Sonia S. Anand | 93 | 446 | 50100 |
| Walter L. Miller | 93 | 339 | 30794 |
| Michael F. Goodchild | 93 | 393 | 35338 |
| Steven J. Cooke | 93 | 937 | 34644 |
| Peter Franks | 92 | 535 | 36485 |
| Robert C. Green | 91 | 526 | 40414 |
| Gang Liu | 90 | 455 | 36158 |
| Laurent Peyrin-Biroulet | 90 | 901 | 34120 |
| Jesse B. Jupiter | 90 | 543 | 26480 |
| Ingmar Skoog | 89 | 458 | 28998 |
| David Henry | 89 | 547 | 45563 |
| Ulrike Lohmann | 88 | 379 | 45843 |
| Peng Zhang | 88 | 1578 | 33705 |