E-Mail: tom.eulenfeld@uni-jena.de
Room: 4006
Phone: +49-3641-9-46484
I am a scientific programmer with a background in physics and seismology. As a side project, I develop sugar, a lightweight Python toolkit for working with DNA/RNA sequences and bioinformatics file formats. Check it out on GitHub along with my other software projects. If you’re curious about my pre-bioinformatics days, older papers are listed on Google Scholar.
Publications
2025
Eulenfeld, Tom; Triebel, Sandra; Marz, Manja
AnchoRNA: Full virus genome alignments through conserved anchor regions Journal Article
In: bioRxiv, 2025.
@article{nokey_67,
title = {AnchoRNA: Full virus genome alignments through conserved anchor regions},
author = {Tom Eulenfeld and Sandra Triebel and Manja Marz},
doi = {10.1101/2025.01.30.635689},
year = {2025},
date = {2025-12-15},
urldate = {2025-02-01},
journal = {bioRxiv},
abstract = {Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), large number of sequences, sequence divergence, and high computational complexity in particular when computing alignments based on RNA secondary structures. Standard alignment methods often face these issues, in particular when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences.
We present an algorithm to determine high quality anchors that define partitions of sequences and guide the alignment of viral genomes to respect well conserved, and therefore functionally significant, regions. This new approach is implemented in the Python-based command line tool AnchoRNA, which is designed to identify conserved regions, or anchors, within coding sequences. By default, anchors are searched in translated coding sequences accounting for high mutation rates in viral genomes. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 55 anchors that are used for guiding the alignment process. The incorporation of these anchors led to improvements across tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in viral genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Multiple sequence alignment of full viral genomes can be challenging due to factors such as long sequences, large insertions/deletions (spanning several 100 nucleotides), large number of sequences, sequence divergence, and high computational complexity in particular when computing alignments based on RNA secondary structures. Standard alignment methods often face these issues, in particular when processing highly variable sequences or when specific phylogenetic analysis is required on selected subsequences.
We present an algorithm to determine high quality anchors that define partitions of sequences and guide the alignment of viral genomes to respect well conserved, and therefore functionally significant, regions. This new approach is implemented in the Python-based command line tool AnchoRNA, which is designed to identify conserved regions, or anchors, within coding sequences. By default, anchors are searched in translated coding sequences accounting for high mutation rates in viral genomes. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 55 anchors that are used for guiding the alignment process. The incorporation of these anchors led to improvements across tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in viral genomes.
We present an algorithm to determine high quality anchors that define partitions of sequences and guide the alignment of viral genomes to respect well conserved, and therefore functionally significant, regions. This new approach is implemented in the Python-based command line tool AnchoRNA, which is designed to identify conserved regions, or anchors, within coding sequences. By default, anchors are searched in translated coding sequences accounting for high mutation rates in viral genomes. AnchoRNA enhances the accuracy and efficiency of full-genome alignment by focusing on these crucial conserved regions. AnchoRNA guided alignments are systematically compared to the results of 3 alignment programs. Utilizing a dataset of 55 representative Pestivirus genomes, AnchoRNA identified 55 anchors that are used for guiding the alignment process. The incorporation of these anchors led to improvements across tested alignment tools, highlighting the effectiveness of AnchoRNA in enhancing alignment quality, especially in viral genomes.
Triebel, Sandra; Eulenfeld, Tom; Ontiveros-Palacios, Nancy; Sweeney, Blake; Tautz, Norbert; Marz, Manja
First full-genome alignment representative for the genus Pestivirus Journal Article
In: bioRxiv, 2025.
@article{nokey_77,
title = {First full-genome alignment representative for the genus \textit{Pestivirus}},
author = {Sandra Triebel and Tom Eulenfeld and Nancy Ontiveros-Palacios and Blake Sweeney and Norbert Tautz and Manja Marz},
url = {https://doi.org/10.5281/zenodo.15490752},
doi = {10.1101/2025.05.22.655560},
year = {2025},
date = {2025-05-27},
journal = {bioRxiv},
abstract = {The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3’ stem-loop essential for genome replication, had already been studied for a few individual pestiviruses.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3’ stem-loop essential for genome replication, had already been studied for a few individual pestiviruses.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.
In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5’ stem-loop structure, the IRES element, and the 3’ stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3’ untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3’ end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.
2024
Ritsch, Muriel; Eulenfeld, Tom; Lamkiewicz, Kevin; Schoen, Andreas; Weber, Friedemann; Hölzer, Martin; Marz, Manja
In: Viruses, vol. 16, iss. 8, 2024, ISSN: 1999-4915.
@article{nokey_66,
title = {Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in \textit{Myotis daubentonii}},
author = {Muriel Ritsch and Tom Eulenfeld and Kevin Lamkiewicz and Andreas Schoen and Friedemann Weber and Martin Hölzer and Manja Marz},
doi = {10.3390/v16081210},
issn = {1999-4915},
year = {2024},
date = {2024-07-27},
urldate = {2024-07-27},
journal = {Viruses},
volume = {16},
issue = {8},
abstract = {Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat \textit{Myotis daubentonii}, EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a \textit{Cultervirus} (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in \textit{Myotis daubentonii} tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 \textit{Yangochiropera<i/> and 12 \textit{Yinpterochiroptera} species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat Myotis daubentonii, EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a Cultervirus (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in Myotis daubentonii tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 Yangochiropera<i/> and 12 Yinpterochiroptera species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.