Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes.

Autor: Pier Luigi Buttigieg, Wolfgang Hankeln, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, Frank Oliver Glöckner

Publikováno v: PLoS ONE, Vol 8, Iss 3, p e50869 (2013)

BackgroundThe proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of

Externí odkaz: https://doaj.org/article/d389fb0ab8994cb0b2e1aa53874a9cd8

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

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

Publikováno v: Nature Biotechnology. 29:415-420

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e4ce19a957f3247a7a2d5328a104024
https://doi.org/10.1038/nbt.1823

Ecological structuring of bacterial and archaeal taxa in surface ocean waters

Autor: Pelin Yilmaz, Wolfgang Hankeln, Renzo Kottmann, Frank Oliver Glöckner, Christian Quast, Morten Hvitfeldt Iversen

Publikováno v: FEMS microbiology ecology. 81(2)

The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::834e6966989382fed90295f3d8ba0f65
https://pubmed.ncbi.nlm.nih.gov/22416918

The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Autor: Frank Oliver Glöckner, Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James Cole, Linda Amaral-Zettler, Jack Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce Birren, Martin Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel Gallery, Richard Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth Glass, Antonio Gonzalez, Jeffrey Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian Lauber, Teresa Legg, Ruth Ley, Catherine Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara Methé, Folker Meyer, Sara Nakielny, Karen Nelson, Diana Nemergut, Josh Neufeld, Norman Pace, Giriprakash Palanisamy, Jörg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James Tiedje, Doyle Ward, George Weinstock, Doug Wendel, Owen White, Andreas Wilke, Jennifer Wortmann

Publikováno v: Nature Precedings.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::9cb498b8e6f0695bddf936d36beff095
https://doi.org/10.1038/npre.2010.5252

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

Autor: Wolfgang, Hankeln, Pier Luigi, Buttigieg, Dennis, Fink, Renzo, Kottmann, Pelin, Yilmaz, Frank Oliver, Glöckner

Publikováno v: BMC Bioinformatics
BMC Bioinformatics, Vol 11, Iss 1, p 358 (2010)

Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. T

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::e3359f57cb1937b3ba9b4307f551dca4
https://hdl.handle.net/21.11116/0000-0001-CB0A-021.11116/0000-0007-72C4-B