Manimozhiyan Arumugam

Manimozhiyan Arumugam

UNVERIFIED PROFILE

Are you Manimozhiyan Arumugam?   Register this Author

Register author
Manimozhiyan Arumugam

Manimozhiyan Arumugam

Publications by authors named "Manimozhiyan Arumugam"

Are you Manimozhiyan Arumugam?   Register this Author

49Publications

3371Reads

13Profile Views

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.

View Article

Download full-text PDF

Source
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 Aug;37(8):852-857

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
August 2019

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

Gut 2019 Jun 15. Epub 2019 Jun 15.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1136/gutjnl-2019-319123DOI Listing
June 2019

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
http://www-huber.embl.de/pub/pdf/Arumugam_Nature_2011.pdf
Web Search
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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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