Robert C Edgar

Robert C Edgar

UNVERIFIED PROFILE

Are you Robert C Edgar?   Register this Author

Register author
Robert C Edgar

Robert C Edgar

Publications by authors named "Robert C Edgar"

Are you Robert C Edgar?   Register this Author

33Publications

1029Reads

32Profile Views

Updating the 97% identity threshold for 16S ribosomal RNA OTUs.

Authors:
Robert C Edgar

Bioinformatics 2018 07;34(14):2371-2375

Sonoma, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty113DOI Listing
July 2018

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences.

Authors:
Robert C Edgar

PeerJ 2018 18;6:e4652. Epub 2018 Apr 18.

Sonoma, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.4652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910792PMC
April 2018

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs.

Authors:
Robert C Edgar

PeerJ 2017 4;5:e3889. Epub 2017 Oct 4.

Sonoma, CA, United States of America.

View Article

Download full-text PDF

Source
https://peerj.com/articles/3889
Publisher Site
http://dx.doi.org/10.7717/peerj.3889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5631090PMC
October 2017

Error filtering, pair assembly and error correction for next-generation sequencing reads.

Bioinformatics 2015 Nov 2;31(21):3476-82. Epub 2015 Jul 2.

Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Lyngby, Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv401DOI Listing
November 2015

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

Microbiome 2015 31;3:34. Epub 2015 Jul 31.

State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-015-0098-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520016PMC
August 2015

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

Microbiome 2015 20;3:20. Epub 2015 May 20.

State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-015-0081-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438525PMC
May 2015

UPARSE: highly accurate OTU sequences from microbial amplicon reads.

Authors:
Robert C Edgar

Nat Methods 2013 Oct 18;10(10):996-8. Epub 2013 Aug 18.

Independent Investigator, Tiburon, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.2604DOI Listing
October 2013

Search and clustering orders of magnitude faster than BLAST.

Authors:
Robert C Edgar

Bioinformatics 2010 Oct 12;26(19):2460-1. Epub 2010 Aug 12.

Tiburon, CA 94920, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btq461DOI Listing
October 2010

Quality measures for protein alignment benchmarks.

Authors:
Robert C Edgar

Nucleic Acids Res 2010 Apr 4;38(7):2145-53. Epub 2010 Jan 4.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkp1196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853116PMC
April 2010

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome.

Proc Natl Acad Sci U S A 2009 Aug 22;106(31):12855-60. Epub 2009 Jul 22.

School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0901282106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722308PMC
August 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Improved repeat identification and masking in Dipterans.

Gene 2007 Mar 12;389(1):1-9. Epub 2006 Oct 12.

Department of Biology, San Francisco State University, San Francisco, CA, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2006.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1945102PMC
March 2007

PILER-CR: fast and accurate identification of CRISPR repeats.

Authors:
Robert C Edgar

BMC Bioinformatics 2007 Jan 20;8:18. Epub 2007 Jan 20.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-8-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1790904PMC
January 2007

Multiple alignment of protein sequences with repeats and rearrangements.

Nucleic Acids Res 2006 26;34(20):5932-42. Epub 2006 Oct 26.

Department of Computer Science, Posts & Telecommunications Institute of Technology, Hanoi, Vietnam.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkl511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635250PMC
December 2006

Multiple sequence alignment.

Curr Opin Struct Biol 2006 Jun 5;16(3):368-73. Epub 2006 May 5.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sbi.2006.04.004DOI Listing
June 2006

PILER: identification and classification of genomic repeats.

Bioinformatics 2005 Jun;21 Suppl 1:i152-8

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bti1003DOI Listing
June 2005

MUSCLE: a multiple sequence alignment method with reduced time and space complexity.

Authors:
Robert C Edgar

BMC Bioinformatics 2004 Aug 19;5:113. Epub 2004 Aug 19.

Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-5-113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC517706PMC
August 2004

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Authors:
Robert C Edgar

Nucleic Acids Res 2004 19;32(5):1792-7. Epub 2004 Mar 19.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkh340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC390337PMC
July 2004

A comparison of scoring functions for protein sequence profile alignment.

Bioinformatics 2004 May 12;20(8):1301-8. Epub 2004 Feb 12.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth090DOI Listing
May 2004

COACH: profile-profile alignment of protein families using hidden Markov models.

Bioinformatics 2004 May 12;20(8):1309-18. Epub 2004 Feb 12.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth091DOI Listing
May 2004

Simultaneous sequence alignment and tree construction using hidden Markov models.

Pac Symp Biocomput 2003 :180-91

Department of Bioengineering, University of California, Berkeley, California 94720, USA.

View Article

Download full-text PDF

Source
http://psb.stanford.edu/psb-online/proceedings/psb03/edgar.p
Web Search
August 2003

Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins.

Biochemistry 2003 Aug;42(30):8988-98

Department of Chemistry, California State Polytechnic University at Pomona, 3801 West Temple Avenue, Pomona, California 91768, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi027435eDOI Listing
August 2003

SATCHMO: sequence alignment and tree construction using hidden Markov models.

Bioinformatics 2003 Jul;19(11):1404-11

195 Roque Moraes Drive, Mill Valley, CA 94941, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btg158DOI Listing
July 2003