Ksenia G. Kuznetsova
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View article: Heterogeneity in paediatric diabetes clinical presentation and its link to disease severity
Heterogeneity in paediatric diabetes clinical presentation and its link to disease severity Open
Background Diabetes subtypes with different clinical profiles have been found and replicated in adults. However, clinical heterogeneity of paediatric-onset diabetes remains unexplored. Better capture of different aetiologies of the disease…
View article: ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets
ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets Open
In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently i…
View article: Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes
Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes Open
Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Like for other rare diseases, multiple genes have been linked to monogenic diabetes with different measures of pathogenicity, but the infor…
View article: Taxonomic diversity and abundance of enchytraeids (Annelida, Clitellata, Enchytraeida) in the Northern Palaearctic. 1. Asian part
Taxonomic diversity and abundance of enchytraeids (Annelida, Clitellata, Enchytraeida) in the Northern Palaearctic. 1. Asian part Open
Enchytraeids, or potworms, are tiny oligochaetes that are distributed worldwide in many terrestrial, freshwater and marine ecosystems. Despite their key role in the functioning of ecosystems, the diversity and abundance of Enchytraeidae ar…
View article: ProHap enables proteomic database generation accounting for population diversity
ProHap enables proteomic database generation accounting for population diversity Open
Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this infor…
View article: Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides
Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides Open
Precision medicine focuses on adapting care to the individual profile of patients, for example, accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promise towar…
View article: Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides Open
Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides" The database directory contains the FASTA files of the four protein sequence databases u…
View article: Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides Open
Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides" The database directory contains the FASTA files of the four protein sequence databases u…
View article: Revising deep learning methods in parking lot occupancy detection
Revising deep learning methods in parking lot occupancy detection Open
Parking guidance systems have recently become a popular trend as a part of the smart cities' paradigm of development. The crucial part of such systems is the algorithm allowing drivers to search for available parking lots across regions of…
View article: Retention time and fragmentation predictors increase confidence in variant peptide identification
Retention time and fragmentation predictors increase confidence in variant peptide identification Open
Precision medicine focuses on adapting care to the individual profile of patients, e.g. accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promises towards this…
View article: A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes
A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes Open
Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Multiple genes have been described to be responsible for monogenic diabetes, but the information on the variants is not unified among diffe…
View article: A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes
A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes Open
Aims Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Multiple genes have been described to be responsible for monogenic diabetes, but the information on the variants is not unified among …
View article: Results fasta files for "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes"
Results fasta files for "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes" Open
Fasta files contain protein sequences for the project "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes"
View article: Supplementary Data: Finding Haplotypic Signatures in Proteins
Supplementary Data: Finding Haplotypic Signatures in Proteins Open
Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excludi…
View article: Supplementary Data: Finding Haplotypic Signatures in Proteins
Supplementary Data: Finding Haplotypic Signatures in Proteins Open
Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excludi…
View article: Taxonomic diversity and abundance of enchytraeids (Annelida: Clitellata: Enchytraeida) in the Northern Palaearctic. 1. Asian part
Taxonomic diversity and abundance of enchytraeids (Annelida: Clitellata: Enchytraeida) in the Northern Palaearctic. 1. Asian part Open
The diversity and abundance of small soil oligochaetes – enchytraeids were studied in the different biomes of the Asiatic part of Northern Palaearctic. We delimited our sampling area by the Ural Mountains in the west and the Central Asian …
View article: Supplementary Data: Retention time and fragmentation predictors increase confidence in variant peptide identification
Supplementary Data: Retention time and fragmentation predictors increase confidence in variant peptide identification Open
Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in variant peptide identification" The database directory contains the FASTA files of the four protein sequence databases used in the…
View article: Finding haplotypic signatures in proteins
Finding haplotypic signatures in proteins Open
Background The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of allele…
View article: Finding Haplotypic Signatures in Proteins
Finding Haplotypic Signatures in Proteins Open
The non-random distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can enco…
View article: Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes
Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes Open
RNA editing by adenosine deaminases of the ADAR family can lead to protein recoding, since inosine formed from adenosine in mRNA is complementary to cytosine; the resulting codon editing might introduce amino acid substitutions into transl…
View article: Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i>
Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i> Open
Venoms of predatory marine cone snails are intensely studied because of the biomedical applications of the neuropeptides that they contain, termed conotoxins. Meanwhile some gastropod lineages have independently acquired secretory glands s…
View article: Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus
Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus Open
Cancer cell lines responded differentially to type I interferon treatment in models of oncolytic therapy using vesicular stomatitis virus (VSV). Two opposite cases were considered in this study, glioblastoma DBTRG-05MG and osteosarcoma HOS…
View article: Interplay between A-to-I Editing and Splicing of RNA: A Potential Point of Application for Cancer Therapy
Interplay between A-to-I Editing and Splicing of RNA: A Potential Point of Application for Cancer Therapy Open
Adenosine-to-inosine RNA editing is a system of post-transcriptional modification widely distributed in metazoans which is catalyzed by ADAR enzymes and occurs mostly in double-stranded RNA (dsRNA) before splicing. This type of RNA editing…
View article: Vexitoxins: a novel class of conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i>
Vexitoxins: a novel class of conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i> Open
Venoms of predatory marine cone snails (the family Conidae, order Neogastropoda) are intensely studied because of the broad range of biomedical applications of the neuropeptides that they contain, conotoxins. Meanwhile anatomy in some othe…
View article: Validating amino acid variants in proteogenomics using sequence coverage by multiple reads
Validating amino acid variants in proteogenomics using sequence coverage by multiple reads Open
Mass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic acid sequences. At the same time, due to the stochastic nature of the method when it com…
View article: Results of the proteomic analysys V. coccineum;Results of the proteomic analysys V. vulpecula;Proteomic search database V. coccineum;Proteomic search database V. vulpecula from Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i>
Results of the proteomic analysys V. coccineum;Results of the proteomic analysys V. vulpecula;Proteomic search database V. coccineum;Proteomic search database V. vulpecula from Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i> Open
peptides predicted from monoisotopic masses aligned to the database entries;peptides predicted from monoisotopic masses aligned to the database entries;fasta file with transcripts of interest used for proteomic search;fasta file with trans…
View article: Supplementary Data: Identifying Protein Haplotypes by Mass Spectrometry
Supplementary Data: Identifying Protein Haplotypes by Mass Spectrometry Open
Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excludi…
View article: Results fasta files for "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes"
Results fasta files for "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes" Open
Fasta files contain protein sequences for the project "A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes"
View article: A history of study and new records of terrestrial enchytraeids (Annelida, Clitellata, Enchytraeidae) from the Russian Far East
A history of study and new records of terrestrial enchytraeids (Annelida, Clitellata, Enchytraeidae) from the Russian Far East Open
A list of terrestrial enchytraeids of the Russian Far East is compiled based on literature and extensive field data collected by the authors in 2019. A database has been created consisting of geographic coordinates, habitat type, species, …
View article: Proteome-Wide Analysis of ADAR-mediated Messenger RNA Editing During Fruit Fly Ontogeny
Proteome-Wide Analysis of ADAR-mediated Messenger RNA Editing During Fruit Fly Ontogeny Open
Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. Some of its functions are enforced through editing of mRNA codons with the resu…