News

08. May 2021
Many laboratories have ramped up nanopore sequencing for SARS-CoV-2 surveillance, but are in dire need of bioinformatics support. Here we present poreCov, a high-throughput software pipeline for reliable genotyping and reference-based genome reconstruction of SARS-CoV-2 samples based on nanopore tiled amplicon sequencing focused around the ARTIC protocol. On GitHub! Big kudos @CaSe Group Jena!

11. April 2021
Our chromosome-level hybrid genome assembly with RNA-Seq-improved annotation of the oleaginous yeast Rhodotorula toruloides is out as a preprint! Great collaboration w/ the Swedish University of Agricultural Sciences, Uppsala (SLU)!

05. April 2021
Finally! Together with great colleagues from ANSES in France (among others) we describe a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae isolated from flamingo! The bioinformatics part actually started with Fabien visiting us in 2016 and 2017 to learn about assembly and finally found its successful conclusion with the analysis of nanopore data and high-quality genomes.

06. March 2021
Questions about the characteristics, spread and significance of mutated variants of SARS-CoV-2 play a major role in the progress of the pandemic. Here, we summarize in the “Deutsches Ärzteblatt International” (in German) how molecular surveillance using whole genome sequencing is carried out at the Robert Koch Institute.

22. February 2021
Are you looking for some easy to run tool w/o dependency-struggle to analyze your hybrid metagenomics data? Including state-of-the-art principals of diff binning and pathways? Out now in PLOS Comp Biol, MUFFIN!

06. December 2020
RNA-Seq workflows are a dime a dozen. Nevertheless, we are happy to present RNAflow as an easy to use pipeline for gene expression calculation with less configuration effort. Made possible by Nextflow and most importantly Marie ;) !

14. November 2020
Genomic surveillance is limited not only by the speed at which genomes can be shared, but also by the speed at which they reach the right person or algorithm to analyze them. DarkQ is a proof-of-concept on how we might share data for genomic surveillance in the future.

10. November 2020
Very happy that this is finally out, a review on workflows and tools that have been developed by the virus bioinformatics community as a rapid reaction to the COVID-19 pandemic! Including a comprehensive (yet incomplete) collection of tools and resources for virus detection, annotation, tracking and drug design.

29. October 2020
Freshly out! Our genome comparison of 33 Chlamydia strains! All started with Lisa’s master thesis, we run into issues defining proper core gene sets (roary n = 7, really?!) and developed RIBAP together with Kevin! All would not have been possible without the supervision of the great post-prof Konrad! Thx to all involved!

20. October 2020
Martin’s first paper as a single author (invited perspective in Molecular Ecology Resources)! Based on a recent publication by Freedman et al. on errors in de novo transcriptome assemblies, Martin shares some thoughts on the current status and future of this area.

01. September 2020
Welcome Kunaphas! For his bioinformatics research internship at the FU Berlin he joins the team to work on the detection of antimicrobial peptides from large collections of publicly available RNA-Seq data.

26. August 2020
The in-depth characterization of model species is important to advance the field of molecular biology. So I’m more than happy that this study about a marine Chlamydomonas sp. as an algal model system is finally accepted in the Journal of Phycology (will add a link asap)!

13. August 2020
Yeah, our joint study (CRC AquaDiva) on hybrid metagenome assembly is out at Environmental Microbiology! We show how including nanopore long reads improves the recovery of microbial and viral genomes from a complex groundwater sample. A great cooperation w/ the Küsel Lab, thx all, and special kudos to Will Overholt for all the hard work!

07. August 2020
After 7 years at the FSU and the legendary RNA Bioinformatics team, I’m pleased to announce that I’ve just moved to the Robert Koch Institute to support the central scientific institution of our government in the field of infectious diseases with applied bioinformatics and research. Great times in Jena, which I will certainly miss, but now new tasks are waiting!

02. August 2020
Detect sites under positive selection with PoSeiDon! Implemented via Nextflow and Docker and now accepted as an Application Note in Bioinformatics.

26. July 2020
Have you ever had trouble getting a number of virus detection tools to work? Stop it! Test “What the Phage”! The preprint of our multitool approach for phage identification and analysis is now available. Implemented in Nextflow with Docker/Singularity support.

24. May 2020
I am very happy to be able to contribute to this review on workflows and tools that have been developed by the virus bioinformatics community as a rapid reaction to the COVID19 pandemic! Also check this comprehensive (yet incomplete) collection of tools and resources for virus detection, annotation, tracking and drug design.

22. May 2020
I am happy to announce that PoSeiDon, a pipeline to detect significantly positive selected sites and possible recombination events in an alignment of multiple protein-coding sequences, is now available as a Nextflow w/ Dockers! And a small preprint is also out.

21. May 2020
You really like Prokka to annotate your bacterial genomes? But sometimes there are so many hypothetical proteins? Try out our small tool HyPro where we extend hypothetical protein annotations from Prokka using additional homology searches against larger databases.

19. May 2020
Interested in the detection of B-cell epitopes? The identification of this small but diagnostically relevant protein regions is a challenging task that usually involves extensive laboratory work. By using a deep neural network EpiDope detects B-cell epitope regions on individual protein sequences!

10. February 2020
Are you looking for some easy to run tool w/o dependency-struggle to analyze your hybrid metagenomics data? Including state-of-the-art principals of diff binning and pathways? Check out MUFFIN!

02. February 2020
Our pipeline RIBAP for the automatic annotation and core gene set calculation/visualization of bacterial genomes is now available as a Nextflow/Docker/Conda workflow. Annotate your protein sequences with Prokka and determine a pan genome with Roary. This genome is refined with the usage of ILPs that solve the best matching for each pairwise strain mmseqs2 comparison.

06. January 2020
Already in the old year Lasse submitted his master’s thesis, which dealt with the efficient clustering of multi-tool transcriptome assemblies. Now he is about to take his bioinformatics knowledge out into the world. We wish him all the best and much success for his future career!

19. December 2019
Just before Christmas, our joint AquaDiva study on the hybrid metagenome assembly of a complex groundwater sample appeared as a new preprint on BioRxiv. We show, that the inclusion of Nanopore long reads improves metagenome assemblies of microbes and phages. A fun read during the holidays ;) Happy X-mas!

10. December 2019
Have you ever downloaded hundreds of GBs for a sequence classification task to ultimately get 10k E. coli strains reported? Thin your genome collections! New preprint.

20. November 2019
Martin went for a hands-on workshop on Nanopore sequencing to the Indian Institute of Technology in Delhi, teaching as a part of a great team about the technology itself, metagenomics analysis and antimicrobial resistance detection.

15. October 2019
Congratulations to Lisa for her Master’s degree in molecular life sciences, which she finally received from the University of Jena. A well done pangenome comparison of different Chlamydia strains that will most likely result in a more biology-focused and a computational publication. Stay tuned.

03. October 2019
Our comprehensive annotation of short and long ncRNAs in 16 bat genome assemblies got published at NAR Genomics and Bioinformatics! Many thanks to Manja and the whole Jena RNA group for this great team effort! Final annotations and all results can be found in our online ressource.

30. September 2019
Martin has just moved to Cambridge UK to work for half a year in Rob Finn’s research group at the European Bioinformatics Institute in Hinxton on metagenomic approaches involving Nanopore long reads. The small associated lab in Jena remains - thanks to Remote, office not required.

23. September 2019
Congratz to Sandra, who just handed in her bachelor thesis about the hybrid assembly of small but highly repetitive bacterial genomes combining Illumina and Nanopore data. Cool work and well done, Sandra! It was a pleasure to be able to support you on this path!

21. September 2019
Today, Martin is presenting his project within CRC AquaDiva at his second fellowship meeting of interdisciplinary life science at the Joachim Herz Stiftung in Hamburg; talking about the detection of viruses from groundwater samples using nanopores.

05. September 2019
Yeah! We made it onto the cover of Genome Research by sequencing and analyzing large and highly complex RNA genomes of coronaviruses in their native form using nanopores! Thx to Beetlebum for the great art and the Jena RNA group for the great science! Thx at John Ziebuhr and Rama Madhugiri, our wet lab partners at the JLU Giessen.

16. August 2019
Our tool PCAGO for the interactive analysis and visualization of RNA-Seq expression data (preprint) can now be simply used locally with the help of an Docker image. Thanks, Lasse!

13. August 2019
Bats are impressive! Our manuscript dealing with the RNA-Seq analysis of cells from a small bat species, Myotis daubentonii, got accepted in iScience! We investigated the transcriptome response to a viral infection or stimulation with interferon (IFN) at two time points. Many thanks to our partners at the Institute for Virology, JLU Giessen.

26. June 2019
Our manuscript about a new Chlamydia species isolated from a red-shouldered hawk got published in Systematic and Applied Microbiology! We are pleased that we were able to help with data evaluation and assembly to ultimately define this new species.

10. June 2019
Martin is now a member of the external advisory board of the EU project “Digital Skills on Computational Biology for Health Professionals” (BioS). BioS aims at advancing the computational skills of medical doctors through the design, development and delivery of new modular vocational curricula on computational biology & bioinformatics.

03. June 2019
This week Martin will visit the European Bioinformatics Institute (EMBl EBI) at Wellcome Genome Campus, Hinxton, UK; to attend a workshop about “Managing a Bioinformatics Core Facility”.

28. May 2019
Sequencing viruses from low amount of DNA is a challenging task. In our recent study, published at Viruses today, we investigated different DNA amplification methods to prep libaries for Illumina sequencing of viral metagenomes obtained from pristine aquifer groundwaters. The work is part of the CRC AquaDiva and will help us to further investigate viruses in the ground water.

16. May 2019
Our work about influenza virus models got published at Viruses today! We applied Chemical Organization Theory to reveal a hierarchy of mathematical infection models and show, among other things, the need for further models for co-infections. It was a crazy and funny journey into a more theoretical field of research.

13. May 2019
Our paper about the comprehensive comparison of de novo short-read transcriptome assembly tools across different species got published in GigaScience today! In short, a combination of assembly tools such as Trinity, rnaSPAdes, and Trans-ABySS, which are still well maintained, should be preferred.

7. May 2019
Today, Martin is visiting Nick Lomans group at the University of Birmingham, School of Biosciences, Institute of Microbiology and Infection. His group is working on microbial genomics and real-time diagnostics using bioinformatics.

18. March 2019
Over the next two weeks we look forward to learning a lot about viruses, sharing our knowledge about bioinformatics and meeting old and new collaboration-friends at two great conferences on viruses, the 29th Annual Meeting of the Society for Virology in Düsseldorf and the 3rd annual meeting of the European Virus Bioinformatics Center in Glasgow.

06. February 2019
Yeah, our application was approved and we receive over 1.3 million euros from the Thuringian Ministry of Science to advance the digitization of life sciences. Together with eleven other researchers from the university, hospital, non-university research institutes and the private sector we will work on new methods to support researchers in life sciences using AI.

13. January 2019
With the support of the University of Jena we have a one-year position for a student assistant at our disposal. You will support us with the data analysis of pre-experiments of direct RNA long-read data for a grant application. Apply now!

10. December 2018
Our paper on hematopoietic stem cell self-renewal in aging and inflammation limited by cohesin-mediated NF-κB signaling is out in the Journal of Experimental Medicine! We had the great honour of contributing the computer-assisted RNA-Seq analysis part to this impressive study.

02. December 2018
Our preprint about the full-lenght direct RNA sequencing of coronaviruses using nanopores is out. The longest reads cover nearly the full 27kb RNA genome of the virus!

20. November 2018
You want to analyze effects of point mutations on the secondary structures of two interacting viral RNAs? Our bioRxiv preprint was just accepted at Virus Research. Check it out!

31. October 2018
Searching for a LaTeX template for your DFG grant proposal? Check out!

01. October 2018
Directly after the GCB, the whole lab is attending the 16. Herbstseminar der Bioinformatik in Doubice, Czech. Looking forward to lots of RNA bioinformatics, viroInformatics, and pivo.

24. September 2018
This week the German Conference on Bioinformatics takes place in Vienna. Meet Martin at poster 8 to discuss about current challenges and advantages in nanopore long-read sequencing.

19. September 2018
Excited to announce that Martin just received a two-year Add-on Fellowship for Interdisciplinary Life Science of the Joachim Herz Stiftung.

10. September 2018
Students asked for it and here it is - our first practical course on virusinformatics! Two weeks of students facing our day-to-day problems in virus bioinformatics.

03. September 2018
Our LaTeX course starts today (2018/09/03-2018/09/07). The second course will be held from 2018/09/17 to 2018/09/21.

26. August 2018
The 23rd International Bioinformatics Workshop on Virus Evolution/Molecular Epidemiology (VEME) starts today in Berlin, Germany. The EVBC supports!

23. July 2018
Today, Martin is going to Vancouver to give a keynote talk about the EVBC as an interface between bioinformatics and virology at the 11th International Conference on Virology and Microbiology.

20. July 2018
Hölzer Lab web page is live!
Thanks to Github Pages, Jekyll, and the Allan Lab template!