Pelin Yilmaz

Pelin Yilmaz

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Pelin Yilmaz

Pelin Yilmaz

Publications by authors named "Pelin Yilmaz"

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43Publications

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Refining the taxonomic structure of the phylum Acidobacteria.

Int J Syst Evol Microbiol 2018 Oct 16. Epub 2018 Oct 16.

2​Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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October 2018

The importance of designating type material for uncultured taxa.

Syst Appl Microbiol 2018 Jul 18. Epub 2018 Jul 18.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia. Electronic address:

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July 2018

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences.

Mar Genomics 2017 Dec 1;36:33-39. Epub 2017 Jun 1.

University of Bremen, Molecular Ecology, BreMarE, Leobener Str. 5, 28359 Bremen, Germany. Electronic address:

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December 2017

25 years of serving the community with ribosomal RNA gene reference databases and tools.

J Biotechnol 2017 Nov 23;261:169-176. Epub 2017 Jun 23.

Department for Microbiology, Technical University Munich, D-85354 Freising, Germany.

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November 2017

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

BMC Bioinformatics 2017 Sep 30;18(1):433. Epub 2017 Sep 30.

Department of Life Sciences & Chemistry, Jacobs University gGmbH, Bremen, Germany.

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September 2017

Plant specimen contextual data consensus.

Gigascience 2016 12;5(1):1-4

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsius str. 1, Bremen 28359, Germany.

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December 2016

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Nucleic Acids Res 2016 06 10;44(11):5022-33. Epub 2016 May 10.

The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany.

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June 2016

Expanding the World of Marine Bacterial and Archaeal Clades.

Front Microbiol 2015 8;6:1524. Epub 2016 Jan 8.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Life Sciences and Chemistry, Jacobs UniversityBremen, Germany.

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January 2016

The magnitude of gonadotoxicity of chemotherapy drugs on ovarian follicles and granulosa cells varies depending upon the category of the drugs and the type of granulosa cells.

Hum Reprod 2015 Dec 13;30(12):2926-35. Epub 2015 Oct 13.

Department of Obstetrics and Gynecology, Koc University School of Medicine, Istanbul, Turkey American Hospital Women's Health Center, Comprehensive Cancer Care and Fertility Preservation Programs, Assisted Reproduction Unit, Istanbul, Turkey

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December 2015

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs.

Environ Microbiol 2015 Sep 4;17(9):3301-13. Epub 2015 Mar 4.

Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany.

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September 2015

Minimum Information about a Biosynthetic Gene cluster.

Authors:
Marnix H Medema Renzo Kottmann Pelin Yilmaz Matthew Cummings John B Biggins Kai Blin Irene de Bruijn Yit Heng Chooi Jan Claesen R Cameron Coates Pablo Cruz-Morales Srikanth Duddela Stephanie Düsterhus Daniel J Edwards David P Fewer Neha Garg Christoph Geiger Juan Pablo Gomez-Escribano Anja Greule Michalis Hadjithomas Anthony S Haines Eric J N Helfrich Matthew L Hillwig Keishi Ishida Adam C Jones Carla S Jones Katrin Jungmann Carsten Kegler Hyun Uk Kim Peter Kötter Daniel Krug Joleen Masschelein Alexey V Melnik Simone M Mantovani Emily A Monroe Marcus Moore Nathan Moss Hans-Wilhelm Nützmann Guohui Pan Amrita Pati Daniel Petras F Jerry Reen Federico Rosconi Zhe Rui Zhenhua Tian Nicholas J Tobias Yuta Tsunematsu Philipp Wiemann Elizabeth Wyckoff Xiaohui Yan Grace Yim Fengan Yu Yunchang Xie Bertrand Aigle Alexander K Apel Carl J Balibar Emily P Balskus Francisco Barona-Gómez Andreas Bechthold Helge B Bode Rainer Borriss Sean F Brady Axel A Brakhage Patrick Caffrey Yi-Qiang Cheng Jon Clardy Russell J Cox René De Mot Stefano Donadio Mohamed S Donia Wilfred A van der Donk Pieter C Dorrestein Sean Doyle Arnold J M Driessen Monika Ehling-Schulz Karl-Dieter Entian Michael A Fischbach Lena Gerwick William H Gerwick Harald Gross Bertolt Gust Christian Hertweck Monica Höfte Susan E Jensen Jianhua Ju Leonard Katz Leonard Kaysser Jonathan L Klassen Nancy P Keller Jan Kormanec Oscar P Kuipers Tomohisa Kuzuyama Nikos C Kyrpides Hyung-Jin Kwon Sylvie Lautru Rob Lavigne Chia Y Lee Bai Linquan Xinyu Liu Wen Liu Andriy Luzhetskyy Taifo Mahmud Yvonne Mast Carmen Méndez Mikko Metsä-Ketelä Jason Micklefield Douglas A Mitchell Bradley S Moore Leonilde M Moreira Rolf Müller Brett A Neilan Markus Nett Jens Nielsen Fergal O'Gara Hideaki Oikawa Anne Osbourn Marcia S Osburne Bohdan Ostash Shelley M Payne Jean-Luc Pernodet Miroslav Petricek Jörn Piel Olivier Ploux Jos M Raaijmakers José A Salas Esther K Schmitt Barry Scott Ryan F Seipke Ben Shen David H Sherman Kaarina Sivonen Michael J Smanski Margherita Sosio Evi Stegmann Roderich D Süssmuth Kapil Tahlan Christopher M Thomas Yi Tang Andrew W Truman Muriel Viaud Jonathan D Walton Christopher T Walsh Tilmann Weber Gilles P van Wezel Barrie Wilkinson Joanne M Willey Wolfgang Wohlleben Gerard D Wright Nadine Ziemert Changsheng Zhang Sergey B Zotchev Rainer Breitling Eriko Takano Frank Oliver Glöckner

Nat Chem Biol 2015 Sep;11(9):625-31

1] Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany. [2] Jacobs University Bremen gGmbH, Bremen, Germany.

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September 2015

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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July 2015

In vitro biological activities and fatty acid profiles of Pistacia terebinthus fruits and Pistacia khinjuk seeds.

Nat Prod Res 2015 12;29(5):444-6. Epub 2014 Aug 12.

a Department of Analytical Chemistry , Faculty of Pharmacy, Bezmialem Vakif University , 34093 Istanbul , Turkey.

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May 2015

Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring.

Appl Environ Microbiol 2015 Mar 9;81(6):2025-31. Epub 2015 Jan 9.

Max Planck Institute for Marine Microbiology, Bremen, Germany Department of Earth Sciences-Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands.

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March 2015

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Nat Rev Microbiol 2014 09;12(9):635-45

Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB)), E-07190 Esporles, Balearic Islands, Spain.

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September 2014

Simultaneous determination of seven phthalic acid esters in beverages using ultrasound and vortex-assisted dispersive liquid-liquid microextraction followed by high-performance liquid chromatography.

J Sep Sci 2014 Aug 27;37(16):2111-7. Epub 2014 Jun 27.

Department of Analytical Chemistry, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.

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August 2014

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

ISME J 2014 Jan 24;8(1):1-3. Epub 2013 Oct 24.

Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.

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January 2014

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Nucleic Acids Res 2014 Jan 28;42(Database issue):D643-8. Epub 2013 Nov 28.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany, Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada, Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada, Ribocon GmbH, D-28359 Bremen, Germany, School of Engineering and Science, Jacobs University Bremen gGmbH, D-28759 Bremen, Germany and Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany.

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January 2014

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

PLoS One 2013 14;8(3):e50869. Epub 2013 Mar 14.

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

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September 2013

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.

Nucleic Acids Res 2013 Jan 28;41(Database issue):D590-6. Epub 2012 Nov 28.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany.

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January 2013

Ecological structuring of bacterial and archaeal taxa in surface ocean waters.

FEMS Microbiol Ecol 2012 Aug 10;81(2):373-85. Epub 2012 Apr 10.

Max Planck Institute for Marine Microbiology, Bremen, Germany.

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August 2012

The genomic standards consortium: bringing standards to life for microbial ecology.

ISME J 2011 Oct 7;5(10):1565-7. Epub 2011 Apr 7.

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

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October 2011

Analysis of 23S rRNA genes in metagenomes - a case study from the Global Ocean Sampling Expedition.

Syst Appl Microbiol 2011 Sep 14;34(6):462-9. Epub 2011 Jun 14.

Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.

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September 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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May 2011

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

BMC Bioinformatics 2010 Jun 30;11:358. Epub 2010 Jun 30.

Max Planck Institute for Marine Microbiology, Bremen, Germany.

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June 2010

Megx.net: integrated database resource for marine ecological genomics.

Nucleic Acids Res 2010 Jan 25;38(Database issue):D391-5. Epub 2009 Oct 25.

Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany. rkottman@mpi-bremen

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January 2010