List of works by Manja Marz

A CRISPR Activation Screen Identifies Genes That Protect against Zika Virus Infection

scientific article published on 30 July 2019

A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

scientific article published on 30 September 2019

A marine Chlamydomonas sp. emerging as an algal model

scientific article published on 11 October 2020

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

scientific article published on 5 September 2017

A new era of virus bioinformatics

scientific article published on 08 May 2018

A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis

scientific article published on 14 February 2012

A survey of nematode SmY RNAs

scientific article

A virtual “Werkstatt” for digitization in the sciences

scholarly article by Sheeba Samuel et al published 11 May 2020 in Research Ideas and Outcomes

Animal snoRNAs and scaRNAs with exceptional structures

scientific article published on November 2011

Bcheck: a wrapper tool for detecting RNase P RNA genes

scientific article

Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon

scientific article published on 20 February 2019

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

scientific article

Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer

scientific article

Carbon fixation rates in groundwater similar to those in oligotrophic marine systems

scientific article published in 2022

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling ⬇️

article

Challenges in RNA virus bioinformatics

scientific article published on 03 March 2014

Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation

scientific article published on 07 December 2018

Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species

scientific article published on 28 October 2020

Comparative analysis of eukaryotic U3 snoRNA

scientific article

Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany

scientific article published on 24 August 2017

Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany

scientific article

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

scientific article published on 04 November 2020

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

scientific article published on 11 May 2015

Conserved aging-related signatures of senescence and inflammation in different tissues and species

scientific article published on 12 October 2019

Conserved introns reveal novel transcripts in Drosophila melanogaster

scientific article published on 20 May 2009

Correction to: A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

scientific article published on 27 November 2019

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

scientific article published on 5 December 2016

Corrigendum: Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

scientific article published on October 2016

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

scientific article

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers

scientific article published on 01 May 2019

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

scientific article

Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology

scientific article

Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection.

scientific article published on 17 January 2017

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

scientific article

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

scientific article published in September 2019

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

scientific article published on 01 December 2018

Dissemination of 6S RNA among bacteria

scientific article published on January 2014

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Effects of allelic variations in the human Myxovirus resistance protein A on its antiviral activity

scientific article published on 12 January 2018

EpiDope: A Deep Neural Network for linear B-cell epitope prediction

scientific article published on 11 September 2020

Erratum for Wegner et al., "Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon"

scholarly article published in Applied and Environmental Microbiology

Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters

scientific article published on 28 May 2019

Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.

scientific article

Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against Ebola, Influenza, and Other RNA Viruses.

scientific article published on 10 May 2017

Evolution of 7SK RNA and its protein partners in metazoa

scientific article published on 4 September 2009

Finding approximate gene clusters with Gecko 3.

scientific article

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

scientific article

Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses

scientific article

Genomewide comparison and novel ncRNAs of Aquificales.

scientific article

Global importance of RNA secondary structures in protein-coding sequences

scientific article published on 01 February 2019

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

scientific article published on 11 September 2014

HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer

scientific article published on 19 August 2020

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

scientific article

Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines

scientific article published on 12 September 2019

Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach

scientific article published on 12 April 2013

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system

scientific article published on 05 August 2020

Invertebrate 7SK snRNAs.

scientific article published on 12 January 2008

Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D.

scientific article published on 17 January 2017

MicroRNAs as biomarker of Parkinson disease? Small but mighty

scientific article published on 16 January 2015

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Multiple roots of fruiting body formation in Amoebozoa

scientific article published on 25 January 2018

Non-coding RNA annotation of the genome of Trichoplax adhaerens

scientific article published on 16 January 2009

Noncoding RNA

article from 2010

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection

scientific article published on 21 May 2020

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection

scientific article published on 31 July 2020

Prediction of conserved long-range RNA-RNA interactions in full viral genomes

scientific article published on 10 June 2016

Proteinortho: detection of (co-)orthologs in large-scale analysis.

scientific article

RNA interactions

scientific article published in January 2011

RNA structure analysis of alphacoronavirus terminal genome regions

scientific article

RNA-RNA interaction prediction based on multiple sequence alignments

scientific article

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

scientific article published on 19 November 2020

Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication

scientific article published on 22 September 2020

SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs

scientific article published on 12 November 2018

SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs

scientific article published on 23 September 2018

Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".

scientific article published on 28 September 2017

Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions.

scientific article

Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis.

scientific article

Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history.

scientific article published in February 2010

The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms

scientific article

The International Virus Bioinformatics Meeting 2020

scientific article published on 06 December 2020

The International Virus Bioinformatics Meeting 2022

publication published on 05 May 2022

The Third Annual Meeting of the European Virus Bioinformatics Center

scientific article published on 05 May 2019

The common ancestral core of vertebrate and fungal telomerase RNAs.

scientific article published on 23 October 2012

The correlation of genome size and DNA methylation rate in metazoans

scientific article published on 7 November 2012

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

scientific article

The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers

scientific article published on 14 December 2021

Tissue-specific Gene Expression Changes Are Associated with Aging in Mice

scientific article published on 10 December 2020

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes

scientific article published on 30 July 2015

Transcriptomic immune response of the cotton stainer Dysdercus fasciatus to experimental elimination of vitamin-supplementing intestinal symbionts

scientific article

U7 snRNAs: a computational survey

scientific article

VIDHOP, viral host prediction with Deep Learning

scientific article published on 10 August 2020

Virologists-Heroes need weapons.

scientific article published on 8 February 2018

Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii

scientific article published on 10 August 2019

Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

scientific article published in December 2014

Whole-Genome Sequence of Chlamydia gallinacea Type Strain 08-1274/3.

scientific article published on 21 July 2016

Women in the European Virus Bioinformatics Center

scientific article published on 13 July 2022

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.

scientific article published on 27 September 2016

pRNA: NoRC-associated RNA of rRNA operons

scientific article published on 20 December 2013

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