Pascal Mutz
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View article: An updated evolutionary classification of CRISPR–Cas systems including rare variants
An updated evolutionary classification of CRISPR–Cas systems including rare variants Open
The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types an…
View article: Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily
Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily Open
Extensive metatranscriptome mining has recently vastly expanded the range of covalently closed circular (ccc) RNA replicons. A notable group of such replicons are Obelisks, cccRNAs of about 1 kilobase (kb) encoding a protein with a unique …
View article: The protein structurome of Orthornavirae and its dark matter
The protein structurome of Orthornavirae and its dark matter Open
Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into t…
View article: The protein structurome of Orthornavirae and its dark matter
The protein structurome of Orthornavirae and its dark matter Open
Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into t…
View article: DNA polymerase swapping in Caudoviricetes bacteriophages
DNA polymerase swapping in Caudoviricetes bacteriophages Open
View article: Jumping DNA polymerases in bacteriophages
Jumping DNA polymerases in bacteriophages Open
Background Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses …
View article: Mriyaviruses: small relatives of giant viruses
Mriyaviruses: small relatives of giant viruses Open
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein str…
View article: Jumping DNA polymerases in bacteriophages
Jumping DNA polymerases in bacteriophages Open
Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nea…
View article: Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates
Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates Open
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and stru…
View article: Mriyaviruses: Small Relatives of Giant Viruses
Mriyaviruses: Small Relatives of Giant Viruses Open
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein str…
View article: Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling
Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling Open
Protein structures are more strongly conserved in evolution than are amino acid sequences. Comparative structural analysis is particularly important for inferring the origins of viral proteins that typically evolve at high rates.
View article: Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling
Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling Open
Viruses with large double-stranded DNA genomes appear to have captured the majority of their genes from the hosts at different stages of evolution. The origin of many virus genes is readily detected through highly significant sequence simi…
View article: Replication Data for: Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling
Replication Data for: Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling Open
Viruses with large double-stranded DNA genomes appear to have captured the majority of their genes from the hosts at different stages of evolution. The origin of many virus genes is readily detected through highly significant sequence simi…
View article: Stochastic dynamics of Type-I interferon responses
Stochastic dynamics of Type-I interferon responses Open
Interferon (IFN) activates the transcription of several hundred of IFN stimulated genes (ISGs) that constitute a highly effective antiviral defense program. Cell-to-cell variability in the induction of ISGs is well documented, but its sour…
View article: Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales
Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales Open
Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from …
View article: Dual role of neddylation in transcription of hepatitis B virus RNAs from cccDNA and production of viral surface antigen
Dual role of neddylation in transcription of hepatitis B virus RNAs from cccDNA and production of viral surface antigen Open
View article: Varidnaviruses in the human gut: a major expansion of the order Vinavirales
Varidnaviruses in the human gut: a major expansion of the order Vinavirales Open
Background Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria , in particular, crAss-like phages. However,…
View article: Varidnaviruses in the human gut: a major expansion of the order <i>Vinavirales</i>
Varidnaviruses in the human gut: a major expansion of the order <i>Vinavirales</i> Open
Background Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria , in particular, crAss-like phages. However,…
View article: Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches
Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches Open
Significance Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineag…
View article: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches Open
Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive populatio…
View article: Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches Open
Alignments ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2. Correlated Subtrees Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format.
View article: Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches Open
Supplementary Data Tables Table S1: Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode o…
View article: Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches Open
Supplementary Data Tables Table S1: Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode o…
View article: Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches Open
Supplementary Data Tables Table S1: Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode o…
View article: Deep mining of the Sequence Read Archive reveals bipartite coronavirus genomes and inter-family Spike glycoprotein recombination
Deep mining of the Sequence Read Archive reveals bipartite coronavirus genomes and inter-family Spike glycoprotein recombination Open
Genetic variation in RNA viruses is generated by point mutation and recombination as well as reassortment in the case of viruses with segmented genomes. While point mutation concerns only few sites per genome copy, recombination and reasso…
View article: Ongoing global and regional adaptive evolution of SARS-CoV-2
Ongoing global and regional adaptive evolution of SARS-CoV-2 Open
Significance Understanding the ongoing evolution of SARS-CoV-2 is essential to control and ultimately end the pandemic. We analyzed more than 300,000 SARS-CoV-2 genomes available as of January 2021 and demonstrate adaptive evolution of the…
View article: Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2 Open
This repository includes: The global tree in Newick format: global_2_13_21.main.tre The global, ultrametric tree in Newick format: global_2_13_21.ultra.tre All metadata used in this study including the GISAID acknowledgements: metadata.tgz…
View article: Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2 Open
This repository includes: The global tree in Newick format: global_2_13_21.main.tre The global, ultrametric tree in Newick format: global_2_13_21.ultra.tre All metadata used in this study including the GISAID acknowledgements: metadata.tgz…
View article: Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2
Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2 Open
Understanding the trends in SARS-CoV-2 evolution is paramount to control the COVID- 19 pandemic. We analyzed more than 300,000 high quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ong…
View article: Secretion of Hepatitis C Virus Replication Intermediates Reduces Activation of Toll-Like Receptor 3 in Hepatocytes
Secretion of Hepatitis C Virus Replication Intermediates Reduces Activation of Toll-Like Receptor 3 in Hepatocytes Open