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1

Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, Da

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 71 KB

english, 2018

2

Correction for Barka et al., Taxonomy, Physiology, and Natural Products of Actinobacteria

Barka, Essaid Ait, Vatsa, Parul, Sanchez, Lisa, Gaveau-Vaillant, Nathalie, Jacquard, Cedric, Meier-Kolthoff, Jan P., Klenk, Hans-Peter, Clément, Christophe, Ouhdouch, Yder, van Wezel, Gilles P.

Journal:

Microbiology and Molecular Biology Reviews

Year:

2016

Language:

english

File:

PDF, 135 KB

english, 2016

3

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, Da

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 4.89 MB

english, 2017

4

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

HÃ¶rdt, Anton, LÃ³pez, Marina GarcÃa, Meier-Kolthoff, Jan P., Schleuning, Marcel, Weinhold, Lisa-Maria, Tindall, Brian J., Gronow, Sabine, Kyrpides, Nikos C., Woyke, Tanja, GÃ¶ker, Markus

Journal:

Frontiers in Microbiology

Year:

2020

File:

PDF, 11.14 MB

2020

5

AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa

Alexandros Stamatakis, Alexander F Auch, Jan Meier-Kolthoff, Markus Göker

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 420 KB

english, 2007

6

When should a DDH experiment be mandatory in microbial taxonomy?

Meier-Kolthoff, Jan P., GÃ¶ker, Markus, SprÃ¶er, Cathrin, Klenk, Hans-Peter

Journal:

Archives of Microbiology

Year:

2013

Language:

english

File:

PDF, 345 KB

english, 2013

7

Genome sequence-based species delimitation with confidence intervals and improved distance functions

Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk…

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 440 KB

english, 2013

8

First genome sequences ofAchromobacterphages reveal new members of the N4 family

Wittmann, Johannes, Dreiseikelmann, Brigitte, Rohde, Manfred, Meier-Kolthoff, Jan P, Bunk, Boyke, Rohde, Christine

Journal:

Virology Journal

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

9

Highly parallelized inference of large genome-based phylogenies

Meier-Kolthoff, Jan P., Auch, Alexander F., Klenk, Hans-Peter, Göker, Markus

Journal:

Concurrency and Computation: Practice and Experience

Year:

2014

Language:

english

File:

PDF, 1.19 MB

english, 2014

10

Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)

Drüppel, Katharina, Hensler, Michael, Trautwein, Kathleen, Koßmehl, Sebastian, Wöhlbrand, Lars, Schmidt-Hohagen, Kerstin, Ulbrich, Marcus, Bergen, Nils, Meier-Kolthoff, Jan P., Göker, Markus, Klenk, H

Journal:

Environmental Microbiology

Year:

2014

Language:

english

File:

PDF, 2.32 MB

english, 2014

11

Welcher Coli ist ein Coli? Sequenzierung des Typstamms vonEscherichia coli

Meier-Kolthoff, Jan P.

Journal:

Year:

2015

Language:

german

File:

PDF, 336 KB

german, 2015

12

Genome sequence of the moderately thermophilic sulfur-reducing bacteriumThermanaerovibrio veloxtype strain (Z-9701T) and emended description of the genusThermanaerovibrio

Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck,

Journal:

Standards in Genomic Sciences

Year:

2014

Language:

english

File:

PDF, 3.15 MB

english, 2014

13

Genome sequence of the chemoheterotrophic soil bacteriumSaccharomonospora cyaneatype strain (NA-134T)

Meier-Kolthoff, Jan P., Lu, Megan, Huntemann, Marcel, Lucas, Susan, Lapidus, Alla, Copeland, Alex, Pitluck, Sam, Goodwin, Lynne A., Han, Cliff, Tapia, Roxanne, Pötter, Gabriele, Land, Miriam, Ivanova,

Journal:

Standards in Genomic Sciences

Year:

2014

Language:

english

File:

PDF, 2.20 MB

english, 2014

14

High-quality draft genome sequence ofFlavobacterium suncheonenseGH29-5T(DSM 17707T) isolated from greenhouse soil in South Korea, and emended description ofFlavobacterium suncheonenseGH29-5T

Tashkandy, Nisreen, Sabban, Sari, Fakieh, Mohammad, Meier-Kolthoff, Jan P., Huang, Sixing, Tindall, Brian J., Rohde, Manfred, Baeshen, Mohammed N., Baeshen, Nabih A., Lapidus, Alla, Copeland, Alex, Pi

Journal:

Standards in Genomic Sciences

Year:

2016

Language:

english

File:

PDF, 1.59 MB

english, 2016

15

Corrigendum: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Lagkouvardos, Ilias, Pukall, Rüdiger, Abt, Birte, Foesel, Bärbel U., Meier-Kolthoff, Jan P., Kumar, Neeraj, Bresciani, Anne, Martínez, Inés, Just, Sarah, Ziegler, Caroline, Brugiroux, Sandrine, Garzet

Journal:

Nature Microbiology

Year:

2016

Language:

english

File:

PDF, 47 KB

english, 2016

16

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Lagkouvardos, Ilias, Pukall, Rüdiger, Abt, Birte, Foesel, Bärbel U., Meier-Kolthoff, Jan P., Kumar, Neeraj, Bresciani, Anne, Martínez, Inés, Just, Sarah, Ziegler, Caroline, Brugiroux, Sandrine, Garzet

Journal:

Nature Microbiology

Year:

2016

Language:

english

File:

PDF, 1.42 MB

english, 2016

17

Genomic insights into the taxonomic status of the Bacillus cereus group

Liu, Yang, Lai, Qiliang, Göker, Markus, Meier-Kolthoff, Jan P., Wang, Meng, Sun, Yamin, Wang, Lei, Shao, Zongze

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 2.14 MB

english, 2015

18

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

Simon, Meinhard, Scheuner, Carmen, Meier-Kolthoff, Jan P, Brinkhoff, Thorsten, Wagner-Döbler, Irene, Ulbrich, Marcus, Klenk, Hans-Peter, Schomburg, Dietmar, Petersen, Jörn, Göker, Markus

Journal:

The ISME Journal

Year:

2017

Language:

english

File:

PDF, 1.76 MB

english, 2017

19

Complete genome sequence of DSM 30083T, the type strain (U5/41T) ofEscherichia coli, and a proposal for delineating subspecies in microbial taxonomy

Jan P Meier-Kolthoff,Richard L Hahnke,Jörn Petersen…

Journal:

Standards in Genomic Sciences

Year:

2014

Language:

english

File:

PDF, 4.02 MB

english, 2014

20

Comparing polysaccharide decomposition between the type strainsGramella echinicolaKMM 6050T(DSM 19838T) andGramella portivictoriaeUST040801-001T(DSM 23547T), and emended description ofGramella echinicolaNedashkovskaya et al. 2005 emend. Shahina et al. 2014 andGramella portivictoriaeLau et al. 2005

Irina Panschin,Sixing Huang,Jan P. Meier-Kolthoff…

Journal:

Standards in Genomic Sciences

Year:

2016

Language:

english

File:

PDF, 2.24 MB

english, 2016

21

The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli

Donner, Jannik, Reck, Michael, Bunk, Boyke, Jarek, Michael, App, Constantin Benjamin, Meier-Kolthoff, Jan P., Overmann, Jörg, Müller, Rolf, Kirschning, Andreas, Wagner-Döbler, Irene, Bradford, Patrici

Journal:

Year:

2017

Language:

english

File:

PDF, 4.27 MB

english, 2017

22

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Meier-Kolthoff, Jan P, Göker, Markus

Journal:

Year:

2017

Language:

english

File:

PDF, 1.13 MB

english, 2017

23

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P., Trujillo, Martha E., Montero-Calasanz, Maria del Carmen, Sahin, Nevzat, Smith, Darren Lee, Kim, Kristi E., Peluso, Paul, Deshpande

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 4.27 MB

english, 2018

24

Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter

Freese, Heike M, Sikorski, Johannes, Bunk, Boyke, Scheuner, Carmen, Meier-Kolthoff, Jan P, Spröer, Cathrin, Gram, Lone, Overmann, Jörg

Journal:

Genome Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 449 KB

english, 2017

25

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes

Hahnke, Richard L., Stackebrandt, Erko, Meier-Kolthoff, Jan P., Tindall, Brian J., Huang, Sixing, Rohde, Manfred, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, T.B.K., Huntemann,

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 2.65 MB

english, 2015

26

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Ahn, Anne-Catherine, Meier-Kolthoff, Jan P., Overmars, Lex, Richter, Michael, Woyke, Tanja, Sorokin, Dimitry Y., Muyzer, Gerard, Thompson, Cristiane

Journal:

Year:

2017

Language:

english

File:

PDF, 4.55 MB

english, 2017

27

Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

Peeters, Charlotte, Meier-Kolthoff, Jan P., Verheyde, Bart, De Brandt, Evie, Cooper, Vaughn S., Vandamme, Peter

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 4.38 MB

english, 2016

28

Genome-Based Taxonomic Classification of Bacteroidetes

Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 7.39 MB

english, 2016

29

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Montero-Calasanz, Maria del Carmen, Meier-Kolthoff, Jan P., Zhang, Dao-Feng, Yaramis, Adnan, Rohde, Manfred, Woyke, Tanja, Kyrpides, Nikos C., Schumann, Peter, Li, Wen-Jun, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2017

Language:

english

File:

PDF, 2.38 MB

english, 2017

30

Investigation of recombination-intense viral groups and their genes in the Earth’s virome

Meier-Kolthoff, Jan P., Uchiyama, Jumpei, Yahara, Hiroko, Paez-Espino, David, Yahara, Koji

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 2.31 MB

english, 2018

31

Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes

Hahnke, Richard L., Meier-Kolthoff, Jan P., García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N., Woyke, Tanja, Kyrpides, Nikos C., Klenk, Hans-Peter, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 136 KB

english, 2018

32

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Nouioui, Imen, Carro, Lorena, García-López, Marina, Meier-Kolthoff, Jan P., Woyke, Tanja, Kyrpides, Nikos C., Pukall, Rüdiger, Klenk, Hans-Peter, Goodfellow, Michael, Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 5.31 MB

english, 2018

33

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems

Bischoff, Vera, Bunk, Boyke, Meier-Kolthoff, Jan P., Spröer, Cathrin, Poehlein, Anja, Dogs, Marco, Nguyen, Mary, Petersen, Jörn, Daniel, Rolf, Overmann, Jörg, Göker, Markus, Simon, Meinhard, Brinkhoff

Journal:

The ISME Journal

Year:

2019

File:

PDF, 4.61 MB

2019

34

Large-Scale Co-Phylogenetic Analysis on the Grid

Stockinger, Heinz, Auch, Alexander F., Göker, Markus, Meier-Kolthoff, Jan, Stamatakis, Alexandros

Journal:

International Journal of Grid and High Performance Computing

Year:

2009

Language:

english

File:

PDF, 1.15 MB

english, 2009

35

Whole-Genome Sequencing Redefines Shewanella Taxonomy

Thorell, Kaisa, Meier-Kolthoff, Jan P., Sjöling, Åsa, Martín-Rodríguez, Alberto J.

Journal:

Frontiers in Microbiology

Year:

2019

Language:

english

File:

PDF, 5.81 MB

english, 2019

36

Whole-Genome Sequencing Redefines Shewanella Taxonomy

Thorell, Kaisa, Meier-Kolthoff, Jan P., Sjöling, Åsa, Martín-Rodríguez, Alberto J.

Journal:

Frontiers in Microbiology

Year:

2019

File:

PDF, 5.81 MB

2019

37

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

García-López, Marina, Meier-Kolthoff, Jan P., Tindall, Brian J., Gronow, Sabine, Woyke, Tanja, Kyrpides, Nikos C., Hahnke, Richard L., Göker, Markus

Journal:

Frontiers in Microbiology

Year:

2019

File:

PDF, 19.27 MB

2019

38

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Strepis, Nikolaos, Naranjo, Henry D., Meier-Kolthoff, Jan, Göker, Markus, Shapiro, Nicole, Kyrpides, Nikos, Klenk, Hans-Peter, Schaap, Peter J., Stams, Alfons J. M., Sousa, Diana Z.

Journal:

Year:

2020

Language:

english

File:

PDF, 1.51 MB

english, 2020

39

Comparative genomics suggests mechanisms of genetic adaptation towards the catabolism of the phenylurea herbicide linuron in Variovorax

ÃztÃ¼rk, BaÅak, Werner, Johannes, Meier-Kolthoff, Jan P, Bunk, Boyke, SprÃ¶er, Cathrin, Springael, Dirk, Katz, Laura A

Journal:

Genome Biology and Evolution

Year:

2020

File:

PDF, 1.02 MB

2020

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