Dr. Jan Meier-Kolthoff – Computer Scientist and Bioinformatician

21. February 202321. February 2023Publications

Paper published on how to establish a universal virus taxonomy

In a previous post from last year I reported on a workshop in Oxford (UK) which I attended in April 2022 to discuss various questions on how to establish a universal virus taxonomy, in view of the (post-)genomic age we are currently in. Finally, last week, our consensus view of that meeting was published in PLoS Biology. The consensus view is the result of both the workshop and longer discussions via email during the drafting phase of the manuscript. My co-authors are renowned experts from various fields (virology, taxonomy, bioinformatics etc.) such as Eugene Koonin, Christian Drosten or Peter Simmonds. […]

15. November 2022Allgemein

I received the title “Highly Cited Researcher” for the third time in a row

Today I received the achievement “Highly Cited Researcher 2022” from Clarivate™ / Web of Science™. It is the third time in a row that I have received the title “Highly Cited Researcher” and I am very happy to see that my work of the last decade is still making a difference in the scientific community worldwide. The online analysis shows that Germany contributes 369 researchers to the overall list of 6,938 researchers. Here is today’s email from Clarivate™: “Each year, Clarivate™ identifies the world’s most influential researchers ─ the select few who have been most frequently cited by their peers […]

11. April 202211. April 2022Conferences

Conference in Oxford, UK, on the future of virus taxonomy

From April 6th-8th, 2022, I was invited participant of the ICTV Workshop – Virus Classification in a Metagenomic Age. My expertise in this field is closely linked to the bioinformatic method VICTOR for genome-based virus classification which I have published some years ago. About 40 experts from the field of (genome-based) virus taxonomy and general virology were invited to discuss various topics either via Zoom or on-site in Oxford, UK. The list of participants included renowned experts such as Christian Drosten, Peter Walker, Eugene Koonin etc. The workshop was split into two parts and roughly followed this outline: Workshop 1 […]

16. November 202116. November 2021General

I have been awarded the title “Highly Cited Researcher 2021”

The list of Highly Cited Researchers 2021 from Clarivate TM identifies scientists and social scientists who have demonstrated significant and broad influence, reflected in the publication of multiple papers frequently cited by their peers during the last decade. 6,602 researchers are named Highly Cited Researchers in 2021 – 3,774 in specific fields and 2,828 for cross-field performance. This is the fourth year that we have identified researchers with cross-field impact. The number of researchers selected in each field is based on the square root of the population of authors listed on the field’s highly cited papers. The number of […]

13. October 202119. October 2021General

Our paper on the TYGS and LPSN databases was just published in Nucleic Acids Research

Our paper “TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes” was recently published in Nucleic Acids Research! The paper presents the current state and recent advancements of the TYGS and LPSN databases and provides insights on how these two databases are interconnected in a synergistic manner. Here is the abstract: Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This poses a challenge for database systems, particularly since it is obviously advantageous if such data are […]

14. December 20207. January 2021General

Web of Science included me in their list “Highly Cited Researchers 2020”

I am humbled to be included in the Web of Science list of “Highly Cited Researchers 2020“. The list of Highly Cited Researchers 2020 from Clarivate / Web of Science identifies scientists and social scientists who have demonstrated significant and broad influence, reflected in the publication of multiple papers frequently cited by their peers during the last decade. 6,389 researchers are named Highly Cited Researchers in 2020 – 3,896 in specific fields and 2,493 for cross-field performance.

16. May 201916. May 2019General

Paper on our new Type (Strain) Genome Server published in Nature Communications

Many years of work have now finally concluded in the publication of our TYGS platform in Nature Communications. Executive summary TYGS, the Type (Strain) Genome Server, is a user-friendly high-throughput web server for genome-based prokaryote taxonomy. Microbial taxonomy needs genome-based analyses but these can be complex and require expert knowledge. TYGS fills this gap. TYGS is as reliable as the GGDC but offers way more features. Citation Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10: 2182. doi:10.1038/s41467-019-10210-3 Weblink https://doi.org/10.1038/s41467-019-10210-3

15. February 201721. March 2017Publications

Launch of VICTOR, the Virus Classification and Tree Building Online Resource

I’m delighted to announce the launch of our novel web service VICTOR. It allows for the comparison of up to 100 bacterial and archaeal viruses (“phages”) using either their genome or proteome sequences. The results include phylogenomic trees inferred using the Genome-BLAST Distance Phylogeny method (GBDP), with branch support, as well as suggestions for the classification at the species, genus and family level. The methods were validated against a comprehensive taxonomic reference dataset accepted by the ICTV with respect to phylogenetic as well as clustering algorithms. We are confident that this service will be beneficial for phage taxonomy in particular […]

29. November 201629. November 2016Publications

A number of important studies have been accepted for publication

A number of highly anticipated works have been accepted in recent weeks. These include (but not limited to): Our very extensive work (Simon et al.) on the phylogenomics of the Rhodobacteraceae which revealed evolutionary adaptation to marine and non-marine habitats A large-scale phylogenomic study (Hahnke et al.) on the genome-based taxonomic classification of Bacteroidetes – a work which elucidated and corrected many previous misclassifications and suggested the emendation of countless species descriptions.

18. August 2016Publications

PNAS publication on comparative genomics of biotechnologically important yeasts is out now

The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these yeasts convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, and can grow in extremes of temperature, salinity, and pH. We compared 29 yeast genomes with the goal of correlating genetics to useful traits. In one rare species, we discovered a genetic code that translates CUG codons to alanine rather than canonical leucine. Genome comparison enabled correlation of genes to useful metabolic properties and showed the synteny of the mating-type locus to be conserved over a billion years of evolution. Our study provides […]