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:

• Microbial bioinformatics
• Genomic surveillance
• Pathogen detection and characterization
• Nanopore real-time sequencing
• Transcriptomics and gene expression
• Metagenomics and metatranscriptomics
• Reproducible genomics (container, WMS)

Highlighted

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

openRxiv  ·  02 Feb 2025  ·  doi:10.1101/2025.01.29.635492

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

All

2026

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Martin Hunt, Angie S. Hinrichs, Daniel Anderson, Lily Karim, Bethany L. Dearlove, …, Tulio de Oliveira, Timothy EA Peto, Derrick Crook, Russell Corbett-Detig, Zamin Iqbal

Nature Methods  ·  09 Feb 2026  ·  doi:10.1038/s41592-025-02947-1

2025

A whole-genome sequencing dataset of nanopore raw signals for bacterial genotyping and methylation analysis

Johanna Dabernig-Heinz, Valentina Galeone, Somayyeh Sedaghatjoo, Ivo Steinmetz, Christian Kohler, Martin Hölzer, Gabriel E. Wagner

Scientific Data  ·  02 Dec 2025  ·  doi:10.1038/s41597-025-06319-4

A public health perspective of SARS-CoV-2 evolution and surveillance strategies in Germany from 2020 to 2023

Djin-Ye Oh, Martin Hölzer, Daniela Börnigen, Sofia Paraskevopoulou, Susanne Duwe, …, Torsten Semmler, Maureen Rebecca Smith, Andrea Thürmer, Wiep van der Toorn, Max von Kleist

Communications Medicine  ·  11 Nov 2025  ·  doi:10.1038/s43856-025-01093-1

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

Accurately assembling nanopore sequencing data of highly pathogenic bacteria

Christine Thomas, Hanka Brangsch, Valentina Galeone, Martin Hölzer, Manja Marz, Jörg Linde

BMC Genomics  ·  28 Aug 2025  ·  doi:10.1186/s12864-025-11793-6

Large-scale Evaluation of Prokaryotic Annotation Tools Across Thousands of Species

Mateusz Jundzill, Martin Hölzer, Serghei Mangul, Mike Marquet, Ralf Ehricht, Mara Lohde, Riccardo Spott, Oliwia Makarewicz, Mathias Pletz, Christian Brandt

Springer Science and Business Media LLC  ·  13 Aug 2025  ·  doi:10.21203/rs.3.rs-7317585/v1

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2

Joshua I. Levy, Praneeth Gangavarapu, Dylan A. Pilz, Maryam Ahmadi Jesvaghane, Allison Steedman, …, Daniel J. Park, Angie S. Hinrichs, Louise C. Laurent, Rob Knight, Kristian G. Andersen

Cold Spring Harbor Laboratory  ·  27 Jul 2025  ·  doi:10.1101/2025.07.26.25332245

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

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

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

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

varVAMP: degenerate primer design for tiled full genome sequencing and qPCR

Jonas Fuchs, Johanna Kleine, Mathias Schemmerer, Julian Kreibich, Wolfgang Maier, …, Sindy Böttcher, Reimar Johne, Jürgen Wenzel, Martin Hölzer, Marcus Panning

Nature Communications  ·  31 May 2025  ·  doi:10.1038/s41467-025-60175-9

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

Valentina Galeone, Johanna Dabernig-Heinz, Mara Lohde, Christian Brandt, Christian Kohler, Gabriel E. Wagner, Martin Hölzer

openRxiv  ·  02 Feb 2025  ·  doi:10.1101/2025.01.29.635492

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

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

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

Martin Hölzer, Charlotte Reuschel, Fabien Vorimore, Karine Laroucau, Konrad Sachse

Access Microbiology  ·  01 Jan 2025  ·  doi:10.1099/acmi.0.000936.v3

2024

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

Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs

Viruses  ·  11 Sep 2024  ·  doi:10.3390/v16091444

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

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

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

Martin Hölzer

Bioinformatics  ·  29 Mar 2024  ·  doi:10.1093/bioinformatics/btae175

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

Hugues Richard, John Wiedenhoeft, Constance Scharff, Iris Adam

openRxiv  ·  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

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

Daria Meyer, Winfried Goettsch, Jannes Spannenberg, Bettina Stieber, Sebastian Krautwurst, …, Christian Höner zu Siederdissen, Akash Srivastava, Milena Zarkovic, Damian Wollny, Manja Marz

openRxiv  ·  07 Dec 2023  ·  doi:10.1101/2023.12.06.570356

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

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

Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard

iScience  ·  01 Nov 2023  ·  doi:10.1016/j.isci.2023.108057

ICTV Virus Taxonomy Profile: Xinmoviridae 2023

Stephen Sharpe, Sofia Paraskevopoulou

Journal of General Virology  ·  26 Oct 2023  ·  doi:10.1099/jgv.0.001906

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

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

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

Jun-Min Li, Fei Wang, Gongyin Ye, Sofia Paraskevopoulou

Journal of General Virology  ·  11 Jul 2023  ·  doi:10.1099/jgv.0.001869

Building alternative splicing and evolution-aware sequence-structure maps for protein repeats

Antoine Szatkownik, Diego Javier Zea, Hugues Richard, Elodie Laine

openRxiv  ·  30 Apr 2023  ·  doi:10.1101/2023.04.29.538821

De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasma bovis strains

Sandra Triebel, Konrad Sachse, Michael Weber, Martin Heller, Celia Diezel, Martin Hölzer, Christiane Schnee, Manja Marz

openRxiv  ·  13 Apr 2023  ·  doi:10.1101/2023.04.13.536562

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

openRxiv  ·  30 Mar 2023  ·  doi:10.1101/2023.03.29.534691

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

Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt

Database  ·  01 Jan 2023  ·  doi:10.1093/database/baad071

2022

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

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

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

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

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

Etienne SIMON-LORIERE, Xavier Montagutelli, Frederic Lemoine, Flora Donati, Franck Touret, …, Yazdan Yazdanpanah, Bruno Coignard, Xavier de Lamballerie, Sylvie van der Werf, Axelle Paquin

Research Square  ·  04 Apr 2022  ·  doi:10.21203/rs.3.rs-1502293/v1

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

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

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

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

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

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

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.

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

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 Lepidium (Brassicaceae)

Lydia Gramzow, Katharina Klupsch, Noé Fernández Pozo, Martin Hölzer, Manja Marz, Stefan A. Rensing, Günter Theißen

openRxiv  ·  01 Nov 2021  ·  doi:10.1101/2021.10.29.466389

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

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

openRxiv  ·  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.

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

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.

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

Christian Brandt, Sebastian Krautwurst, Riccardo Spott, Mara Lohde, Mateusz Jundzill, Mike Marquet, Martin Hölzer

openRxiv  ·  07 May 2021  ·  doi:10.1101/2021.05.07.443089

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

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

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

Marie Lataretu, Martin Hölzer

Genes  ·  10 Dec 2020  ·  doi:10.3390/genes11121487

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

Diego Javier Zea, Sofya Laskina, Alexis Baudin, Hugues Richard, Elodie Laine

openRxiv  ·  15 Nov 2020  ·  doi:10.1101/2020.11.14.382820

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.

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

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