MF1 Research and Innovation

Research

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.

Our research currently focuses on metagenomics, pangenomics, and wastewater surveillance in the context of infectious diseases and public health improvement.

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.

2024

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

2023

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
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
Thomas B. K. Watkins, Emma C. Colliver, Matthew R. Huska, Tom L. Kaufmann, Emilia L. Lim, ..., Kerstin Haase, Peter Van Loo, Charles Swanton, Nicholas McGranahan, Roland F. Schwarz
PLOS Computational Biology   ·   23 Oct 2023   ·   doi:10.1371/journal.pcbi.1011379
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
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
Targeted decontamination of sequencing data with CLEAN
Marie Lataretu, Sebastian Krautwurst, Adrian Viehweger, Christian Brandt, Martin Hölzer
Cold Spring Harbor Laboratory   ·   06 Aug 2023   ·   doi:10.1101/2023.08.05.552089
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
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
Antoine Szatkownik, Diego Javier Zea, Hugues Richard, Elodie Laine
Cold Spring Harbor Laboratory   ·   30 Apr 2023   ·   doi:10.1101/2023.04.29.538821
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
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
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

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
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
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
DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors
[no author info]
[no publisher info]   ·   07 Jun 2022   ·   hal:hal-01574630
Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs
[no author info]
Genome Research   ·   07 Jun 2022   ·   hal:hal-03274456
Statistical methods for analysing high throughput sequencing data
[no author info]
[no publisher info]   ·   07 Jun 2022   ·   hal:tel-03636135
Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.
Michaël Bekaert, Hughes Richard, Bernard Prum, Jean-Pierre Rousset
Genome research   ·   30 May 2022   ·   pmid:16882864
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.
Michael I Love, Matthew R Huska, Marcel Jurk, Robert Schöpflin, Stephan R Starick, ..., Samantha B Cooper, Keith R Yamamoto, Morgane Thomas-Chollier, Martin Vingron, Sebastiaan H Meijsing
Nucleic acids research   ·   25 May 2022   ·   pmid:27903902
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
Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions
Karin Schmelz, Joern Toedling, Matt Huska, Maja C. Cwikla, Louisa-Marie Kruetzfeldt, ..., Patrick Hundsdoerfer, Anton G. Henssen, Roland F. Schwarz, Johannes H. Schulte, Angelika Eggert
Nature Communications   ·   23 Nov 2021   ·   doi:10.1038/s41467-021-26870-z
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
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
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
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.
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, ..., Yang Zhang, Shu Zhang, Amy Zhang, Yuanting Zheng, Stas Zubenko
Cell   ·   01 Jun 2021   ·   doi:10.1016/j.cell.2021.05.002
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)
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
A marine Chlamydomonas sp. emerging as an algal model
David Carrasco Flores, Markus Fricke, Valentin Wesp, Daniel Desirò, Anja Kniewasser, Martin Hölzer, Manja Marz, Maria Mittag
Journal of Phycology   ·   22 Nov 2020   ·   doi:10.1111/jpy.13083
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?
Martin Hölzer
Molecular Ecology Resources   ·   29 Oct 2020   ·   doi:10.1111/1755-0998.13268
Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species
Martin Hölzer, Lisa-Marie Barf, Kevin Lamkiewicz, Fabien Vorimore, Marie Lataretu, Alison Favaroni, Christiane Schnee, Karine Laroucau, Manja Marz, Konrad Sachse
Pathogens   ·   28 Oct 2020   ·   doi:10.3390/pathogens9110899
Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system
Will A. Overholt, Martin Hölzer, Patricia Geesink, Celia Diezel, Manja Marz, Kirsten Küsel
Environmental Microbiology   ·   20 Aug 2020   ·   doi:10.1111/1462-2920.15186
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
Cold Spring Harbor Laboratory   ·   25 Jul 2020   ·   doi:10.1101/2020.07.24.219899
Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research
Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, ..., Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
MDPI AG   ·   23 May 2020   ·   doi:10.20944/preprints202005.0376.v1
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
Martin Hölzer, Manja Marz
Cold Spring Harbor Laboratory   ·   20 May 2020   ·   doi:10.1101/2020.05.18.102731
EpiDope: A Deep neural network for linear B-cell epitope prediction
Maximilian Collatz, Florian Mock, Martin Hölzer, Emanuel Barth, Konrad Sachse, Manja Marz
Cold Spring Harbor Laboratory   ·   13 May 2020   ·   doi:10.1101/2020.05.12.090019
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A
Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone
Bioinformatics   ·   24 Apr 2020   ·   doi:10.1093/bioinformatics/btaa272
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
Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)
Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam-Rudloff, Christian Brandt
Cold Spring Harbor Laboratory   ·   08 Feb 2020   ·   doi:10.1101/2020.02.08.939843

2019

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system
Will A. Overholt, Martin Hölzer, Patricia Geesink, Celia Diezel, Manja Marz, Kirsten Küsel
Cold Spring Harbor Laboratory   ·   19 Dec 2019   ·   doi:10.1101/2019.12.18.880807
Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content
A. Viehweger, M. Hoelzer, C. Brandt
Cold Spring Harbor Laboratory   ·   25 Nov 2019   ·   doi:10.1101/855262
Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk
K. Laroucau, F. Vorimore, R. Aaziz, L. Solmonson, R.C. Hsia, P.M. Bavoil, P. Fach, M. Hölzer, A. Wuenschmann, K. Sachse
Systematic and Applied Microbiology   ·   01 Sep 2019   ·   doi:10.1016/j.syapm.2019.06.002
Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii
Martin Hölzer, Andreas Schoen, Julia Wulle, Marcel A. Müller, Christian Drosten, Manja Marz, Friedemann Weber
iScience   ·   01 Sep 2019   ·   doi:10.1016/j.isci.2019.08.016
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
Nelly Mostajo Berrospi, Marie Lataretu, Sebastian Krautwurst, Florian Mock, Daniel Desirò, ..., Maximilian Collatz, Andreas Schoen, Friedemann Weber, Manja Marz, Martin Hölzer
Cold Spring Harbor Laboratory   ·   19 Aug 2019   ·   doi:10.1101/738526
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, ..., Jun Wu, María M Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E Mason
Cold Spring Harbor Laboratory   ·   05 Aug 2019   ·   doi:10.1101/724526
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John Anders, Manja Marz, Antonis Chatzinotas
Viruses   ·   28 May 2019   ·   doi:10.3390/v11060484
Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis
Stephan Peter, Martin Hölzer, Kevin Lamkiewicz, Pietro Speroni di Fenizio, Hassan Al Hwaeer, Manja Marz, Stefan Schuster, Peter Dittrich, Bashar Ibrahim
Viruses   ·   16 May 2019   ·   doi:10.3390/v11050449
De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
Martin Hölzer, Manja Marz
GigaScience   ·   01 May 2019   ·   doi:10.1093/gigascience/giz039
The Anti-amyloid Compound DO1 Decreases Plaque Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice
Annett Boeddrich, Julius T. Babila, Thomas Wiglenda, Lisa Diez, Manuela Jacob, ..., David P. Wolfer, Maarten Loos, Dieter Beule, Miguel A. Andrade-Navarro, Erich E. Wanker
Cell Chemical Biology   ·   01 Jan 2019   ·   doi:10.1016/j.chembiol.2018.10.013
SilentMutations (SIM): A tool for analyzing long-range RNA–RNA interactions in viral genomes and structured RNAs
Daniel Desirò, Martin Hölzer, Bashar Ibrahim, Manja Marz
Virus Research   ·   01 Jan 2019   ·   doi:10.1016/j.virusres.2018.11.005

2018

Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation
Zhiyang Chen, Elias Moris Amro, Friedrich Becker, Martin Hölzer, Seyed Mohammad Mahdi Rasa, ..., Manja Marz, Alessandro Ori, Francesco Neri, Yohei Morita, K. Lenhard Rudolph
Journal of Experimental Medicine   ·   07 Dec 2018   ·   doi:10.1084/jem.20181505
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz
Cold Spring Harbor Laboratory   ·   30 Nov 2018   ·   doi:10.1101/483693
PCAGO: An interactive web service to analyze RNA-Seq data with principal component analysis
Ruman Gerst, Martin Hölzer
Cold Spring Harbor Laboratory   ·   03 Oct 2018   ·   doi:10.1101/433078
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   ·   doi:10.1186/s12859-018-2215-1
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   ·   doi:10.1371/journal.pcbi.1005992

2017

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
Sabrina Krakau, Hugues Richard, Annalisa Marsico
Genome Biology   ·   01 Dec 2017   ·   doi:10.1186/s13059-017-1364-2
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   ·   22 Nov 2017   ·   doi:10.1093/nar/gkx1175
Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
Petra Möbius, Martin Hölzer, Marius Felder, Gabriele Nordsiek, Marco Groth, Heike Köhler, Kathrin Reichwald, Matthias Platzer, Manja Marz
Genome biology and evolution   ·   24 Oct 2017   ·   pmc:PMC4607514
Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany
Petra Möbius, Gabriele Nordsiek, Martin Hölzer, Michael Jarek, Manja Marz, Heike Köhler
Genome Announcements   ·   24 Aug 2017   ·   doi:10.1128/genomea.00870-17
Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against Ebola, Influenza, and Other RNA Viruses
Jonas Fuchs, Martin Hölzer, Mirjam Schilling, Corinna Patzina, Andreas Schoen, ..., Gert Zimmer, Manja Marz, Friedemann Weber, Marcel A. Müller, Georg Kochs
Journal of Virology   ·   01 Aug 2017   ·   doi:10.1128/jvi.00361-17
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data
Sabrina Krakau, Hugues Richard, Annalisa Marsico
Cold Spring Harbor Laboratory   ·   07 Jun 2017   ·   doi:10.1101/146704
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, Lelia Polit, Hugues Richard, Elodie Laine
Cold Spring Harbor Laboratory   ·   23 Mar 2017   ·   doi:10.1101/119891
Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculsis and presence of intestinal lesions characteristic of paratuberculosis
Petra Möbius, Elisabeth Liebler-Tenorio, Martin Hölzer, Heike Köhler
Veterinary Microbiology   ·   01 Mar 2017   ·   doi:10.1016/j.vetmic.2017.01.026
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D
Konstantin Riege, Martin Hölzer, Tilman E. Klassert, Emanuel Barth, Julia Bräuer, ..., Nelly Mostajo, Magdalena Stock, Bertram Vogel, Hortense Slevogt, Manja Marz
Scientific Reports   ·   17 Jan 2017   ·   doi:10.1038/srep40598
Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection
Tilman E. Klassert, Julia Bräuer, Martin Hölzer, Magdalena Stock, Konstantin Riege, ..., Mario M. Müller, Silke Rummler, Christine Skerka, Manja Marz, Hortense Slevogt
Scientific Reports   ·   17 Jan 2017   ·   doi:10.1038/srep40599
Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
Martin Hölzer, Manja Marz
In Loeffler’s Footsteps – Viral Genomics in the Era of High-Throughput Sequencing   ·   01 Jan 2017   ·   doi:10.1016/bs.aivir.2017.08.004

2016

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns
Matthew Huska, Martin Vingron
PLOS Computational Biology   ·   16 Dec 2016   ·   doi:10.1371/journal.pcbi.1005249
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, ..., Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, Manja Marz
Scientific Reports   ·   07 Oct 2016   ·   doi:10.1038/srep34589
Predicting enhancers using a small subset of high confidence examples and co-training
Matthew R Huska, Anna Ramisch, Martin Vingron, Annalisa Marsico
PeerJ   ·   01 Sep 2016   ·   doi:10.7287/peerj.preprints.2407
Predicting enhancers using a small subset of high confidence examples and co-training
Matthew R Huska, Anna Ramisch, Martin Vingron, Annalisa Marsico
PeerJ   ·   01 Sep 2016   ·   doi:10.7287/peerj.preprints.2407v1
Whole-Genome Sequence of Chlamydia gallinacea Type Strain 08-1274/3
Martin Hölzer, Karine Laroucau, Heather Huot Creasy, Sandra Ott, Fabien Vorimore, Patrik M. Bavoil, Manja Marz, Konrad Sachse
Genome Announcements   ·   25 Aug 2016   ·   doi:10.1128/genomea.00708-16
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
[no author info]
Microbiome   ·   03 Jun 2016   ·   doi:10.1186/s40168-016-0168-z

2015

SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival
F Schmid, Q Wang, M R Huska, M A Andrade-Navarro, M Lemm, ..., D Kobelt, W Walther, J Smith, P M Schlag, U Stein
Oncogene   ·   21 Dec 2015   ·   doi:10.1038/onc.2015.451
Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes
Abdullah H. Sahyoun, Martin Hölzer, Frank Jühling, Christian Höner zu Siederdissen, Marwa Al-Arab, Kifah Tout, Manja Marz, Martin Middendorf, Peter F. Stadler, Matthias Bernt
Nucleic Acids Research   ·   30 Jul 2015   ·   doi:10.1093/nar/gkv746
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
H Hu, S A Haas, J Chelly, H Van Esch, M Raynaud, ..., J Gecz, T J Jentsch, W Chen, H-H Ropers, V M Kalscheuer
Molecular Psychiatry   ·   03 Feb 2015   ·   doi:10.1038/mp.2014.193

2014

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries
Alexandre Gillet-Markowska, Hugues Richard, Gilles Fischer, Ingrid Lafontaine
Bioinformatics   ·   07 Nov 2014   ·   doi:10.1093/bioinformatics/btu730
Fiona: a parallel and automatic strategy for read error correction
Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard
Bioinformatics   ·   22 Aug 2014   ·   doi:10.1093/bioinformatics/btu440
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum
Alessandra Rogato, Hugues Richard, Alexis Sarazin, Björn Voss, Soizic Cheminant Navarro, Raphaël Champeimont, Lionel Navarro, Alessandra Carbone, Wolfgang R Hess, Angela Falciatore
BMC Genomics   ·   20 Aug 2014   ·   doi:10.1186/1471-2164-15-698
Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Marion Fehlker, Matthew R Huska, Thomas Jöns, Miguel A Andrade-Navarro, Wolfgang Kemmner
BMC Cancer   ·   05 Feb 2014   ·   doi:10.1186/1471-2407-14-64
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
Bogdan Mirauta, Pierre Nicolas, Hugues Richard
Bioinformatics   ·   27 Jan 2014   ·   doi:10.1093/bioinformatics/btu042

2013

Assessment of transcript reconstruction methods for RNA-seq
Tamara Steijger, Josep F Abril, Pär G Engström, Felix Kokocinski, Tim J Hubbard, Roderic Guigó, Jennifer Harrow, Paul Bertone
Nature Methods   ·   03 Nov 2013   ·   doi:10.1038/nmeth.2714
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
Annalisa Marsico, Matthew R Huska, Julia Lasserre, Haiyang Hu, Dubravka Vucicevic, Anne Musahl, Ulf Orom, Martin Vingron
Genome Biology   ·   01 Jan 2013   ·   doi:10.1186/gb-2013-14-8-r84

2011

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods
Ulrike Mäder, Pierre Nicolas, Hugues Richard, Philippe Bessières, Stéphane Aymerich
Current Opinion in Biotechnology   ·   01 Feb 2011   ·   doi:10.1016/j.copbio.2010.10.003

2010

The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo
Annabel Christ, Sara Terryn, Vanessa Schmidt, Erik I. Christensen, Matthew R. Huska, Miguel A. Andrade-Navarro, Norbert Hübner, Olivier Devuyst, Annette Hammes, Thomas E. Willnow
Kidney International   ·   01 Sep 2010   ·   doi:10.1038/ki.2010.169
The genome of a songbird
Wesley C. Warren, David F. Clayton, Hans Ellegren, Arthur P. Arnold, LaDeana W. Hillier, ..., Joanne Nelson, Asif Chinwalla, Shunfeng Hou, Elaine R. Mardis, Richard K. Wilson
Nature   ·   01 Apr 2010   ·   doi:10.1038/nature08819
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
Hugues Richard, Marcel H. Schulz, Marc Sultan, Asja Nürnberger, Sabine Schrinner, ..., Axel Rasche, Hans Lehrach, Martin Vingron, Stefan A. Haas, Marie-Laure Yaspo
Nucleic Acids Research   ·   11 Feb 2010   ·   doi:10.1093/nar/gkq041

2009

Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing
Hao Hu, Klaus Wrogemann, Vera Kalscheuer, Andreas Tzschach, Hugues Richard, ..., Martine Raynaud, Hans Van Bokhoven, Jamel Chelly, Hilger Ropers, Wei Chen
The HUGO Journal   ·   01 Dec 2009   ·   doi:10.1007/s11568-010-9137-y
Erratum to: Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing
Hao Hu, Klaus Wrogemann, Vera Kalscheuer, Andreas Tzschach, Hugues Richard, ..., Martine Raynaud, Hans Van Bokhoven, Jamel Chelly, Hilger Ropers, Wei Chen
The HUGO Journal   ·   01 Dec 2009   ·   doi:10.1007/s11568-010-9142-1
DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction
Ann-Marie Bröske, Lena Vockentanz, Shabnam Kharazi, Matthew R Huska, Elena Mancini, ..., Claus Nerlov, Achim Leutz, Miguel A Andrade-Navarro, Sten Eirik W Jacobsen, Frank Rosenbauer
Nature Genetics   ·   04 Oct 2009   ·   doi:10.1038/ng.463
MedlineRanker: flexible ranking of biomedical literature
Jean-Fred Fontaine, Adriano Barbosa-Silva, Martin Schaefer, Matthew R. Huska, Enrique M. Muro, Miguel A. Andrade-Navarro
Nucleic Acids Research   ·   07 May 2009   ·   doi:10.1093/nar/gkp353
Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin
Gareth A. Palidwor, Sergey Shcherbinin, Matthew R. Huska, Tamas Rasko, Ulrich Stelzl, ..., Raphaele Foulle, Pablo Porras, Luis Sanchez-Pulido, Erich E. Wanker, Miguel A. Andrade-Navarro
PLoS Computational Biology   ·   13 Mar 2009   ·   doi:10.1371/journal.pcbi.1000304
Recent developments in StemBase: a tool to study gene expression in human and murine stem cells
Reatha Sandie, Gareth A Palidwor, Matthew R Huska, Christopher J Porter, Paul M Krzyzanowski, Enrique M Muro, Carolina Perez-Iratxeta, Miguel A Andrade-Navarro
BMC Research Notes   ·   01 Jan 2009   ·   doi:10.1186/1756-0500-2-39

2008

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
Marc Sultan, Marcel H. Schulz, Hugues Richard, Alon Magen, Andreas Klingenhoff, ..., Sean O'Keeffe, Stefan Haas, Martin Vingron, Hans Lehrach, Marie-Laure Yaspo
Science   ·   15 Aug 2008   ·   doi:10.1126/science.1160342

2007

BiasViz: visualization of amino acid biased regions in protein alignments
Matthew R. Huska, Henrik Buschmann, Miguel A. Andrade-Navarro
Bioinformatics   ·   06 Oct 2007   ·   doi:10.1093/bioinformatics/btm489

2005

Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
Michaël Bekaert, Hugues Richard, Bernard Prum, Jean-Pierre Rousset
Genome Research   ·   01 Oct 2005   ·   doi:10.1101/gr.4258005
seq++: analyzing biological sequences with a range of Markov-related models
V. Miele, P.-Y. Bourguignon, D. Robelin, G. Nuel, H. Richard
Bioinformatics   ·   17 Mar 2005   ·   doi:10.1093/bioinformatics/bti389
Study of stem cell function using microarray experiments
Carolina Perez-Iratxeta, Gareth Palidwor, Christopher J. Porter, Neal A. Sanche, Matthew R. Huska, ..., Paul M. Krzyzanowski, Evan Hughes, Pearl A. Campbell, Michael A. Rudnicki, Miguel A. Andrade
FEBS Letters   ·   23 Feb 2005   ·   doi:10.1016/j.febslet.2005.02.020

2003

SPA: simple web tool to assess statistical significance of DNA patterns
H. Richard
Nucleic Acids Research   ·   01 Jul 2003   ·   doi:10.1093/nar/gkg613
SIC: a tool to detect short inverted segments in a biological sequence
D. Robelin
Nucleic Acids Research   ·   01 Jul 2003   ·   doi:10.1093/nar/gkg596

2002

Occurrence Probability of Structured Motifs in Random Sequences
S. Robin, J.-J. Daudin, H. Richard, M.-F. Sagot, S. Schbath
Journal of Computational Biology   ·   01 Dec 2002   ·   doi:10.1089/10665270260518254