Michael Menzel, Mihaela Martis-Thiele, Hannah Goldschmid, Alexander Ott, Eva Romanovsky, Janna Siemanowski-Hrach, Lancelot Seillier, Nadina Ortiz Brüchle, Angela Maurer, Kjong-Van Lehmann, Matthias Begemann, Miriam Elbracht, Robert Meyer, Sebastian Dintner, Rainer Claus, Jan Meier-Kolthoff, Eric Blanc, Markus M?bs, Maria Joosten, Manuela Benary, Patrick Basitta, Florian H?lscher, Verena Tischler, Thomas Gro?, Oliver Kutz, Rebecca Prause, Doreen William, Kai Horny, Wolfgang Goering, Sugirthan Sivalingam, Arndt Borkhardt, Cornelia Blank, Stefanie Junk, Layal Yasin, Evgeny A. Moskalev, Maria Giulia Carta, Fulvia Ferrazzi, Lars T?gel, Steffen Wolter, Eugen Adam, Uta Matysiak, Tessa Rosenthal, Jürgen D?nitz, Ulrich Lehmann, Gunnar Schmidt, Stephan Bartels, Winfried Hofmann, Steffen Hirsch, Nicola Dikow, Kirsten G?bel, Rouzbeh Banan, Stefan Hamelmann, Annette Fink, Markus Ball, Olaf Neumann, Jan Rehker, Michael Kloth, Justin Murtagh, Nils Hartmann, Phillip Jurmeister, Andreas Mock, J?rg Kumbrink, Andreas Jung, Eva-Maria Mayr, Anne Jacob, Marcel Trautmann, Santina Kirmse, Kim Falkenberg, Christian Ruckert, Daniela Hirsch, Alexander Immel, Wolfgang Dietmaier, Tobias Haack, Ralf Marienfeld, Axel Fürstberger, Jakob Niew?hner, Uwe Gerstenmaier, Timo Eberhardt, Phillip Greif, Silke Appenzeller, Katja Maurus, Julia Doll, Yvonne Jelting, Danny Jonigk, Bruno M?rkl, Dieter Beule, David Horst, Anna-Lena Wulf, Daniela Aust, Martin Werner, Kirsten Reuter-Jessen, Philipp Str?bel, Bernd Auber, Felix Sahm, Sabine Merkelbach-Bruse, Udo Siebolts, Wilfried Roth, Silke Lassmann, Frederick Klauschen, Nadine T. Gaisa, Wilko Weichert, Matthias Evert, Sorin Armeanu-Ebinger, Stephan Ossowski, Christopher Schroeder, Christian P. Schaaf, Nisar Malek, Peter Schirmacher, Daniel Kazdal, Nicole Pfarr, Jan Budczies and Albrecht Stenzinger. in press. Benchmarking whole exome sequencing in the German Network for Personalized Medicine. European Journal of Cancer 114306. DOI: 10.1016/j.ejca.2024.114306
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Peter Simmonds, Evelien M. Adriaenssens, F. Murilo Zerbini, Nicola G. A. Abrescia, Pakorn Aiewsakun, Poliane Alfenas-Zerbini, Yiming Bao, Jakub Barylski, Christian Drosten, Siobain Duffy, W. Paul Duprex, Bas E. Dutilh, Santiago F. Elena, Maria Laura García, Sandra Junglen, Aris Katzourakis, Eugene V. Koonin, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Ma?gorzata ?obocka, Cédric Lood, Jennifer Mahony, Jan P. Meier-Kolthoff, Arcady R. Mushegian, Hanna M. Oksanen, Minna M. Poranen, Alejandro Reyes-Mu?oz, David L. Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Stuart Siddell, Tim Skern, Donald B. Smith, Matthew B. Sullivan, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani and Nikos Vasilakis. 2023. Four principles to establish a universal virus taxonomy. PLoS Biology 21, 2, e3001922. DOI: 10.1371/journal.pbio.3001922
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Isabel Schober, Boyke Bunk, Gabriela Carril, Heike M. Freese, Nicolás Ojeda, Thomas Riedel, Jan P. Meier-Kolthoff, Markus G?ker, Cathrin Spr?er, Patricio A. Flores-Herrera, Guillermo Nourdin-Galindo, Fernando Gómez, Constanza Cárdenas, Felipe Vásquez-Ponce, Alvaro Labra, Jaime Figueroa, Jorge Olivares-Pacheco, Ulrich Nübel, Johannes Sikorski, Sergio H. Marshall and J?rg Overmann. 2023. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. The ISME Journal 17, 12, 2247-2258. DOI: 10.1038/s41396-023-01531-9
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Maria del Carmen Montero-Calasanz, Adnan Yaramis, Manfred Rohde, Peter Schumann, Hans-Peter Klenk and Jan P. Meier-Kolthoff. 2022. Genotype–phenotype correlations within the Geodermatophilaceae. Frontiers in Microbiology 13, 975365. DOI: 10.3389/fmicb.2022.975365
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Correction published at: https://doi.org/10.3389/fmicb.2022.1100319

Hao Li, Jan P. Meier-Kolthoff, Canxin Hu, Zhongjie Wang, Jun Zhu, Wei Zheng, Yun Tian and Feng Guo. 2022. Panoramic insights into microevolution and macroevolution of a Prevotella copri-containing lineage in primate guts. Genomics, Proteomics & Bioinformatics 20, 2, 334-349. DOI: 10.1016/j.gpb.2021.10.006
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Jan P. Meier-Kolthoff, Joaquim Sardà Carbasse, Rosa L. Peinado-Olarte and Markus G?ker. 2022. TYGS and LPSN:?a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Research 50, D1, D801-D807. DOI: 10.1093/nar/gkab902
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Alberto J. Martín-Rodríguez and Jan P. Meier-Kolthoff. 2022. Whole genome-based taxonomy of Shewanella and Parashewanella. International Journal of Systematic and Evolutionary Microbiology 72, 7, 005438. DOI: 10.1099/ijsem.0.005438
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Doina Ciobanu, Alicia Clum, Steven Ahrendt, William B. Andreopoulos, Asaf Salamov, Sandy Chan, C. Alisha Quandt, Brian Foster, Jan P. Meier-Kolthoff, Yung Tsu Tang, Patrick Schwientek, Gerald L. Benny, Matthew E. Smith, Diane Bauer, Shweta Deshpande, Kerrie Barry, Alex Copeland, Steven W. Singer, Tanja Woyke, Igor V. Grigoriev, Timothy Y. James and Jan-Fang Cheng. 2021. A single-cell genomics pipeline for environmental microbial eukaryotes. iScience 24, 4, 102290. DOI: 10.1016/j.isci.2021.102290
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Michael E. J. Buhl, Jan P. Meier-Kolthoff and Matthias Marschal. 2021. Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid. International Journal of Systematic and Evolutionary Microbiology 71, 12. DOI: 10.1099/ijsem.0.005146
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Peter Schumann, Franziska Kalensee, Jialan Cao, Alexis Criscuolo, Dominique Clermont, Johann Michael K?hler, Jan P. Meier-Kolthoff, Meina Neumann-Schaal, Brian J. Tindall and Rüdiger Pukall. 2021. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter. International Journal of Systematic and Evolutionary Microbiology 71, 4. DOI: 10.1099/ijsem.0.004769
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David Heidler von Heilborn, Jessica Reinmüller, Georg H?lzl, Jan P. Meier-Kolthoff, Christian Woehle, Magdalena Marek, Bruno Hüttel and André Lipski. 2021. Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere. International Journal of Systematic and Evolutionary Microbiology 71, 8. DOI: 10.1099/ijsem.0.004973
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Svetlana N. Dedysh, Petra Henke, Anastasia A. Ivanova, Irina S. Kulichevskaya, Dmitriy A. Philippov, Jan P. Meier-Kolthoff, Markus G?ker, Sixing Huang and J?rg Overmann. 2020. 100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii. Environmental Microbiology 22, 1, 198-211. DOI: 10.1111/1462-2920.14838
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Martinique Frentrup, Zhemin Zhou, Matthias Steglich, Jan P. Meier-Kolthoff, Markus G?ker, Thomas Riedel, Boyke Bunk, Cathrin Spr?er, J?rg Overmann, Marion Blaschitz, Alexander Indra, Lutz von Müller, Thomas A. Kohl, Stefan Niemann, Christian Seyboldt, Frank Klawonn, Nitin Kumar, Trevor D. Lawley, Sergio García-Fernández, Rafael Cantón, Rosa del Campo, Ortrud Zimmermann, Uwe Gro?, Mark Achtman and Ulrich Nübel. 2020. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. Microbial Genomics 6, 8. DOI: 10.1099/mgen.0.000410
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Anton H?rdt, Marina García López, Jan P. Meier-Kolthoff, Marcel Schleuning, Lisa-Maria Weinhold, Brian J. Tindall, Sabine Gronow, Nikos C. Kyrpides, Tanja Woyke and Markus G?ker. 2020. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Frontiers in Microbiology 11, 468. DOI: 10.3389/fmicb.2020.00468
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Ba?ak ?ztürk, Johannes Werner, Jan P. Meier-Kolthoff, Boyke Bunk, Cathrin Spr?er and Dirk Springael. 2020. Comparative genomics suggests mechanisms of genetic adaptation toward the catabolism of the phenylurea herbicide linuron in Variovorax. Genome Biology and Evolution 12, 6, 827-841. DOI: 10.1093/gbe/evaa085
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Nikolaos Strepis, Henry D. Naranjo, Jan P. Meier-Kolthoff, Markus G?ker, Nicole Shapiro, Nikos Kyrpides, Hans-Peter Klenk, Peter J. Schaap, Alfons J. M. Stams and Diana Z. Sousa. 2020. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics 21, 1, 24. DOI: 10.1186/s12864-019-6410-x
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Aidan C. Parte, Joaquim Sardà Carbasse, Jan P. Meier-Kolthoff, Lorenz C. Reimer and Markus G?ker. 2020. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology 70, 11, 5607-5612. DOI: 10.1099/ijsem.0.004332
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Marina García-López, Jan P. Meier-Kolthoff, Brian J. Tindall, Sabine Gronow, Tanja Woyke, Nikos C. Kyrpides, Richard L. Hahnke and Markus G?ker. 2019. Analysis of 1,000 type-strain genomes improves taxonomic classification of bacteroidetes. Frontiers in Microbiology 10, 2083. DOI: 10.3389/fmicb.2019.02083
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Vera Bischoff, Boyke Bunk, Jan P. Meier-Kolthoff, Cathrin Spr?er, Anja Poehlein, Marco Dogs, Mary Nguyen, J?rn Petersen, Rolf Daniel, J?rg Overmann, Markus G?ker, Meinhard Simon, Thorsten Brinkhoff and Cristina Moraru. 2019. Cobaviruses?–?a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. The ISME Journal 13, 6, 1404-1421. DOI: 10.1038/s41396-019-0362-7
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Jan P. Meier-Kolthoff. 2019. Moderne genombasierte Klassifikation von Bakterien und Archaeen. BIOspektrum 25, 6, 624-627. DOI: 10.1007/s12268-019-0211-2
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Imke H. E. Korf, Jan P. Meier-Kolthoff, Evelien M. Adriaenssens, Andrew M. Kropinski, Manfred Nimtz, Manfred Rohde, Mark J. van Raaij and Johannes Wittmann. 2019. Still something to discover: novel insights into Escherichia coli phage diversity and taxonomy. Viruses 11, 5, 454. DOI: 10.3390/v11050454
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Jan P. Meier-Kolthoff and Markus G?ker. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications 10, 1, 2182. DOI: 10.1038/s41467-019-10210-3
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Kaisa Thorell, Jan P. Meier-Kolthoff, ?sa Sj?ling and Alberto J. Martín-Rodríguez. 2019. Whole-genome sequencing redefines Shewanella taxonomy. Frontiers in Microbiology 10, 1861. DOI: 10.3389/fmicb.2019.01861
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Lorena Carro, Imen Nouioui, Vartul Sangal, Jan P. Meier-Kolthoff, Martha E. Trujillo, Maria del Carmen Montero-Calasanz, Nevzat Sahin, Darren Lee Smith, Kristi E. Kim, Paul Peluso, Shweta Deshpande, Tanja Woyke, Nicole Shapiro, Nikos C. Kyrpides, Hans-Peter Klenk, Markus G?ker and Michael Goodfellow. 2018. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Scientific Reports 8, 1, 525. DOI: 10.1038/s41598-017-17392-0
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Imen Nouioui, Lorena Carro, Marina García-López, Jan P. Meier-Kolthoff, Tanja Woyke, Nikos C. Kyrpides, Rüdiger Pukall, Hans-Peter Klenk, Michael Goodfellow and Markus G?ker. 2018. Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology 9, 2007. DOI: 10.3389/fmicb.2018.02007
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Jan P. Meier-Kolthoff, Jumpei Uchiyama, Hiroko Yahara, David Paez-Espino and Koji Yahara. 2018. Investigation of recombination-intense viral groups and their genes in the Earth's virome. Scientific Reports 8, 1, 11496. DOI: 10.1038/s41598-018-29272-2
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Fabini D. Orata, Jan P. Meier-Kolthoff, Dominic Sauvageau and Lisa Y. Stein. 2018. Phylogenomic analysis of the Gammaproteobacterial Methanotrophs (order methylococcales) calls for the reclassification of members at the genus and species levels. Frontiers in Microbiology 9, 3162. DOI: 10.3389/fmicb.2018.03162
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Supratim Mukherjee, Rekha Seshadri, Neha J. Varghese, Emiley A. Eloe-Fadrosh, Jan P. Meier-Kolthoff, Markus G?ker, R. Cameron Coates, Michalis Hadjithomas, Georgios A. Pavlopoulos, David Paez-Espino, Yasuo Yoshikuni, Axel Visel, William B. Whitman, George M. Garrity, Jonathan A. Eisen, Philip Hugenholtz, Amrita Pati, Natalia N. Ivanova, Tanja Woyke, Hans-Peter Klenk and Nikos C. Kyrpides. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35, 7, 676-683. DOI: 10.1038/nbt.3886
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Erratum published at: https://doi.org/10.1038/nbt0418-368c

Maria del Carmen Montero-Calasanz, Jan P. Meier-Kolthoff, Dao-Feng Zhang, Adnan Yaramis, Manfred Rohde, Tanja Woyke, Nikos C. Kyrpides, Peter Schumann, Wen-Jun Li and Markus G?ker. 2017. Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Frontiers in Microbiology 8, 2501. DOI: 10.3389/fmicb.2017.02501
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Anne-Catherine Ahn, Jan P. Meier-Kolthoff, Lex Overmars, Michael Richter, Tanja Woyke, Dimitry Y. Sorokin and Gerard Muyzer. 2017. Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio. PLoS ONE 12, 3, e0173517. DOI: 10.1371/journal.pone.0173517
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Meinhard Simon, Carmen Scheuner, Jan P. Meier-Kolthoff, Thorsten Brinkhoff, Irene Wagner-D?bler, Marcus Ulbrich, Hans-Peter Klenk, Dietmar Schomburg, J?rn Petersen and Markus G?ker. 2017. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. The ISME Journal 11, 6, 1483-1499. DOI: 10.1038/ismej.2016.198
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Annika R?ttig, Ewelina Atasayar, Jan P. Meier-Kolthoff, Cathrin Spr?er, Peter Schumann, Jennifer Schauer and Alexander Steinbüchel. 2017. Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil. International Journal of Systematic and Evolutionary Microbiology 67, 6, 1676-1682. DOI: 10.1099/ijsem.0.001839
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Jannik Donner, Michael Reck, Boyke Bunk, Michael Jarek, Constantin Benjamin App, Jan P. Meier-Kolthoff, J?rg Overmann, Rolf Müller, Andreas Kirschning and Irene Wagner-D?bler. 2017. The biofilm inhibitor carolacton enters gram-negative cells: studies using a TolC-deficient strain of Escherichia coli. mSphere 2, 5, e00375-17. DOI: 10.1128/mspheredirect.00375-17
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Heike M. Freese, Johannes Sikorski, Boyke Bunk, Carmen Scheuner, Jan P. Meier-Kolthoff, Cathrin Spr?er, Lone Gram and J?rg Overmann. 2017. Trajectories and drivers of genome evolution in surface-associated marine Phaeobacter. Genome Biology and Evolution 9, 12, 3297-3311. DOI: 10.1093/gbe/evx249
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Jan P. Meier-Kolthoff and Markus G?ker. 2017. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33, 21, 3396-3404. DOI: 10.1093/bioinformatics/btx440
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Robert Riley, Sajeet Haridas, Kenneth H. Wolfe, Mariana R. Lopes, Chris Todd Hittinger, Markus G?ker, Asaf A. Salamov, Jennifer H. Wisecaver, Tanya M. Long, Christopher H. Calvey, Andrea L. Aerts, Kerrie W. Barry, Cindy Choi, Alicia Clum, Aisling Y. Coughlan, Shweta Deshpande, Alexander P. Douglass, Sara J. Hanson, Hans-Peter Klenk, Kurt M. LaButti, Alla Lapidus, Erika A. Lindquist, Anna M. Lipzen, Jan P. Meier-Kolthoff, Robin A. Ohm, Robert P. Otillar, Jasmyn L. Pangilinan, Yi Peng, Antonis Rokas, Carlos A. Rosa, Carmen Scheuner, Andriy A. Sibirny, Jason C. Slot, J. Benjamin Stielow, Hui Sun, Cletus P. Kurtzman, Meredith Blackwell, Igor V. Grigoriev and Thomas W. Jeffries. 2016. Comparative genomics of biotechnologically important yeasts. PNAS 113, 35, 9882-9887. DOI: 10.1073/pnas.1603941113
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Irina Panschin, Sixing Huang, Jan P. Meier-Kolthoff, Brian J. Tindall, Manfred Rohde, Susanne Verbarg, Alla Lapidus, James Han, Stephan Trong, Matthew Haynes, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Natalia N. Ivanova, Konstantinos Mavromatis, Victor Markowitz, Tanja Woyke, Markus G?ker, Hans-Peter Klenk, Nikos C. Kyrpides and Richard L. Hahnke. 2016. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. Standards in Genomic Sciences 11, 1, 37. DOI: 10.1186/s40793-016-0163-9
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Richard L. Hahnke, Jan P. Meier-Kolthoff, Marina García-López, Supratim Mukherjee, Marcel Huntemann, Natalia N. Ivanova, Tanja Woyke, Nikos C. Kyrpides, Hans-Peter Klenk and Markus G?ker. 2016. Genome-based taxonomic classification of Bacteroidetes. Frontiers in Microbiology 7, 2003. DOI: 10.3389/fmicb.2016.02003
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Correction published at: 10.3389/fmicb.2018.00304

Daniel Garrido-Sanz, Jan P. Meier-Kolthoff, Markus G?ker, Marta Martín, Rafael Rivilla and Miguel Redondo-Nieto. 2016. Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS ONE 11, 2, e0150183. DOI: 10.1371/journal.pone.0150183
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Correction published at: 10.1371/journal.pone.0153733

Nisreen Tashkandy, Sari Sabban, Mohammad Fakieh, Jan P. Meier-Kolthoff, Sixing Huang, Brian J. Tindall, Manfred Rohde, Mohammed N. Baeshen, Nabih A. Baeshen, Alla Lapidus, Alex Copeland, Manoj Pillay, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Natalia Ivanova, Victor Markowitz, Tanja Woyke, Markus G?ker, Hans-Peter Klenk, Nikos C. Kyrpides and Richard L. Hahnke. 2016. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T. Standards in Genomic Sciences 11, 1, 42. DOI: 10.1186/s40793-016-0159-5
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Aitor Blanco-Míguez, Jan P. Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus G?ker, Florentino Fdez-Riverola, Borja Sánchez and Anália Louren?o. 2016. Improving phylogeny reconstruction at the strain level using peptidome datasets. PLoS Computational Biology 12, 12, e1005271. DOI: 10.1371/journal.pcbi.1005271
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Charlotte Peeters, Jan P. Meier-Kolthoff, Bart Verheyde, Evie De Brandt, Vaughn S. Cooper and Peter Vandamme. 2016. Phylogenomic study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Frontiers in Microbiology 7, 877. DOI: 10.3389/fmicb.2016.00877
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Imen Nouioui, Faten Ghodhbane-Gtari, Maria del Carmen Montero-Calasanz, Markus G?ker, Jan P. Meier-Kolthoff, Peter Schumann, Manfred Rohde, Michael Goodfellow, Maria P. Fernandez, Philippe Normand, Louis S. Tisa, Hans-Peter Klenk and Maher Gtari. 2016. Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov.. International Journal of Systematic and Evolutionary Microbiology 66, 12, 5201-5210. DOI: 10.1099/ijsem.0.001496
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Alex J. La Reau, Jan P. Meier-Kolthoff and Garret Suen. 2016. Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. Microbial Genomics 2, 12, 000099. DOI: 10.1099/mgen.0.000099
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Essaid Ait Barka, Parul Vatsa, Lisa Sanchez, Nathalie Gaveau-Vaillant, Cedric Jacquard, Jan P. Meier-Kolthoff, Hans-Peter Klenk, Christophe Clément, Yder Ouhdouch and Gilles P. van Wezel. 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews 80, 1, 1-43. DOI: 10.1128/mmbr.00019-15
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Correction published at: 10.1128/MMBR.00044-16

Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, B?rbel U. Foesel, Jan P. Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz, Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt, Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, J?rg Overmann, B?rbel Stecher and Thomas Clavel. 2016. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology 1, 10, 16131. DOI: 10.1038/nmicrobiol.2016.131
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Correction published at: 10.1038/nmicrobiol.2016.219

Yang Liu, Qiliang Lai, Markus G?ker, Jan P. Meier-Kolthoff, Meng Wang, Yamin Sun, Lei Wang and Zongze Shao. 2015. Genomic insights into the taxonomic status of the Bacillus cereus group. Scientific Reports 5, 1, 14082. DOI: 10.1038/srep14082
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Richard L. Hahnke, Erko Stackebrandt, Jan P. Meier-Kolthoff, Brian J. Tindall, Sixing Huang, Manfred Rohde, Alla Lapidus, James Han, Stephan Trong, Matthew Haynes, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Natalia N. Ivanova, Konstantinos Mavromatis, Victor Markowitz, Tanja Woyke, Markus G?ker, Nikos C. Kyrpides and Hans-Peter Klenk. 2015. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes. Standards in Genomic Sciences 10, 1, 46. DOI: 10.1186/s40793-015-0032-y
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Jan P. Meier-Kolthoff. 2015. Welcher Coli ist ein Coli? Sequenzierung des Typstamms von Escherichia coli. BIOspektrum 21, 4, 455. DOI: 10.1007/s12268-015-0600-0
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Jan P. Meier-Kolthoff. 2014. Comparison of nucleotide and protein sequences for genome-based classification and identification. .
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Diss., Universit?t Braunschweig, 2014

Jan P. Meier-Kolthoff, Richard L. Hahnke, J?rn Petersen, Carmen Scheuner, Victoria Michael, Anne Fiebig, Christine Rohde, Manfred Rohde, Berthold Fartmann, Lynne A. Goodwin, Olga Chertkov, T. B. K. Reddy, Amrita Pati, Natalia N. Ivanova, Victor Markowitz, Nikos C. Kyrpides, Tanja Woyke, Markus G?ker and Hans-Peter Klenk. 2014. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Standards in Genomic Sciences 9, 1, 2. DOI: 10.1186/1944-3277-9-2
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Johannes Wittmann, Brigitte Dreiseikelmann, Manfred Rohde, Jan P. Meier-Kolthoff, Boyke Bunk and Christine Rohde. 2014. First genome sequences of Achromobacter phages reveal new members of the N4 family. Virology Journal 11, 1, 14. DOI: 10.1186/1743-422x-11-14
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Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk and Markus G?ker. 2014. GBDP on the grid: a genome-based approach for species delimitation adjusted for an automated and highly parallel processing of large data sets. In Janne Chr. Schulz and Sven Hermann (Ed.). Hochleistungsrechnen in Baden-Württemberg-Ausgew?hlte Aktivit?ten im bwGRiD 2012: Beitr?ge zu Anwenderprojekten und Infrastruktur im bwGRiD im Jahr 2012. KIT Scientific Publishing, Karlsruhe, 83-102. DOI: 10.5445/KSP/1000039516
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Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk and Markus G?ker. 2014. Highly parallelized inference of large genome-based phylogenies. Concurrency and Computation: Practice and Experience 26, 10, 1715-1729. DOI: 10.1002/cpe.3112
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Katharina Drüppel, Michael Hensler, Kathleen Trautwein, Sebastian Ko?mehl, Lars W?hlbrand, Kerstin Schmidt‐Hohagen, Marcus Ulbrich, Nils Bergen, Jan P. Meier-Kolthoff, Markus G?ker, Hans‐Peter Klenk, Dietmar Schomburg and Ralf Rabus. 2014. Pathways and substrate‐specific regulation of amino acid degradation in Phaeobacter inhibens?DSM 17395 (archetype of the marine Roseobacter clade). Environmental Microbiology 16, 1, 218-238. DOI: 10.1111/1462-2920.12276
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Jan P. Meier-Kolthoff, Hans-Peter Klenk and Markus G?ker. 2014. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. International Journal of Systematic and Evolutionary Microbiology 64, 2, 352-356. DOI: 10.1099/ijs.0.056994-0
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Jan P. Meier-Kolthoff, Megan Lu, Marcel Huntemann, Susan Lucas, Alla Lapidus, Alex Copeland, Sam Pitluck, Lynne A. Goodwin, Cliff Han, Roxanne Tapia, Gabriele P?tter, Miriam Land, Natalia Ivanova, Manfred Rohde, Markus G?ker, John C. Detter, Tanja Woyke, Nikos C. Kyrpides and Hans-Peter Klenk. 2013. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T). Standards in Genomic Sciences 9, 1, 28-41. DOI: 10.4056/sigs.4207886
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Krishna Palaniappan, Jan P. Meier-Kolthoff, Hazuki Teshima, Matt Nolan, Alla Lapidus, Hope Tice, Tijana Glavina Del Rio, Jan-Fang Cheng, Cliff Han, Roxanne Tapia, Lynne A. Goodwin, Sam Pitluck, Konstantinos Liolios, Konstantinos Mavromatis, Ioanna Pagani, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Amy Chen, Manfred Rohde, Shanmugam Mayilraj, Stefan Spring, John C. Detter, Markus G?ker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk and Tanja Woyke. 2013. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences 9, 1, 57-70. DOI: 10.4056/sigs.4237901
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Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk and Markus G?ker. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 1, 60. DOI: 10.1186/1471-2105-14-60
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Jan P. Meier-Kolthoff, Markus G?ker, Cathrin Spr?er and Hans-Peter Klenk. 2013. When should a DDH experiment be mandatory in microbial taxonomy?. Archives of Microbiology 195, 6, 413-418. DOI: 10.1007/s00203-013-0888-4
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Heinz Stockinger, Alexander F. Auch, Markus G?ker, Jan P. Meier-Kolthoff and Alexandros Stamatakis. 2011. Large-scale co-phylogenetic analysis on the grid. In Emmanuel Udoh (Ed.). Cloud, grid and high performance computing: emerging applications. IGI Global, Hershey, PA, 222-237. DOI: 10.4018/978-1-60960-603-9.ch014
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Alexandros Stamatakis, Alexander F. Auch, Jan P. Meier-Kolthoff and Markus G?ker. 2007. AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 8, 1, 405. DOI: 10.1186/1471-2105-8-405
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Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson and Markus G?ker. 2007. CopyCat: cophylogenetic analysis tool. Bioinformatics 23, 7, 898-900. DOI: 10.1093/bioinformatics/btm027
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