Ivan Kuzmin
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View article: SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic
SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic Open
Background The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet …
View article: eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs Open
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex trai…
View article: Andes virus mRNA vaccines: comparison of unmodified and modified mRNA platforms
Andes virus mRNA vaccines: comparison of unmodified and modified mRNA platforms Open
Andes virus (ANDV) is a rodent-borne zoonotic orthohantavirus endemic in South America that causes hantavirus pulmonary syndrome in humans, with up to a 40% case fatality rate. We developed ANDV mRNA vaccines based on the M segment of the …
View article: The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations
The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations Open
Mutagenic outcomes of CRISPR/Cas9-generated double-stranded breaks depend on both the sequence flanking the cut and cellular DNA damage repair. The interaction of these features has been largely unexplored, limiting our ability to understa…
View article: g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)
g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update) Open
g:Profiler is a reliable and up-to-date functional enrichment analysis tool that supports various evidence types, identifier types and organisms. The toolset integrates many databases, including Gene Ontology, KEGG and TRANSFAC, to provide…
View article: Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci
Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci Open
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data no…
View article: gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler Open
g:Profiler (https://biit.cs.ut.ee/gprofiler) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the acc…
View article: gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler Open
g:Profiler (https://biit.cs.ut.ee/gprofiler) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the acc…
View article: eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs Open
An increasing number of gene expression quantitative trait locus (eQTL) studies have made summary statistics publicly available, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and c…
View article: PAWER: Protein Array Web ExploreR
PAWER: Protein Array Web ExploreR Open
Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while existing solutions are either outd…
View article: g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Open
Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to the…
View article: Additional file 3 of funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Additional file 3 of funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data Open
List of significantly enriched GO functions for the cluster shown in Fig. 7. (XLSX 17 kb)
View article: Additional file 3 of funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Additional file 3 of funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data Open
List of significantly enriched GO functions for the cluster shown in Fig. 7. (XLSX 17 kb)
View article: Using bio.tools to generate and annotate workbench tool descriptions
Using bio.tools to generate and annotate workbench tool descriptions Open
Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration o…
View article: bio-tools/ToolDog: v0.3.4 for F1000 submission
bio-tools/ToolDog: v0.3.4 for F1000 submission Open
Fix CWL stdout by removing the "None" string appearing at the end of file.
View article: In Vivo Efficacy of a Cocktail of Human Monoclonal Antibodies (CL184) Against Diverse North American Bat Rabies Virus Variants
In Vivo Efficacy of a Cocktail of Human Monoclonal Antibodies (CL184) Against Diverse North American Bat Rabies Virus Variants Open
Following rabies virus (RABV) exposure, a combination of thorough wound washing, multiple-dose vaccine administration and the local infiltration of rabies immune globulin (RIG) are essential components of modern post-exposure prophylaxis (…