Publications by authors named "Manimozhiyan Arumugam"

54Publications

Perturbation of gut microbiota decreases susceptibility but does not modulate ongoing autoimmune neurological disease.

J Neuroinflammation 2020 Mar 6;17(1):79. Epub 2020 Mar 6.

Research group Neuroinflammation and mucosal Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.

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http://dx.doi.org/10.1186/s12974-020-01766-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060541PMC
March 2020

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 Sep;37(9):1091

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0252-6DOI Listing
September 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam Rivers Michael S Robeson Patrick Rosenthal Nicola Segata Michael Shaffer Arron Shiffer Rashmi Sinha Se Jin Song John R Spear Austin D Swafford Luke R Thompson Pedro J Torres Pauline Trinh Anupriya Tripathi Peter J Turnbaugh Sabah Ul-Hasan Justin J J van der Hooft Fernando Vargas Yoshiki Vázquez-Baeza Emily Vogtmann Max von Hippel William Walters Yunhu Wan Mingxun Wang Jonathan Warren Kyle C Weber Charles H D Williamson Amy D Willis Zhenjiang Zech Xu Jesse R Zaneveld Yilong Zhang Qiyun Zhu Rob Knight J Gregory Caporaso

Nat Biotechnol 2019 08;37(8):852-857

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015180PMC
August 2019

Trust is good, control is better: technical considerations in blood microbiome analysis.

Gut 2020 Jul 15;69(7):1362-1363. Epub 2019 Jun 15.

The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1136/gutjnl-2019-319123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306979PMC
July 2020

Genes controlling the activation of natural killer lymphocytes are epigenetically remodeled in intestinal cells from germ-free mice.

FASEB J 2019 02 10;33(2):2719-2731. Epub 2018 Oct 10.

Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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https://www.fasebj.org/doi/10.1096/fj.201800787R
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http://dx.doi.org/10.1096/fj.201800787RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338647PMC
February 2019

Circulating microbiome in blood of different circulatory compartments.

Gut 2019 03 26;68(3):578-580. Epub 2018 Mar 26.

The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1136/gutjnl-2018-316227DOI Listing
March 2019

Complete Genome Sequences of Type Strain GUR, with Antitumor Activity, and Its Derivative Strain GURSA1 with an Inactivated Gene.

Genome Announc 2017 Sep 21;5(38). Epub 2017 Sep 21.

The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

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http://dx.doi.org/10.1128/genomeA.00939-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609411PMC
September 2017

Gut microbiome development along the colorectal adenoma-carcinoma sequence.

Nat Commun 2015 Mar 11;6:6528. Epub 2015 Mar 11.

1] BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia [4] Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China.

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http://dx.doi.org/10.1038/ncomms7528DOI Listing
March 2015

An integrated catalog of reference genes in the human gut microbiome.

Nat Biotechnol 2014 Aug 6;32(8):834-41. Epub 2014 Jul 6.

1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [4] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [5] Macau University of Science and Technology, Macau, China.

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http://dx.doi.org/10.1038/nbt.2942DOI Listing
August 2014

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.

Cell 2011 Jul;146(2):277-89

Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany.

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http://dx.doi.org/10.1016/j.cell.2011.06.039DOI Listing
July 2011

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:
Pelin Yilmaz Renzo Kottmann Dawn Field Rob Knight James R Cole Linda Amaral-Zettler Jack A Gilbert Ilene Karsch-Mizrachi Anjanette Johnston Guy Cochrane Robert Vaughan Christopher Hunter Joonhong Park Norman Morrison Philippe Rocca-Serra Peter Sterk Manimozhiyan Arumugam Mark Bailey Laura Baumgartner Bruce W Birren Martin J Blaser Vivien Bonazzi Tim Booth Peer Bork Frederic D Bushman Pier Luigi Buttigieg Patrick S G Chain Emily Charlson Elizabeth K Costello Heather Huot-Creasy Peter Dawyndt Todd DeSantis Noah Fierer Jed A Fuhrman Rachel E Gallery Dirk Gevers Richard A Gibbs Inigo San Gil Antonio Gonzalez Jeffrey I Gordon Robert Guralnick Wolfgang Hankeln Sarah Highlander Philip Hugenholtz Janet Jansson Andrew L Kau Scott T Kelley Jerry Kennedy Dan Knights Omry Koren Justin Kuczynski Nikos Kyrpides Robert Larsen Christian L Lauber Teresa Legg Ruth E Ley Catherine A Lozupone Wolfgang Ludwig Donna Lyons Eamonn Maguire Barbara A Methé Folker Meyer Brian Muegge Sara Nakielny Karen E Nelson Diana Nemergut Josh D Neufeld Lindsay K Newbold Anna E Oliver Norman R Pace Giriprakash Palanisamy Jörg Peplies Joseph Petrosino Lita Proctor Elmar Pruesse Christian Quast Jeroen Raes Sujeevan Ratnasingham Jacques Ravel David A Relman Susanna Assunta-Sansone Patrick D Schloss Lynn Schriml Rohini Sinha Michelle I Smith Erica Sodergren Aymé Spo Jesse Stombaugh James M Tiedje Doyle V Ward George M Weinstock Doug Wendel Owen White Andrew Whiteley Andreas Wilke Jennifer R Wortman Tanya Yatsunenko Frank Oliver Glöckner

Nat Biotechnol 2011 May;29(5):415-20

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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https://darchive.mblwhoilibrary.org/bitstream/handle/1912/46
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http://www.nature.com/doifinder/10.1038/nbt.1823
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http://dx.doi.org/10.1038/nbt.1823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367316PMC
May 2011

Enterotypes of the human gut microbiome.

Nature 2011 May 20;473(7346):174-80. Epub 2011 Apr 20.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://www-huber.embl.de/pub/pdf/Arumugam_Nature_2011.pdf
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http://www.nature.com/doifinder/10.1038/nature09944
Publisher Site
http://dx.doi.org/10.1038/nature09944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728647PMC
May 2011

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Bioinformatics 2010 Dec 21;26(23):2979-80. Epub 2010 Oct 21.

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982155PMC
December 2010

SmashCommunity: a metagenomic annotation and analysis tool.

Bioinformatics 2010 Dec 19;26(23):2977-8. Epub 2010 Oct 19.

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq536DOI Listing
December 2010

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Bioinformatics 2009 Jul 4;25(13):1587-93. Epub 2009 May 4.

Department of Computer Science and Center for Genome Sciences, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732315PMC
July 2009

The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.

Bioinformatics 2007 Mar 18;23(5):545-54. Epub 2007 Jan 18.

Laboratory for Computational Genomics, Campus Box 1045, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl659DOI Listing
March 2007

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

Genome Biol 2006 7;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

Laboratory for Computational Genomics and Department of Computer Science, Washington University, One Brookings Drive, St, Louis, MO 63130, USA.

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http://dx.doi.org/10.1186/gb-2006-7-s1-s5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810554PMC
September 2006

Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions.

Genome Res 2005 Apr;15(4):577-82

Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA.

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http://dx.doi.org/10.1101/gr.3329005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074372PMC
April 2005

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

Genome Res 2004 Apr;14(4):665-71

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.1959604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383311PMC
April 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004