Bioinformatics and Translational Research

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. 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.

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
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
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

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
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity
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
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
Targeted decontamination of sequencing data with CLEAN
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
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
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
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
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
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
Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions
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 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
Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry LC-MS1 and in Silico Peptide Mass Libraries
Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries
Peter Lasch, Andy Schneider, Christian Blumenscheit, Joerg Doellinger
Molecular & Cellular Proteomics  ·  01 Dec 2020  ·  doi:10.1074/mcp.tir120.002061
A marine i Chlamydomonas i sp. emerging as an algal model
A marineChlamydomonassp. 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
Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam
Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam
Le Thi Thanh Tam, Jennifer Jähne, Pham Thi Luong, Le Thi Phuong Thao, Le Thi Kim Chung, Andy Schneider, Christian Blumenscheit, Peter Lasch, Thomas Schweder, Rainer Borriss
Microbiology Resource Announcements  ·  19 Nov 2020  ·  doi:10.1128/mra.01154-20
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
Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species
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
Isolation Window Optimization of Data-Independent Acquisition Using Predicted Libraries for Deep and Accurate Proteome Profiling
Isolation Window Optimization of Data-Independent Acquisition Using Predicted Libraries for Deep and Accurate Proteome Profiling
Joerg Doellinger, Christian Blumenscheit, Andy Schneider, Peter Lasch
Analytical Chemistry  ·  25 Aug 2020  ·  doi:10.1021/acs.analchem.0c00994
Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome assembled genomes from a complex aquifer system
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
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
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
Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research
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
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
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
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
Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis MUFFIN
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
The N terminal domains of the paralogous HycE and Nuo scp CD scp govern assembly of the respective formate hydrogenlyase and scp NADH scp dehydrogenase complexes
The N‐terminal domains of the paralogous HycE and NuoCD govern assembly of the respective formate hydrogenlyase and NADH dehydrogenase complexes
Philipp Skorupa, Ute Lindenstrauß, Sabrina Burschel, Christian Blumenscheit, Thorsten Friedrich, Constanze Pinske
FEBS Open Bio  ·  04 Feb 2020  ·  doi:10.1002/2211-5463.12787

2019

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system
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
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
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
Nelly F Mostajo, Marie Lataretu, Sebastian Krautwurst, Florian Mock, Daniel Desirò, …, Maximilian Collatz, Andreas Schoen, Friedemann Weber, Manja Marz, Martin Hölzer
NAR Genomics and Bioinformatics  ·  30 Sep 2019  ·  doi:10.1093/nargab/lqz006
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
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
Genome Research  ·  22 Aug 2019  ·  doi:10.1101/gr.247064.118
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
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
Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii.
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  ·  10 Aug 2019  ·  pmid:31465999
Chlamydia buteonis, a new Chlamydia species isolated from a red-shouldered hawk.
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  ·  19 Jun 2019  ·  pmid:31257045
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
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
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
i De novo i transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
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
SilentMutations SIM : A tool for analyzing long-range RNA RNA interactions in viral genomes and structured RNAs
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
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
The Anti-amyloid Compound DO1 Decreases Plaque Pathology and Neuroinflammation-Related Expression Changes in 5xFAD Transgenic Mice.
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  ·  21 Nov 2018  ·  pmid:30472115
PCAGO: An interactive web service to analyze RNA-Seq data with principal component analysis
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
SilentMutations SIM : a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
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
Cold Spring Harbor Laboratory  ·  23 Sep 2018  ·  doi:10.1101/424002
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
Low input long-read DNA isolation for Nanopore sequencing v1
Low input long-read DNA isolation for Nanopore sequencing v1
Christian Blumenscheit, Adrian Viehweger, Celia Diezel
[no publisher info]  ·  20 Feb 2018  ·  doi:dx.doi.org/10.17504/protocols.io.nc2daye
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

2017

PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.
Sabrina Krakau, Hugues Richard, Annalisa Marsico
Genome biology  ·  28 Dec 2017  ·  pmid:29284540
Software Dedicated to Virus Sequence Analysis Bioinformatics Goes Viral .
Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".
Martin Hölzer, Manja Marz
Advances in virus research  ·  28 Sep 2017  ·  pmid:29029728
Complete Genome Sequence of JII-1961, a Bovine
Complete Genome Sequence of JII-1961, a Bovine
Petra Möbius, Gabriele Nordsiek, Martin Hölzer, Michael Jarek, Manja Marz, Heike Köhler
Genome announcements  ·  24 Aug 2017  ·  pmid:28839035
Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against Ebola, Influenza, and Other RNA Viruses.
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  ·  12 Jul 2017  ·  pmid:28490593
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.
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  ·  28 Feb 2017  ·  pmid:27903902
Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculsis and presence of intestinal lesions characteristic of paratuberculosis.
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  ·  22 Jan 2017  ·  pmid:28284609
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D.
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  ·  pmid:28094339
Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection.
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  ·  pmid:28094291

2016

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.
Matthew Huska, Martin Vingron
PLoS computational biology  ·  16 Dec 2016  ·  pmid:27984582
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.
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  ·  pmid:27713552
Predicting enhancers using a small subset of high confidence examples and co-training
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.
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  ·  21 Jul 2016  ·  pmid:27445388
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

2015

SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival
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
Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
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  ·  17 Sep 2015  ·  pmid:26384038
Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.
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  ·  pmid:26227972
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.
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  ·  pmid:25644381

2014

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.
Alexandre Gillet-Markowska, Hugues Richard, Gilles Fischer, Ingrid Lafontaine
Bioinformatics (Oxford, England)  ·  07 Nov 2014  ·  pmid:25380961
Fiona: a parallel and automatic strategy for read error correction.
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 (Oxford, England)  ·  01 Sep 2014  ·  pmid:25161220
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.
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  ·  pmid:25142710
Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
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.
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models.
Bogdan Mirauta, Pierre Nicolas, Hugues Richard
Bioinformatics (Oxford, England)  ·  27 Jan 2014  ·  pmid:24470570

2013

Assessment of transcript reconstruction methods for RNA-seq.
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  ·  pmid:24185837
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
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 Andersson Orom, Martin Vingron
Genome Biology  ·  16 Aug 2013  ·  doi:10.1186/gb-2013-14-8-r84

2010

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods.
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  ·  10 Nov 2010  ·  pmid:21074401
The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo
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
Erratum to: Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing.
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  ·  11 Apr 2010  ·  pmid:20535404
The genome of a songbird.
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  ·  pmid:20360741
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
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  ·  pmid:20150413

2009

Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing
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
DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction
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
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
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
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.
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 (New York, N.Y.)  ·  03 Jul 2008  ·  pmid:18599741

2007

BiasViz: visualization of amino acid biased regions in protein alignments
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

2006

Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.
Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.
Michaël Bekaert, Hughes Richard, Bernard Prum, Jean-Pierre Rousset
Genome research  ·  01 Aug 2006  ·  pmid:16882864

2005

Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae.
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  ·  pmid:16204194
seq : analyzing biological sequences with a range of Markov-related models.
seq++: analyzing biological sequences with a range of Markov-related models.
Vincent Miele, Pierre-Yves Bourguignon, David Robelin, Grégory Nuel, Hugues Richard
Bioinformatics (Oxford, England)  ·  17 Mar 2005  ·  pmid:15774554
Study of stem cell function using microarray experiments
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.
SPA: Simple web tool to assess statistical significance of DNA patterns.
H Richard, G Nuel
Nucleic acids research  ·  01 Jul 2003  ·  pmid:12824392
SIC: A tool to detect short inverted segments in a biological sequence.
SIC: A tool to detect short inverted segments in a biological sequence.
David Robelin, Hugues Richard, Bernard Prum
Nucleic acids research  ·  01 Jul 2003  ·  pmid:12824390

2002

Occurrence probability of structured motifs in random sequences.
Occurrence probability of structured motifs in random sequences.
S Robin, J-J Daudin, H Richard, M-F Sagot, S Schbath
Journal of computational biology : a journal of computational molecular cell biology  ·  01 Jan 2002  ·  pmid:12614545

Europe PMC
Europe PMC
[no publisher info]  ·  [no date info]  ·  ppr:PPR88097