Literature DB >> 30377368

Striped UniFrac: enabling microbiome analysis at unprecedented scale.

Daniel McDonald1, Yoshiki Vázquez-Baeza1, David Koslicki2, Jason McClelland2, Nicolai Reeve1,3, Zhenjiang Xu1, Antonio Gonzalez1, Rob Knight4,5,6,7.   

Abstract

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Year:  2018        PMID： 30377368      PMCID： PMC7250580          DOI： 10.1038/s41592-018-0187-8

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  9 in total

1.  QIIME allows analysis of high-throughput community sequencing data.

Authors:  J Gregory Caporaso; Justin Kuczynski; Jesse Stombaugh; Kyle Bittinger; Frederic D Bushman; Elizabeth K Costello; Noah Fierer; Antonio Gonzalez Peña; Julia K Goodrich; Jeffrey I Gordon; Gavin A Huttley; Scott T Kelley; Dan Knights; Jeremy E Koenig; Ruth E Ley; Catherine A Lozupone; Daniel McDonald; Brian D Muegge; Meg Pirrung; Jens Reeder; Joel R Sevinsky; Peter J Turnbaugh; William A Walters; Jeremy Widmann; Tanya Yatsunenko; Jesse Zaneveld; Rob Knight
Journal:  Nat Methods       Date:  2010-04-11       Impact factor: 28.547

2.  UniFrac: a new phylogenetic method for comparing microbial communities.

Authors:  Catherine Lozupone; Rob Knight
Journal:  Appl Environ Microbiol       Date:  2005-12       Impact factor: 4.792

3.  Associating microbiome composition with environmental covariates using generalized UniFrac distances.

Authors:  Jun Chen; Kyle Bittinger; Emily S Charlson; Christian Hoffmann; James Lewis; Gary D Wu; Ronald G Collman; Frederic D Bushman; Hongzhe Li
Journal:  Bioinformatics       Date:  2012-06-17       Impact factor: 6.937

4.  Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny.

Authors:  Qin Chang; Yihui Luan; Fengzhu Sun
Journal:  BMC Bioinformatics       Date:  2011-04-25       Impact factor: 3.169

5.  Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.

Authors:  Amnon Amir; Daniel McDonald; Jose A Navas-Molina; Evguenia Kopylova; James T Morton; Zhenjiang Zech Xu; Eric P Kightley; Luke R Thompson; Embriette R Hyde; Antonio Gonzalez; Rob Knight
Journal:  mSystems       Date:  2017-03-07       Impact factor: 6.496

6.  American Gut: an Open Platform for Citizen Science Microbiome Research.

Authors:  Daniel McDonald; Embriette Hyde; Justine W Debelius; James T Morton; Antonio Gonzalez; Gail Ackermann; Alexander A Aksenov; Bahar Behsaz; Caitriona Brennan; Yingfeng Chen; Lindsay DeRight Goldasich; Pieter C Dorrestein; Robert R Dunn; Ashkaan K Fahimipour; James Gaffney; Jack A Gilbert; Grant Gogul; Jessica L Green; Philip Hugenholtz; Greg Humphrey; Curtis Huttenhower; Matthew A Jackson; Stefan Janssen; Dilip V Jeste; Lingjing Jiang; Scott T Kelley; Dan Knights; Tomasz Kosciolek; Joshua Ladau; Jeff Leach; Clarisse Marotz; Dmitry Meleshko; Alexey V Melnik; Jessica L Metcalf; Hosein Mohimani; Emmanuel Montassier; Jose Navas-Molina; Tanya T Nguyen; Shyamal Peddada; Pavel Pevzner; Katherine S Pollard; Gholamali Rahnavard; Adam Robbins-Pianka; Naseer Sangwan; Joshua Shorenstein; Larry Smarr; Se Jin Song; Timothy Spector; Austin D Swafford; Varykina G Thackray; Luke R Thompson; Anupriya Tripathi; Yoshiki Vázquez-Baeza; Alison Vrbanac; Paul Wischmeyer; Elaine Wolfe; Qiyun Zhu; Rob Knight
Journal:  mSystems       Date:  2018-05-15       Impact factor: 6.496

7.  A communal catalogue reveals Earth's multiscale microbial diversity.

Authors:  Luke R Thompson; Jon G Sanders; Daniel McDonald; Amnon Amir; Joshua Ladau; Kenneth J Locey; Robert J Prill; Anupriya Tripathi; Sean M Gibbons; Gail Ackermann; Jose A Navas-Molina; Stefan Janssen; Evguenia Kopylova; Yoshiki Vázquez-Baeza; Antonio González; James T Morton; Siavash Mirarab; Zhenjiang Zech Xu; Lingjing Jiang; Mohamed F Haroon; Jad Kanbar; Qiyun Zhu; Se Jin Song; Tomasz Kosciolek; Nicholas A Bokulich; Joshua Lefler; Colin J Brislawn; Gregory Humphrey; Sarah M Owens; Jarrad Hampton-Marcell; Donna Berg-Lyons; Valerie McKenzie; Noah Fierer; Jed A Fuhrman; Aaron Clauset; Rick L Stevens; Ashley Shade; Katherine S Pollard; Kelly D Goodwin; Janet K Jansson; Jack A Gilbert; Rob Knight
Journal:  Nature       Date:  2017-11-01       Impact factor: 49.962

8.  phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

Authors:  Paul J McMurdie; Susan Holmes
Journal:  PLoS One       Date:  2013-04-22       Impact factor: 3.240

9.  Qiita: rapid, web-enabled microbiome meta-analysis.

Authors:  Antonio Gonzalez; Jose A Navas-Molina; Tomasz Kosciolek; Daniel McDonald; Yoshiki Vázquez-Baeza; Gail Ackermann; Jeff DeReus; Stefan Janssen; Austin D Swafford; Stephanie B Orchanian; Jon G Sanders; Joshua Shorenstein; Hannes Holste; Semar Petrus; Adam Robbins-Pianka; Colin J Brislawn; Mingxun Wang; Jai Ram Rideout; Evan Bolyen; Matthew Dillon; J Gregory Caporaso; Pieter C Dorrestein; Rob Knight
Journal:  Nat Methods       Date:  2018-10-01       Impact factor: 28.547
  9 in total
  21 in total

1.  Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples.

Authors:  Kai Kang; Hui Chong; Kang Ning
Journal:  Gigascience       Date:  2022-07-28       Impact factor: 7.658

2.  Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.

Authors:  Cameron Martino; Daniel McDonald; Kalen Cantrell; Amanda Hazel Dilmore; Yoshiki Vázquez-Baeza; Liat Shenhav; Justin P Shaffer; Gibraan Rahman; George Armstrong; Celeste Allaband; Se Jin Song; Rob Knight
Journal:  mSystems       Date:  2022-04-28       Impact factor: 7.324

3.  Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound.

Authors:  Emily Kunselman; Jeremiah J Minich; Micah Horwith; Jack A Gilbert; Eric E Allen
Journal:  Microbiol Spectr       Date:  2022-05-10

4.  Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase.

Authors:  Igor Sfiligoi; George Armstrong; Antonio Gonzalez; Daniel McDonald; Rob Knight
Journal:  mSystems       Date:  2022-05-31       Impact factor: 7.324

5.  Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.

Authors:  Anupriya Tripathi; Yoshiki Vázquez-Baeza; Julia M Gauglitz; Mingxun Wang; Kai Dührkop; Mélissa Nothias-Esposito; Deepa D Acharya; Madeleine Ernst; Justin J J van der Hooft; Qiyun Zhu; Daniel McDonald; Asker D Brejnrod; Antonio Gonzalez; Jo Handelsman; Markus Fleischauer; Marcus Ludwig; Sebastian Böcker; Louis-Félix Nothias; Rob Knight; Pieter C Dorrestein
Journal:  Nat Chem Biol       Date:  2020-11-16       Impact factor: 15.040

6.  QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.

Authors:  Mehrbod Estaki; Lingjing Jiang; Nicholas A Bokulich; Daniel McDonald; Antonio González; Tomasz Kosciolek; Cameron Martino; Qiyun Zhu; Amanda Birmingham; Yoshiki Vázquez-Baeza; Matthew R Dillon; Evan Bolyen; J Gregory Caporaso; Rob Knight
Journal:  Curr Protoc Bioinformatics       Date:  2020-06

7.  Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces.

Authors:  Aleksandra Checinska Sielaff; Camilla Urbaniak; Ganesh Babu Malli Mohan; Victor G Stepanov; Quyen Tran; Jason M Wood; Jeremiah Minich; Daniel McDonald; Teresa Mayer; Rob Knight; Fathi Karouia; George E Fox; Kasthuri Venkateswaran
Journal:  Microbiome       Date:  2019-04-08       Impact factor: 14.650

8.  Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances.

Authors:  Julia Fukuyama
Journal:  Genome Biol       Date:  2019-06-28       Impact factor: 13.583

9.  High Resistance of a Sludge Enriched with Nitrogen-Fixing Bacteria to Ammonium Salts and Its Potential as a Biofertilizer.

Authors:  Claudia Rodriguez-Gonzalez; Carolina Ospina-Betancourth; Janeth Sanabria
Journal:  Bioengineering (Basel)       Date:  2021-05-01

Review 10.  Towards multi-label classification: Next step of machine learning for microbiome research.

Authors:  Shunyao Wu; Yuzhu Chen; Zhiruo Li; Jian Li; Fengyang Zhao; Xiaoquan Su
Journal:  Comput Struct Biotechnol J       Date:  2021-04-28       Impact factor: 7.271
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