Complete list

Please note: citation statistics are found on my Google Scholar profile

2017

Meier-Kolthoff JP, Göker M: VICTOR: Genome-based Phylogeny and Classification of Prokaryotic Viruses. Bioinformatics 2017 (in press).

Ahn A-C, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin D, Muyzer G: Genetic diversity within the haloalkaliphilic genus Thioalkalivibrio. PLoS One 2017, 12:e0173517. http://dx.doi.org/10.1371/journal.pone.0173517

Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Espino DP, Yoshikuni Y, Visel A, Whitman WB, Garrity G, Eisen JA, Hugenholtz P, Pati A, Ivanova N, Woyke T, Klenk H-P, Kyrpides NC: 1,003 Reference Genomes of Bacterial and Archaeal Isolates Expand Coverage of the Tree of Life. Nat Biotechnol 2017 (advance online publication). http://dx.doi.org/10.1038/nbt.3886

Meier-Kolthoff JP, Göker M: VICTOR: Genome-based Phylogeny and Classification of Prokaryotic Viruses. bioRxiv 2017, preprint. https://doi.org/10.1101/107862

Röttig A, Atasayar E, Meier-Kolthoff JP, Spröer C, Schumann P, Schauer J, Steinbüchel A: Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil. Int J Syst Evol Microbiol 2017, epub ahead of print. http://dx.doi.org/10.1099/ijsem.0.001839

Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk H-P, Schomburg D, Petersen J, Göker M: Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 2017:1–17. http://dx.doi.org/10.1038/ismej.2016.198

2016

Hahnke RL, Meier-Kolthoff JP, García-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk H-P, Göker M: Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016, 7:2003. http://dx.doi.org/10.3389/fmicb.2016.02003

† contributed equally

Blanco-Míguez A, Meier-Kolthoff JP, Gutiérrez-Jácome A, Göker M, Fdez-Riverola F, Sánchez B, Lourenço A: Improving phylogeny reconstruction at the strain level using peptidome datasets. PLOS Comput Biol 2016, 12:e1005271. http://dx.doi.org/10.1371/JOURNAL.PCBI.1005271

Reau AJ La, Meier-Kolthoff JP, Suen G: A sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host-association. Microb Genomics 2016 (published ahead of print). http://dx.doi.org/10.1099/mgen.0.000099

Barka EA, Vatsa P, Sanchez L, Gaveau-vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk H-P, Clément C, Ouhdouch Y, van Wezel GP: Correction for Barka et al., Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016, 80:iii. http://dx.doi.org/10.1128/MMBR.00044-16

Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz M del C, Göker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk H-P, Gtar M: 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. Int J Syst Evol Microbiol 2016 (epub ahead of print). http://dx.doi.org/10.1099/ijsem.0.001496

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov A, Wisecaver J, Long TM, Aerts AL, Choi C, Clum A, Coughlan AY, Deshpande S, Alexander P, Hanson SJ, Klenk H-P, Labutti K, Lapidus A, Lindquist E, Lipzen A, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan J, Rokas A, Rosa CA, Scheuner C, Sibirny A, Slot JC, et al.: Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA 2016 (early edition). http://dx.doi.org/10.1073/pnas.1603941113

Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F, Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 2016, 1(August):16131. http://dx.doi.org/10.1038/nmicrobiol.2016.131

Tashkandy N, Sabban S, Fakieh M, Meier-Kolthoff JP, Huang S, Tindall BJ, Rohde M, Baeshen MN, Baeshen NA, Lapidus A, Copeland A, Pillay M, Reddy TBK, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Göker M, Klenk H-P, Kyrpides NC, Hahnke RL: 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. Stand Genomic Sci 2016, 11:42. http://dx.doi.org/10.1186/s40793-016-0159-5

Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P: Phylogenomic Study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 2016, 7:1-19. http://dx.doi.org/10.3389/fmicb.2016.00877

Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TBK, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Klenk H-P, Kyrpides NC, Hahnke RL: 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. Stand Genomic Sci 2016, 11:37. http://dx.doi.org/10.1186/s40793-016-0163-9

Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M: Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 2016, 11:e0150183. http://dx.doi.org/10.1371/journal.pone.0150183

2015

Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L and Shao Z (2015) Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5:14082. http://dx.doi.org/10.1038/srep14082
† contributed equally

Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, et al. (2015) High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci 10: 46. http://dx.doi.org/10.1186/s40793-015-0032-y

Meier-Kolthoff JP (2015) Welcher Coli ist ein Coli? Sequenzierung des Typstamms von Escherichia coli. BIOspektrum 21: 455–455. http://dx.doi.org/10.1007/s12268-015-0600-0

2014

Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, et al. (2014e) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 10: 2. http://dx.doi.org/10.1186/1944-3277-9-2

Meier-Kolthoff JP (2014d) Comparison of nucleotide and protein sequences for genome-based classification and identification. PhD dissertation, Brunswick (Germany), Technical University. http://d-nb.info/105476994X.

Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2014c) Highly parallelized inference of large genome‐based phylogenies. Concurr Comput Pr Exper 26: 1715–1729. http://dx.doi.org/10.1002/cpe.3112.

Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2014b) GBDP on the grid: a genome-based approach for species delimitation adjusted for an automated and highly parallel processing of large data sets. In: Schulz J, Hermann S, editors. Hochleistungsrechnen in Baden-Württemberg — Ausgewählte Aktivitäten im bwGRiD 2012. Karlsruhe: KIT Scientific Publishing. pp. 83–102. http://dx.doi.org/10.5445/KSP/1000039516.

Meier-Kolthoff JP, Klenk H-P, Goker M (2014a) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64: 352–356. http://dx.doi.org/10.1099/ijs.0.056994-0.

Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, et al. (2014) First genome sequences of Achromobacter phages reveal new members of the N4 family. Virol J 11: 14. http://dx.doi.org/10.1186/1743-422X-11-14.

Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, et al. (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Env Microbiol 16: 218–238. http://dx.doi.org/10.1111/1462-2920.12276.

2013

Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013a) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60. http://dx.doi.org/10.1186/1471-2105-14-60.

Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P (2013b) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195: 413–418. http://dx.doi.org/10.1007/s00203-013-0888-4.

Meier-Kolthoff JP, Lu M, Huntemann M, Lucas S, Lapidus A, et al. (2013c) Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T). Stand Genomic Sci 9: 14–27. http://dx.doi.org/10.4056/sigs.4207886.

Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, et al. (2013) Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Stand Genomic Sci 9: 56–70. http://dx.doi.org/10.4056/sigs.4237901.

2009

Stockinger H, Auch AF, Göker M, Meier-Kolthoff JP, Stamatakis A (2009) Large-scale co-phylogenetic analysis on the grid. Int J Grid High Perform Comput 1: 39–54. http://dx.doi.org/10.4018/978-1-60566-374-6.ch035.

2007

Stamatakis A, Auch AF, Meier-Kolthoff JP, Göker M (2007) AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 10: 1–10. http://dx.doi.org/10.1186/1471-2105-8-405.

Meier-Kolthoff JP, Auch AF, Huson DH, Göker M (2007) CopyCat: cophylogenetic analysis tool. Bioinformatics 23: 898–900. http://dx.doi.org/10.1093/bioinformatics/btm027.