Publications by authors named "Pelin Yilmaz"

49Publications

Proposal to reclassify the proteobacterial classes and , and the phylum into four phyla reflecting major functional capabilities.

Authors:
David W Waite Maria Chuvochina Claus Pelikan Donovan H Parks Pelin Yilmaz Michael Wagner Alexander Loy Takeshi Naganuma Ryosuke Nakai William B Whitman Martin W Hahn Jan Kuever Philip Hugenholtz

Int J Syst Evol Microbiol 2020 Nov 5;70(11):5972-6016. Epub 2020 Nov 5.

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.

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November 2020

Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat.

Authors:
Judith M Klatt Gonzalo V Gomez-Saez Steffi Meyer Petra Pop Ristova Pelin Yilmaz Michael S Granitsiotis Jennifer L Macalady Gaute Lavik Lubos Polerecky Solveig I Bühring

ISME J 2020 Dec 7;14(12):3024-3037. Epub 2020 Aug 7.

Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany.

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December 2020

Role of Temperature and Growth Period in the Synthesis of Hydrothermally Grown TiO₂ Nanorods.

Authors:
Ananthakumar Soosaimanickam Pelin Yilmaz Xuan Li Joe Briscoe Ann-Louise Anderson Steve Dunn Moorthy Babu Sridharan

J Nanosci Nanotechnol 2020 Jun;20(6):3873-3878

Crystal Growth Centre, Anna University, Chennai 600 025, India.

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June 2020

Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework.

Authors:
Gemma Henderson Pelin Yilmaz Sandeep Kumar Robert J Forster William J Kelly Sinead C Leahy Le Luo Guan Peter H Janssen

PeerJ 2019 5;7:e6496. Epub 2019 Mar 5.

Grasslands Research Centre, AgResearch, Palmerston North, New Zealand.

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March 2019

Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research.

Authors:
Gerhard Rambold Pelin Yilmaz Janno Harjes Sabrina Klaster Veronica Sanz Anton Link Frank Oliver Glöckner Dagmar Triebel

Database (Oxford) 2019 01 1;2019. Epub 2019 Jan 1.

SNSB IT Center, Menzinger Straße 67, München, Germany.

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January 2019

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Authors:
Simon Roux Evelien M Adriaenssens Bas E Dutilh Eugene V Koonin Andrew M Kropinski Mart Krupovic Jens H Kuhn Rob Lavigne J Rodney Brister Arvind Varsani Clara Amid Ramy K Aziz Seth R Bordenstein Peer Bork Mya Breitbart Guy R Cochrane Rebecca A Daly Christelle Desnues Melissa B Duhaime Joanne B Emerson François Enault Jed A Fuhrman Pascal Hingamp Philip Hugenholtz Bonnie L Hurwitz Natalia N Ivanova Jessica M Labonté Kyung-Bum Lee Rex R Malmstrom Manuel Martinez-Garcia Ilene Karsch Mizrachi Hiroyuki Ogata David Páez-Espino Marie-Agnès Petit Catherine Putonti Thomas Rattei Alejandro Reyes Francisco Rodriguez-Valera Karyna Rosario Lynn Schriml Frederik Schulz Grieg F Steward Matthew B Sullivan Shinichi Sunagawa Curtis A Suttle Ben Temperton Susannah G Tringe Rebecca Vega Thurber Nicole S Webster Katrine L Whiteson Steven W Wilhelm K Eric Wommack Tanja Woyke Kelly C Wrighton Pelin Yilmaz Takashi Yoshida Mark J Young Natalya Yutin Lisa Zeigler Allen Nikos C Kyrpides Emiley A Eloe-Fadrosh

Nat Biotechnol 2019 01 17;37(1):29-37. Epub 2018 Dec 17.

US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.

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January 2019

Refining the taxonomic structure of the phylum Acidobacteria.

Authors:
Svetlana N Dedysh Pelin Yilmaz

Int J Syst Evol Microbiol 2018 Dec 16;68(12):3796-3806. Epub 2018 Oct 16.

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

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December 2018

The importance of designating type material for uncultured taxa.

Authors:
Maria Chuvochina Christian Rinke Donovan H Parks Michael S Rappé Gene W Tyson Pelin Yilmaz William B Whitman Philip Hugenholtz

Syst Appl Microbiol 2019 Jan 18;42(1):15-21. 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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January 2019

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:
Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A M Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2018 07;36(7):660

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July 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:
Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A Murat Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2018 02;36(2):196

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February 2018

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer .

Authors:
Jessika Füssel Sebastian Lücker Pelin Yilmaz Boris Nowka Maartje A H J van Kessel Patric Bourceau Philipp F Hach Sten Littmann Jasmine Berg Eva Spieck Holger Daims Marcel M M Kuypers Phyllis Lam

Sci Adv 2017 11 1;3(11):e1700807. Epub 2017 Nov 1.

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

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November 2017

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

Authors:
Alan Beccati Jan Gerken Christian Quast Pelin Yilmaz Frank Oliver Glöckner

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

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors:
Robert M Bowers Nikos C Kyrpides Ramunas Stepanauskas Miranda Harmon-Smith Devin Doud T B K Reddy Frederik Schulz Jessica Jarett Adam R Rivers Emiley A Eloe-Fadrosh Susannah G Tringe Natalia N Ivanova Alex Copeland Alicia Clum Eric D Becraft Rex R Malmstrom Bruce Birren Mircea Podar Peer Bork George M Weinstock George M Garrity Jeremy A Dodsworth Shibu Yooseph Granger Sutton Frank O Glöckner Jack A Gilbert William C Nelson Steven J Hallam Sean P Jungbluth Thijs J G Ettema Scott Tighe Konstantinos T Konstantinidis Wen-Tso Liu Brett J Baker Thomas Rattei Jonathan A Eisen Brian Hedlund Katherine D McMahon Noah Fierer Rob Knight Rob Finn Guy Cochrane Ilene Karsch-Mizrachi Gene W Tyson Christian Rinke Alla Lapidus Folker Meyer Pelin Yilmaz Donovan H Parks A M Eren Lynn Schriml Jillian F Banfield Philip Hugenholtz Tanja Woyke

Nat Biotechnol 2017 Aug;35(8):725-731

Department of Energy Joint Genome Institute, Walnut Creek, California, USA.

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August 2017

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

Authors:
Frank Oliver Glöckner Pelin Yilmaz Christian Quast Jan Gerken Alan Beccati Andreea Ciuprina Gerrit Bruns Pablo Yarza Jörg Peplies Ralf Westram Wolfgang Ludwig

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

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

Authors:
Pablo Yarza Pelin Yilmaz Katrin Panzer Frank Oliver Glöckner Marlis Reich

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

Plant specimen contextual data consensus.

Authors:
Petra Ten Hoopen Ramona L Walls Ethalinda Ks Cannon Guy Cochrane James Cole Anjanette Johnston Ilene Karsch-Mizrachi Pelin Yilmaz

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

UniEuk: Time to Speak a Common Language in Protistology!

Authors:
Cédric Berney Andreea Ciuprina Sara Bender Juliet Brodie Virginia Edgcomb Eunsoo Kim Jeena Rajan Laura Wegener Parfrey Sina Adl Stéphane Audic David Bass David A Caron Guy Cochrane Lucas Czech Micah Dunthorn Stefan Geisen Frank Oliver Glöckner Frédéric Mahé Christian Quast Jonathan Z Kaye Alastair G B Simpson Alexandros Stamatakis Javier Del Campo Pelin Yilmaz Colomban de Vargas

J Eukaryot Microbiol 2017 05 21;64(3):407-411. Epub 2017 Apr 21.

Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France.

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May 2017

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle.

Authors:
Clara Martínez-Pérez Wiebke Mohr Carolin R Löscher Julien Dekaezemacker Sten Littmann Pelin Yilmaz Nadine Lehnen Bernhard M Fuchs Gaute Lavik Ruth A Schmitz Julie LaRoche Marcel M M Kuypers

Nat Microbiol 2016 Sep 12;1(11):16163. Epub 2016 Sep 12.

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

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September 2016

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources.

Authors:
Nicolas Tsesmetzis Pelin Yilmaz Peter C Marks Nikos C Kyrpides Ian M Head Bart P Lomans

Stand Genomic Sci 2016 12;11:78. Epub 2016 Oct 12.

Shell Global Solutions International B.V., Rijswijk, Netherlands.

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October 2016

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

Authors:
Alex R Hardisty Finn Bacall Niall Beard Maria-Paula Balcázar-Vargas Bachir Balech Zoltán Barcza Sarah J Bourlat Renato De Giovanni Yde de Jong Francesca De Leo Laura Dobor Giacinto Donvito Donal Fellows Antonio Fernandez Guerra Nuno Ferreira Yuliya Fetyukova Bruno Fosso Jonathan Giddy Carole Goble Anton Güntsch Robert Haines Vera Hernández Ernst Hannes Hettling Dóra Hidy Ferenc Horváth Dóra Ittzés Péter Ittzés Andrew Jones Renzo Kottmann Robert Kulawik Sonja Leidenberger Päivi Lyytikäinen-Saarenmaa Cherian Mathew Norman Morrison Aleksandra Nenadic Abraham Nieva de la Hidalga Matthias Obst Gerard Oostermeijer Elisabeth Paymal Graziano Pesole Salvatore Pinto Axel Poigné Francisco Quevedo Fernandez Monica Santamaria Hannu Saarenmaa Gergely Sipos Karl-Heinz Sylla Marko Tähtinen Saverio Vicario Rutger Aldo Vos Alan R Williams Pelin Yilmaz

BMC Ecol 2016 10 20;16(1):49. Epub 2016 Oct 20.

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

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October 2016

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Authors:
Alexey M Kozlov Jiajie Zhang Pelin Yilmaz Frank Oliver Glöckner Alexandros Stamatakis

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.

Authors:
Pelin Yilmaz Pablo Yarza Josephine Z Rapp Frank O Glöckner

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.

Authors:
Aytac Yuksel Gamze Bildik Filiz Senbabaoglu Nazli Akin Macit Arvas Fehmi Unal Yagmur Kilic Isil Karanfil Baldan Eryılmaz Pelin Yilmaz Can Ozkanbaş Cagatay Taskiran Senai Aksoy Yılmaz Guzel Basak Balaban Umit Ince Akira Iwase Bulent Urman Ozgur Oktem

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

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

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Authors:
Katrin Panzer Pelin Yilmaz Michael Weiß Lothar Reich Michael Richter Jutta Wiese Rolf Schmaljohann Antje Labes Johannes F Imhoff Frank Oliver Glöckner Marlis Reich

PLoS One 2015 30;10(7):e0134377. Epub 2015 Jul 30.

University of Bremen, Molecular Ecology, FB2, Leobener Str. 2, 28359, Bremen, Germany.

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May 2016

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

Authors:
Brigitte Boeckmann Marina Marcet-Houben Jonathan A Rees Kristoffer Forslund Jaime Huerta-Cepas Matthieu Muffato Pelin Yilmaz Ioannis Xenarios Peer Bork Suzanna E Lewis Toni Gabaldón

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

Chemical constituents and biological activities of Cirsium leucopsis, C. sipyleum, and C. eriophorum.

Authors:
Mehmet Boğa Pelin Köseoğlu Yilmaz Deniz Bariş Cebe Mashhad Fatima Bina S Siddiqui Ufuk Kolak

Z Naturforsch C J Biosci 2014 Sep-Oct;69(9-10):381-90

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March 2015

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

Authors:
Judith M Klatt Sebastian Haas Pelin Yilmaz Dirk de Beer Lubos Polerecky

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

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

Authors:
Judith M Klatt Mohammad A A Al-Najjar Pelin Yilmaz Gaute Lavik Dirk de Beer Lubos Polerecky

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

Genomic standards consortium projects.

Authors:
Dawn Field Peter Sterk Renzo Kottmann J Wim De Smet Linda Amaral-Zettler Guy Cochrane James R Cole Neil Davies Peter Dawyndt George M Garrity Jack A Gilbert Frank Oliver Glöckner Lynette Hirschman Hans-Peter Klenk Rob Knight Nikos Kyrpides Folker Meyer Ilene Karsch-Mizrachi Norman Morrison Robert Robbins Inigo San Gil Susanna Sansone Lynn Schriml Tatiana Tatusova Dave Ussery Pelin Yilmaz Owen White John Wooley Gregory Caporaso

Stand Genomic Sci 2014 Jun 15;9(3):599-601. Epub 2014 Feb 15.

Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA .

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June 2014

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

Authors:
Pablo Yarza Pelin Yilmaz Elmar Pruesse Frank Oliver Glöckner Wolfgang Ludwig Karl-Heinz Schleifer William B Whitman Jean Euzéby Rudolf Amann Ramon Rosselló-Móra

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

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

Authors:
Işil Hacıbekiroğlu Pelin Köseoğlu Yılmaz Nesrin Haşimi Ersin Kılınç Veysel Tolan Ufuk Kolak

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

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

Authors:
Pelin Köseoğlu Yılmaz Abdulselam Ertaş Ufuk Kolak

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

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

Authors:
Pelin Yilmaz Laura Wegener Parfrey Pablo Yarza Jan Gerken Elmar Pruesse Christian Quast Timmy Schweer Jörg Peplies Wolfgang Ludwig Frank Oliver Glöckner

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

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

Authors:
Elizabeth M Glass Yekaterina Dribinsky Pelin Yilmaz Hal Levin Robert Van Pelt Doug Wendel Andreas Wilke Jonathan A Eisen Sue Huse Anna Shipanova Mitch Sogin Jason Stajich Rob Knight Folker Meyer Lynn M Schriml

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

A metagenomics portal for a democratized sequencing world.

Authors:
Andreas Wilke Elizabeth M Glass Daniela Bartels Jared Bischof Daniel Braithwaite Mark D'Souza Wolfgang Gerlach Travis Harrison Kevin Keegan Hunter Matthews Renzo Kottmann Tobias Paczian Wei Tang William L Trimble Pelin Yilmaz Jared Wilkening Narayan Desai Folker Meyer

Methods Enzymol 2013 ;531:487-523

Argonne National Laboratory, Lemont, Illinois, USA; University of Chicago, Chicago, Illinois, USA.

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April 2014

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

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

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

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012).

Authors:
Eamonn Ó Tuama John Deck Gabriel Dröge Markus Döring Dawn Field Renzo Kottmann Juncai Ma Hiroshi Mori Norman Morrison Peter Sterk Hideaki Sugawara John Wieczorek Linhuan Wu Pelin Yilmaz

Stand Genomic Sci 2012 Oct 28;7(1):166-70. Epub 2012 Sep 28.

Global Biodiversity Information Facility, GBIF Secretariat, Copenhagen, Denmark.

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October 2012

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

Authors:
Christian Quast Elmar Pruesse Pelin Yilmaz Jan Gerken Timmy Schweer Pablo Yarza Jörg Peplies Frank Oliver Glöckner

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.

Authors:
Pelin Yilmaz Morten H Iversen Wolfgang Hankeln Renzo Kottmann Christian Quast Frank O Glöckner

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

CDinFusion--submission-ready, on-line integration of sequence and contextual data.

Authors:
Wolfgang Hankeln Norma Johanna Wendel Jan Gerken Jost Waldmann Pier Luigi Buttigieg Ivaylo Kostadinov Renzo Kottmann Pelin Yilmaz Frank Oliver Glöckner

PLoS One 2011 13;6(9):e24797. Epub 2011 Sep 13.

Max Planck Institute for Marine Microbiology, Bremen, Germany.

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February 2012

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

Authors:
Norman Morrison David Hancock Lynette Hirschman Peter Dawyndt Bert Verslyppe Nikos Kyrpides Renzo Kottmann Pelin Yilmaz Frank Oliver Glöckner Jeff Grethe Tim Booth Peter Sterk Goran Nenadic Dawn Field

Stand Genomic Sci 2011 Apr;4(2):286-92

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April 2011

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

Authors:
Pelin Yilmaz Renzo Kottmann Elmar Pruesse Christian Quast Frank Oliver Glöckner

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

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

Authors:
Pelin Yilmaz Jack A Gilbert Rob Knight Linda Amaral-Zettler Ilene Karsch-Mizrachi Guy Cochrane Yasukazu Nakamura Susanna-Assunta Sansone Frank Oliver Glöckner Dawn Field

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

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010.

Authors:
Jack A Gilbert Folker Meyer Rob Knight Dawn Field Nikos Kyrpides Pelin Yilmaz John Wooley

Stand Genomic Sci 2010 Dec 15;3(3):235-9. Epub 2010 Dec 15.

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December 2010

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.

Authors:
Lynette Hirschman Peter Sterk Dawn Field John Wooley Guy Cochrane Jack Gilbert Eugene Kolker Nikos Kyrpides Folker Meyer Ilene Mizrachi Yasukazu Nakamura Susanna-Assunta Sansone Lynn Schriml Tatiana Tatusova Owen White Pelin Yilmaz

Stand Genomic Sci 2010 Jun 15;2(3):357-60. Epub 2010 Jun 15.

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June 2010

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

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

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.

Authors:
Renzo Kottmann Ivalyo Kostadinov Melissa Beth Duhaime Pier Luigi Buttigieg Pelin Yilmaz Wolfgang Hankeln Jost Waldmann Frank Oliver Glöckner

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