Bioinformatics and Translational Research

Publications

We conduct research to bridge the gap between life sciences and computer science, employing advanced sequencing technologies to analyze (meta-)genomic and transcriptomic datasets related to infectious diseases, immunology, and medical sciences. With this interdisciplinary approach, we aim to improve our understanding of pathogen-host interactions and support genomic surveillance and containment. We perform research in the following areas:

Highlighted

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D. Finn
PLOS Computational Biology  ·  28 Aug 2023  ·  doi:10.1371/journal.pcbi.1011422
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Eva Aßmann, Shelesh Agrawal, Laura Orschler, Sindy Böttcher, Susanne Lackner, Martin Hölzer
Cold Spring Harbor Laboratory  ·  02 Jun 2023  ·  doi:10.1101/2023.06.02.543047

All

Note: this list currently includes all publications by lab members, including work they may have published while they were in previous labs.

2025

Genomic Donor-Recipient Mismatches in Kidney Transplantation: A Focus on the Techniques and Approaches
Genomic Donor-Recipient Mismatches in Kidney Transplantation: A Focus on the Techniques and Approaches
Stephen Shoebridge, Andreas Heinzel, Michael Kammer, Adèle Dhuyser, Hugues Richard, Laurent Mesnard, Rainer Oberbauer
Current Transplantation Reports  ·  30 Aug 2025  ·  doi:10.1007/s40472-025-00492-6
Next-Generation Sequencing Analysis in Greek Patients with Predominantly Antibody Deficiencies
Next-Generation Sequencing Analysis in Greek Patients with Predominantly Antibody Deficiencies
Achilleas P. Galanopoulos, Sofia Raftopoulou, Styliani Sarrou, Alexia Matziri, Stamatia Papoutsopoulou, …, Varvara A. Mouchtouri, Martin Hölzer, Christos Hadjichristodoulou, Fani Kalala, Matthaios Speletas
Immuno  ·  16 Jul 2025  ·  doi:10.3390/immuno5030027
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest
Katrina Norwood, Zhi-Luo Deng, Susanne Reimering, Gary Robertson, Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Martin Hölzer, Frank Klawonn, Alice C. McHardy
Nature Communications  ·  08 Jul 2025  ·  doi:10.1038/s41467-025-60231-4
Targeted decontamination of sequencing data with CLEAN
Targeted decontamination of sequencing data with CLEAN
Marie Lataretu, Sebastian Krautwurst, Matthew R Huska, Mike Marquet, Adrian Viehweger, Sascha D Braun, Christian Brandt, Martin Hölzer
NAR Genomics and Bioinformatics  ·  04 Jul 2025  ·  doi:10.1093/nargab/lqaf105
Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance
Augmentation of wastewater-based epidemiology with machine learning to support global health surveillance
Eva Aßmann, Timo Greiner, Hugues Richard, Matthew Wade, Shelesh Agrawal, …, Alexander Ullrich, Max von Kleist, Emanuel Wyler, Martin Hölzer, Christopher Irrgang
Nature Water  ·  02 Jun 2025  ·  doi:10.1038/s44221-025-00444-5
Leveraging wastewater sequencing to strengthen global public health surveillance
Leveraging wastewater sequencing to strengthen global public health surveillance
Victor Gordeev, Martin Hölzer, Daniel Desirò, Iryna V. Goraichuk, Sergey Knyazev, …, Mihai Covasa, Roel A. Ophoff, Alex Zelikovsky, Mihai Dimian, Serghei Mangul
BMC Global and Public Health  ·  21 Mar 2025  ·  doi:10.1186/s44263-025-00138-w
Decoding bacterial methylomes in four public health-relevant microbial species: Nanopore sequencing enables reproducible analysis of DNA modifications
Decoding bacterial methylomes in four public health-relevant microbial species: Nanopore sequencing enables reproducible analysis of DNA modifications
Valentina Galeone, Johanna Dabernig-Heinz, Mara Lohde, Christian Brandt, Christian Kohler, Gabriel E. Wagner, Martin Hölzer
Cold Spring Harbor Laboratory  ·  02 Feb 2025  ·  doi:10.1101/2025.01.29.635492
SARS-CoV-2 evolution on a dynamic immune landscape
SARS-CoV-2 evolution on a dynamic immune landscape
N. Alexia Raharinirina, Nils Gubela, Daniela Börnigen, Maureen Rebecca Smith, Djin-Ye Oh, …, Ralf Dürrwald, Thorsten Wolff, Martin Hölzer, Sofia Paraskevopoulou, Max von Kleist
Nature  ·  29 Jan 2025  ·  doi:10.1038/s41586-024-08477-8
Exploring the genomic landscape of Chlamydiifrater species: Novel features include multiple truncated major outer membrane proteins MOMP , unique genes, and chlamydial plasticity zone orthologs
Exploring the genomic landscape of Chlamydiifrater species: Novel features include multiple truncated major outer membrane proteins (MOMP), unique genes, and chlamydial plasticity zone orthologs
Martin Hölzer, Charlotte Reuschel, Fabien Vorimore, Karine Laroucau, Konrad Sachse
Microbiology Society  ·  06 Jan 2025  ·  doi:10.1099/acmi.0.000936.v2
VirusWarn: A mutation-based early warning system to prioritize concerning SARS-CoV-2 and influenza virus variants from sequencing data
VirusWarn: A mutation-based early warning system to prioritize concerning SARS-CoV-2 and influenza virus variants from sequencing data
Christina Kirschbaum, Kunaphas Kongkitimanon, Stefan Frank, Martin Hölzer, Sofia Paraskevopoulou, Hugues Richard
Computational and Structural Biotechnology Journal  ·  01 Jan 2025  ·  doi:10.1016/j.csbj.2025.03.010
Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs
Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs
Martin Hölzer, Charlotte Reuschel, Fabien Vorimore, Karine Laroucau, Konrad Sachse
Access Microbiology  ·  01 Jan 2025  ·  doi:10.1099/acmi.0.000936.v3

2024

Exploring the genomic landscape of Chlamydiifrater species: Novel features include multiple truncated CDS of the major outer membrane porin MOMP , more than 150 unique genes, and an ortholog of the chlamydial plasticity zone
Exploring the genomic landscape of Chlamydiifrater species: Novel features include multiple truncated CDS of the major outer membrane porin (MOMP), more than 150 unique genes, and an ortholog of the chlamydial plasticity zone
Martin Hölzer, Charlotte Reuschel, Fabien Vorimore, Karine Laroucau, Konrad Sachse
Microbiology Society  ·  23 Oct 2024  ·  doi:10.1099/acmi.0.000936.v1
Systematic Screening of Autosomal Dominant Tubulointerstitial Kidney Disease MUC1 27dupC Pathogenic Variant through Exome Sequencing
Systematic Screening of Autosomal Dominant Tubulointerstitial Kidney Disease–MUC1 27dupC Pathogenic Variant through Exome Sequencing
Ilias Bensouna, Thomas Robert, Xavier Vanhoye, Marine Dancer, Laure Raymond, Pierre Delaugère, Pascale Hilbert, Hugues Richard, Laurent Mesnard
Journal of the American Society of Nephrology  ·  26 Sep 2024  ·  doi:10.1681/ASN.0000000503
CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection
CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection
Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs
Viruses  ·  11 Sep 2024  ·  doi:10.3390/v16091444
Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics
Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics
Christian Blumenscheit, Yvonne Pfeifer, Guido Werner, Charlyn John, Franziska Layer-Nicolaou, Andy Schneider, Peter Lasch, Joerg Doellinger
Cold Spring Harbor Laboratory  ·  09 Sep 2024  ·  doi:10.1101/2024.09.09.612008
Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in Myotis daubentonii
Endogenous Bornavirus-like Elements in Bats: Evolutionary Insights from the Conserved Riboviral L-Gene in Microbats and Its Antisense Transcription in Myotis daubentonii
Muriel Ritsch, Tom Eulenfeld, Kevin Lamkiewicz, Andreas Schoen, Friedemann Weber, Martin Hölzer, Manja Marz
Viruses  ·  27 Jul 2024  ·  doi:10.3390/v16081210
RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level
RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level
Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer
Genome Biology  ·  01 Jul 2024  ·  doi:10.1186/s13059-024-03312-9
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
F1000Research  ·  16 Apr 2024  ·  doi:10.12688/f1000research.136683.2
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy
Martin Hölzer
Bioinformatics  ·  29 Mar 2024  ·  doi:10.1093/bioinformatics/btae175
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest
Katrina Norwood, Zhi-Luo Deng, Susanne Reimering, Gary Robertson, Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Martin Hoelzer, Alice Carolyn McHardy
Cold Spring Harbor Laboratory  ·  08 Mar 2024  ·  doi:10.1101/2024.03.07.583829
ICTV Virus Taxonomy Profile: Kolmioviridae 2024
ICTV Virus Taxonomy Profile: Kolmioviridae 2024
Jens H. Kuhn, Artem Babaian, Laura M. Bergner, Paul Dény, Dieter Glebe, …, Mart Krupovic, Sofia Paraskevopoulou, Marcos de la Peña, Teemu Smura, Jussi Hepojoki
Journal of General Virology  ·  29 Feb 2024  ·  doi:10.1099/jgv.0.001963
Reannotation of the zebra finch genome reveals undiscovered transcriptional complexity
Reannotation of the zebra finch genome reveals undiscovered transcriptional complexity
Hugues Richard, John Wiedenhoeft, Constance Scharff, Iris Adam
Cold Spring Harbor Laboratory  ·  09 Jan 2024  ·  doi:10.1101/2024.01.09.574630
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Eva Aßmann, Shelesh Agrawal, Laura Orschler, Sindy Böttcher, Susanne Lackner, Martin Hölzer
GigaScience  ·  01 Jan 2024  ·  doi:10.1093/gigascience/giae051

2023

Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques
Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques
Daria Meyer, Winfried Goettsch, Jannes Spannenberg, Bettina Stieber, Sebastian Krautwurst, …, Christian Höner zu Siederdissen, Akash Srivastava, Milena Zarkovic, Damian Wollny, Manja Marz
Cold Spring Harbor Laboratory  ·  07 Dec 2023  ·  doi:10.1101/2023.12.06.570356
Dicer dependent heterochromatic small scp RNAs scp in the model diatom species i Phaeodactylum tricornutum i
Dicer‐dependent heterochromatic small RNAs in the model diatom species Phaeodactylum tricornutum
Emilia Grypioti, Hugues Richard, Nikoleta Kryovrysanaki, Marianne Jaubert, Angela Falciatore, Frédéric Verret, Kriton Kalantidis
New Phytologist  ·  03 Dec 2023  ·  doi:10.1111/nph.19429
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi
Microbiome  ·  06 Nov 2023  ·  doi:10.1186/s40168-023-01670-3
aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
iScience  ·  01 Nov 2023  ·  doi:10.1016/j.isci.2023.108057
Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds
Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds
Joachim Vater, Le Thi Thanh Tam, Jennifer Jähne, Stefanie Herfort, Christian Blumenscheit, …, Jochen Blom, Silke R. Klee, Thomas Schweder, Peter Lasch, Rainer Borriss
Microorganisms  ·  31 Oct 2023  ·  doi:10.3390/microorganisms11112677
ICTV Virus Taxonomy Profile: Xinmoviridae 2023
ICTV Virus Taxonomy Profile: Xinmoviridae 2023
Stephen Sharpe, Sofia Paraskevopoulou
Journal of General Virology  ·  26 Oct 2023  ·  doi:10.1099/jgv.0.001906
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
F1000Research  ·  01 Sep 2023  ·  doi:10.12688/f1000research.136683.1
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D. Finn
PLOS Computational Biology  ·  28 Aug 2023  ·  doi:10.1371/journal.pcbi.1011422
Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020 2022
Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020–2022
Christian Kohler, Jacqueline King, Lina Stacker, Katja V. Goller, Juliane Moritz, …, Janine Ziemann, Lars Kaderali, Martin Beer, Nils-Olaf Hübner, Karsten Becker
Emerging Microbes & Infections  ·  22 Aug 2023  ·  doi:10.1080/22221751.2023.2245916
Targeted decontamination of sequencing data with CLEAN
Targeted decontamination of sequencing data with CLEAN
Marie Lataretu, Sebastian Krautwurst, Matthew R. Huska, Mike Marquet, Adrian Viehweger, Sascha D. Braun, Christian Brandt, Martin Hölzer
Cold Spring Harbor Laboratory  ·  06 Aug 2023  ·  doi:10.1101/2023.08.05.552089
Annual 2023 taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses realm
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm
Jens H Kuhn, Junya Abe, Scott Adkins, Sergey V Alkhovsky, Tatjana Avšič-Županc, …, Guilin Zhang, Song Zhang, Yong-Zhen Zhang, Lu Zhao, Arnfinn Lodden Økland
The Journal of general virology  ·  01 Aug 2023  ·  pmid:37622664
ICTV Virus Taxonomy Profile: Lispiviridae 2023
ICTV Virus Taxonomy Profile: Lispiviridae 2023
Jun-Min Li, Fei Wang, Gongyin Ye, Sofia Paraskevopoulou
Journal of General Virology  ·  11 Jul 2023  ·  doi:10.1099/jgv.0.001869
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Eva Aßmann, Shelesh Agrawal, Laura Orschler, Sindy Böttcher, Susanne Lackner, Martin Hölzer
Cold Spring Harbor Laboratory  ·  02 Jun 2023  ·  doi:10.1101/2023.06.02.543047
Sequential disruption of SPLASH-identified vRNA vRNA interactions challenges their role in influenza A virus genome packaging
Sequential disruption of SPLASH-identified vRNA–vRNA interactions challenges their role in influenza A virus genome packaging
Celia Jakob, Gabriel L Lovate, Daniel Desirò, Lara Gießler, Redmond P Smyth, Roland Marquet, Kevin Lamkiewicz, Manja Marz, Martin Schwemmle, Hardin Bolte
Nucleic Acids Research  ·  24 May 2023  ·  doi:10.1093/nar/gkad442
Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs
Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs
Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer
Cold Spring Harbor Laboratory  ·  07 May 2023  ·  doi:10.1101/2023.05.05.539552
Building alternative splicing and evolution-aware sequence-structure maps for protein repeats
Building alternative splicing and evolution-aware sequence-structure maps for protein repeats
Antoine Szatkownik, Diego Javier Zea, Hugues Richard, Elodie Laine
Cold Spring Harbor Laboratory  ·  30 Apr 2023  ·  doi:10.1101/2023.04.29.538821
Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition Proteomics
Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition Proteomics
Joerg Doellinger, Christian Blumenscheit, Andy Schneider, Peter Lasch
Journal of Proteome Research  ·  18 Apr 2023  ·  doi:10.1021/acs.jproteome.3c00078
i De novo i genome assembly resolving repetitive structures enables genomic analysis of 35 European i Mycoplasma bovis i strains
De novogenome assembly resolving repetitive structures enables genomic analysis of 35 EuropeanMycoplasma bovisstrains
Sandra Triebel, Konrad Sachse, Michael Weber, Martin Heller, Celia Diezel, Martin Hölzer, Christiane Schnee, Manja Marz
Cold Spring Harbor Laboratory  ·  13 Apr 2023  ·  doi:10.1101/2023.04.13.536562
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Wang Liu-Wei, Wiep van der Toorn, Patrick Bohn, Martin Hölzer, Redmond Smyth, Max von Kleist
Cold Spring Harbor Laboratory  ·  30 Mar 2023  ·  doi:10.1101/2023.03.29.534691
Nanopore-based enrichment of antimicrobial resistance genes a case-based study
Nanopore-based enrichment of antimicrobial resistance genes – a case-based study
Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias W. Pletz, Christian Brandt
Gigabyte  ·  25 Jan 2023  ·  doi:10.46471/gigabyte.75
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2
Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt
Database  ·  01 Jan 2023  ·  doi:10.1093/database/baad071

2022

Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity
Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity
Thomas BK Watkins, Emma C Colliver, Mathew R Huska, Tom L Kaufmann, Emilia L Lim, Kerstin Haase, Peter Van Loo, Charles Swanton, Nicholas McGranahan, Roland F Schwarz
Cold Spring Harbor Laboratory  ·  17 Oct 2022  ·  doi:10.1101/2022.10.13.511885
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility.
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility.
Aaztli Coria, Anastacia Wienecke, Michael L Knight, Daniel Desirò, Alain Laederach, Alexander Borodavka
Nucleic acids research  ·  23 Sep 2022  ·  pmid:36062555
Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics
Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics
Joerg Doellinger, Christian Blumenscheit, Andy Schneider, Peter Lasch
Cold Spring Harbor Laboratory  ·  13 Sep 2022  ·  doi:10.1101/2022.09.12.507556
VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina Sakharova, Manja Marz, Alejandro Reyes Muñoz, Martin Hölzer, Robert D. Finn
Cold Spring Harbor Laboratory  ·  22 Aug 2022  ·  doi:10.1101/2022.08.22.504484
Women in the European Virus Bioinformatics Center
Women in the European Virus Bioinformatics Center
Franziska Hufsky, Ana Abecasis, Patricia Agudelo-Romero, Magda Bletsa, Katherine Brown, …, Lore Van Espen, Anne-Mieke Vandamme, Maryam Zaheri, Neta Zuckerman, Manja Marz
Viruses  ·  12 Jul 2022  ·  doi:10.3390/v14071522
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M Bartoszewicz, …, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y Renard, Stephan Fuchs
Bioinformatics  ·  07 Jul 2022  ·  doi:10.1093/bioinformatics/btac411
Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021
Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021
Djin Ye Oh, Martin Hölzer, Sofia Paraskevopoulou, Maria Trofimova, Felix Hartkopf, …, Markus Petzold, Thomas Schwanz, Florian Szabados, Friedemann Tewald, Carsten Tiemann
Clinical Infectious Diseases  ·  25 Jun 2022  ·  doi:10.1093/cid/ciac399
Synopse virologischer Analysen im Nationalen Referenzzentrum für Influenzaviren während der COVID-19-Pandemie
Synopse virologischer Analysen im Nationalen Referenzzentrum für Influenzaviren während der COVID-19-Pandemie
Ralf Dürrwald, Marianne Wedde, Susanne Duwe, Barbara Biere, Janine Reiche, …, Katja Winter, Martin Mielke, Silke Buda, Djin-Ye Oh, Thorsten Wolff
Robert Koch-Institut  ·  02 Jun 2022  ·  doi:10.25646/10118
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome
Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann, Andrea Volkamer
Journal of Chemical Information and Modeling  ·  10 May 2022  ·  doi:10.1021/acs.jcim.2c00050
History and classification of Aigai virus formerly Crimean Congo haemorrhagic fever virus genotype VI
History and classification of Aigai virus (formerly Crimean–Congo haemorrhagic fever virus genotype VI)
Anna Papa (Άννα Παπά), Marco Marklewitz, Sofia Paraskevopoulou (Σοφία Παρασκευοπούλου), Aura R. Garrison, Sergey V. Alkhovsky (Альховский Сергей Владимирович), …, Amadou Alpha Sall, Jessica R. Spengler, Thomas S. Postler, Gustavo Palacios, Jens H. Kuhn
Journal of General Virology  ·  12 Apr 2022  ·  doi:10.1099/jgv.0.001734
Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe
Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe
Etienne SIMON-LORIERE, Xavier Montagutelli, Frederic Lemoine, Flora Donati, Franck Touret, …, Yazdan Yazdanpanah, Bruno Coignard, Xavier de Lamballerie, Sylvie van der Werf, Axelle Paquin
Springer Science and Business Media LLC  ·  04 Apr 2022  ·  doi:10.21203/rs.3.rs-1502293/v1
Genome sequence data of Bacillus velezensis BP1.2A and BT2.4
Genome sequence data of Bacillus velezensis BP1.2A and BT2.4
Christian Blumenscheit, Jennifer Jähne, Andy Schneider, Jochen Blom, Thomas Schweder, Peter Lasch, Rainer Borriss
Data in Brief  ·  01 Apr 2022  ·  doi:10.1016/j.dib.2022.107978
i Jingchuvirales i : a New Taxonomical Framework for a Rapidly Expanding Order of Unusual Monjiviricete Viruses Broadly Distributed among Arthropod Subphyla
Jingchuvirales : a New Taxonomical Framework for a Rapidly Expanding Order of Unusual Monjiviricete Viruses Broadly Distributed among Arthropod Subphyla
Nicholas Di Paola, Nolwenn M. Dheilly, Sandra Junglen, Sofia Paraskevopoulou, Thomas S. Postler, Mang Shi, Jens H. Kuhn
Applied and Environmental Microbiology  ·  22 Mar 2022  ·  doi:10.1128/aem.01954-21
Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence
Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence
Giselle C. Martín-Hernández, Bettina Müller, Christian Brandt, Martin Hölzer, Adrian Viehweger, Volkmar Passoth
Journal of Fungi  ·  22 Mar 2022  ·  doi:10.3390/jof8040323
ASES: visualizing evolutionary conservation of alternative splicing in proteins
ASES: visualizing evolutionary conservation of alternative splicing in proteins
Diego Javier Zea, Hugues Richard, Elodie Laine
Bioinformatics  ·  21 Feb 2022  ·  doi:10.1093/bioinformatics/btac105
Investigation of a Limited but Explosive COVID-19 Outbreak in a German Secondary School
Investigation of a Limited but Explosive COVID-19 Outbreak in a German Secondary School
Sigrid Baumgarte, Felix Hartkopf, Martin Hölzer, Max von Kleist, Sabine Neitz, Martin Kriegel, Kirsten Bollongino
Viruses  ·  04 Jan 2022  ·  doi:10.3390/v14010087
What the Phage: a scalable workflow for the identification and analysis of phage sequences
What the Phage: a scalable workflow for the identification and analysis of phage sequences
Mike Marquet, Martin Hölzer, Mathias W Pletz, Adrian Viehweger, Oliwia Makarewicz, Ralf Ehricht, Christian Brandt
GigaScience  ·  01 Jan 2022  ·  doi:10.1093/gigascience/giac110

2021

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
Sara Saheb Kashaf, Diana M. Proctor, Clay Deming, Paul Saary, Martin Hölzer, …, Monica E. Taylor, Heidi H. Kong, Julia A. Segre, Alexandre Almeida, Robert D. Finn
Nature Microbiology  ·  24 Dec 2021  ·  doi:10.1038/s41564-021-01011-w
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae
Adrian Viehweger, Christian Blumenscheit, Norman Lippmann, Kelly L. Wyres, Christian Brandt, …, Sören Gatermann, Christoph Lübbert, Mathias W. Pletz, Kathryn E. Holt, Brigitte König
Microbial Genomics  ·  24 Dec 2021  ·  doi:10.1099/mgen.0.000741
2021 Taxonomic update of phylum Negarnaviricota Riboviria: Orthornavirae , including the large orders Bunyavirales and Mononegavirales.
2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Jens H Kuhn, Scott Adkins, Bernard R Agwanda, Rim Al Kubrusli, Sergey V Alkhovsky, …, Yong-Zhen Zhang, Song Zhang, Jinguo Zhang, Zhe Zhang, Xueping Zhou
Archives of virology  ·  01 Dec 2021  ·  pmid:34463877
ICTV Virus Taxonomy Profile: Nyamiviridae 2021
ICTV Virus Taxonomy Profile: Nyamiviridae 2021
Ralf G. Dietzgen, Andrew E. Firth, Dàohóng Jiāng, Sandra Junglen, Hideki Kondo, Jens H. Kuhn, Sofia Paraskevopoulou, Nikos Vasilakis
Journal of General Virology  ·  05 Nov 2021  ·  doi:10.1099/jgv.0.001681
Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in i Lepidium i Brassicaceae
Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)
Lydia Gramzow, Katharina Klupsch, Noé Fernández Pozo, Martin Hölzer, Manja Marz, Stefan A. Rensing, Günter Theißen
Cold Spring Harbor Laboratory  ·  01 Nov 2021  ·  doi:10.1101/2021.10.29.466389
Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics
Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics
Christian Blumenscheit, Yvonne Pfeifer, Guido Werner, Charlyn John, Andy Schneider, Peter Lasch, Joerg Doellinger
Analytical Chemistry  ·  26 Oct 2021  ·  doi:10.1021/acs.analchem.1c00594
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants
Anna Sommer, Stephan Fuchs, Franziska Layer, Christoph Schaudinn, Robert E. Weber, …, Mareike B. Erdmann, Michael Laue, Christopher F. Schuster, Guido Werner, Birgit Strommenger
Microbial Genomics  ·  09 Sep 2021  ·  doi:10.1099/mgen.0.000623
Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany
Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany
Sébastien Calvignac-Spencer, Matthias Budt, Matthew Huska, Hugues Richard, Luca Leipold, …, Torsten Semmler, Max von Kleist, Stefan Kröger, Thorsten Wolff, Martin Hölzer
Viruses  ·  29 Jul 2021  ·  doi:10.3390/v13081491
The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers
The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers
Narendrakumar M. Chaudhari, Will A. Overholt, Perla Abigail Figueroa-Gonzalez, Martin Taubert, Till L. V. Bornemann, Alexander J. Probst, Martin Hölzer, Manja Marz, Kirsten Küsel
Cold Spring Harbor Laboratory  ·  29 Jul 2021  ·  doi:10.1101/2021.07.28.454184
Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo Phoenicopterus roseus : Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.
Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.
F. Vorimore, M. Hölzer, E.M. Liebler-Tenorio, L.-M. Barf, S. Delannoy, …, R.C. Hsia, P.M. Bavoil, R. Rosselló-Móra, K. Laroucau, K. Sachse
Systematic and Applied Microbiology  ·  01 Jul 2021  ·  doi:10.1016/j.syapm.2021.126200
Assessing conservation of alternative splicing with evolutionary splicing graphs
Assessing conservation of alternative splicing with evolutionary splicing graphs
Diego Javier Zea, Sofya Laskina, Alexis Baudin, Hugues Richard, Elodie Laine
Genome Research  ·  15 Jun 2021  ·  doi:10.1101/gr.274696.120
A global metagenomic map of urban microbiomes and antimicrobial resistance.
A global metagenomic map of urban microbiomes and antimicrobial resistance.
David Danko, Daniela Bezdan, Evan E Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, …, Jun Wu, María M Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E Mason
Cell  ·  26 May 2021  ·  pmid:34043940
poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing
poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing
Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer
Cold Spring Harbor Laboratory  ·  07 May 2021  ·  doi:10.1101/2021.05.07.443089
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis MUFFIN
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam-Rudloff, Christian Brandt
PLOS Computational Biology  ·  09 Feb 2021  ·  doi:10.1371/journal.pcbi.1008716
Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening
Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening
Denis Schmidt, Magdalena M. Scharf, Dominique Sydow, Eva Aßmann, Maria Martí-Solano, Marina Keul, Andrea Volkamer, Peter Kolb
Molecules  ·  26 Jan 2021  ·  doi:10.3390/molecules26030629
RUNX3 Transcript Variants Have Distinct Roles in Ovarian Carcinoma and Differently Influence Platinum Sensitivity and Angiogenesis
RUNX3 Transcript Variants Have Distinct Roles in Ovarian Carcinoma and Differently Influence Platinum Sensitivity and Angiogenesis
Karolin Heinze, Martin Hölzer, Martin Ungelenk, Melanie Gerth, Jürgen Thomale, …, Kirk J. McManus, Alexander S. Mosig, Matthias Dürst, Ingo B. Runnebaum, Norman Häfner
Cancers  ·  26 Jan 2021  ·  doi:10.3390/cancers13030476
SLC35F2, a Transporter Sporadically Mutated in the Untranslated Region, Promotes Growth, Migration, and Invasion of Bladder Cancer Cells
SLC35F2, a Transporter Sporadically Mutated in the Untranslated Region, Promotes Growth, Migration, and Invasion of Bladder Cancer Cells
Roland Kotolloshi, Martin Hölzer, Mieczyslaw Gajda, Marc-Oliver Grimm, Daniel Steinbach
Cells  ·  06 Jan 2021  ·  doi:10.3390/cells10010080

2020

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
Marie Lataretu, Martin Hölzer
Genes  ·  10 Dec 2020  ·  doi:10.3390/genes11121487
The International Virus Bioinformatics Meeting 2020
The International Virus Bioinformatics Meeting 2020
Franziska Hufsky, Niko Beerenwinkel, Irmtraud M. Meyer, Simon Roux, Georgia May Cook, …, Jenna Kelly, Philippe Le Mercier, Manja Marz, Alban Ramette, Volker Thiel
Viruses  ·  06 Dec 2020  ·  doi:10.3390/v12121398
Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs
Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs
Diego Javier Zea, Sofya Laskina, Alexis Baudin, Hugues Richard, Elodie Laine
Cold Spring Harbor Laboratory  ·  15 Nov 2020  ·  doi:10.1101/2020.11.14.382820
A decade of de novo transcriptome assembly: Are we there yet
A decade of de novo transcriptome assembly: Are we there yet?
Martin Hölzer
Molecular Ecology Resources  ·  29 Oct 2020  ·  doi:10.1111/1755-0998.13268
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.
Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone
Bioinformatics (Oxford, England)  ·  01 Jul 2020  ·  pmid:32330240
Transcripts Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family
Transcripts’ Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family
Adel Ait-hamlat, Diego Javier Zea, Antoine Labeeuw, Lélia Polit, Hugues Richard, Elodie Laine
Journal of Molecular Biology  ·  01 Mar 2020  ·  doi:10.1016/j.jmb.2020.01.032

2018

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data.
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data.
Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, Hélène Touzet, Martin Figeac
BMC bioinformatics  ·  11 Jun 2018  ·  pmid:29890948
Meet-U: Educating through research immersion.
Meet-U: Educating through research immersion.
Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, …, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes
PLoS computational biology  ·  15 Mar 2018  ·  pmid:29543809
Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.
Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.
Anish M S Shrestha, Martin C Frith, Kiyoshi Asai, Hugues Richard
Nucleic acids research  ·  16 Feb 2018  ·  pmid:29182778

2016

The Metagenomics and Metadesign of the Subways and Urban Biomes MetaSUB International Consortium inaugural meeting report.
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.
Microbiome  ·  03 Jun 2016  ·  pmid:27255532