Igor Snapkov
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View article: Hazard identification and characterization of leachable chemicals from plastic products – a new PARC project
Hazard identification and characterization of leachable chemicals from plastic products – a new PARC project Open
A recent study has suggested that plastics may contain more than 16,000 chemicals, including additives, processing aids, starting substances, intermediates and Non-Intentionally Added Substances. Plastic chemicals are released throughout t…
View article: Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases Open
The circulating antibody (Ab) repertoire is crucial for immune protection, holding significant immunological and biotechnological value. While bottom-up mass spectrometry (MS) is widely used for profiling the sequence diversity of circulat…
View article: Hazard characterization of the mycotoxins enniatins and beauvericin to identify data gaps and improve risk assessment for human health
Hazard characterization of the mycotoxins enniatins and beauvericin to identify data gaps and improve risk assessment for human health Open
Enniatins (ENNs) and beauvericin (BEA) are cyclic hexadepsipeptide fungal metabolites which have demonstrated antibiotic, antimycotic, and insecticidal activities. The substantial toxic potentials of these mycotoxins are associated with th…
View article: Gene expression profiling of peripheral blood and endometrial cancer risk factors: Systems epidemiology approach in the NOWAC Postgenome Cohort Study
Gene expression profiling of peripheral blood and endometrial cancer risk factors: Systems epidemiology approach in the NOWAC Postgenome Cohort Study Open
The increasing incidence of endometrial cancer (EC) requires an extensive search for novel preventive tools and early intervention approaches. However, the establishment of reliable predictive models is impossible without knowledge of gene…
View article: Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases Open
The circulating antibody repertoire is crucial for immune protection, holding significant immunological and biotechnological value. While bottom-up mass spectrometry (MS) is the most widely used proteomics technique for profiling the seque…
View article: Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability
Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability Open
Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as “developability”, which reflects an antibody’s ability to progress through development stages based on its physicochemical p…
View article: In silico proof of principle of machine learning-based antibody design at unconstrained scale
In silico proof of principle of machine learning-based antibody design at unconstrained scale Open
Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility …
View article: Trajectories of gene expression, seasonal influenza, and within-host seasonal immunity: transfer value to covid-19
Trajectories of gene expression, seasonal influenza, and within-host seasonal immunity: transfer value to covid-19 Open
As a novel approach we will combine trajectories or longitudinal studies of gene expression with information on annual influenza epidemics. Seasonality of gene expression in immune cells from blood could be a consequence of within-host sea…
View article: Reference-based comparison of adaptive immune receptor repertoires
Reference-based comparison of adaptive immune receptor repertoires Open
B- and T-cell receptor (immune) repertoires can represent an individual’s immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of…
View article: Individualized VDJ recombination predisposes the available Ig sequence space
Individualized VDJ recombination predisposes the available Ig sequence space Open
The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and, consequently, (auto)antigen recognition. VDJ recombination follows prob…
View article: The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires Open
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns rende…
View article: The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort
The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort Open
Epithelial ovarian cancer (EOC) has a 5-year relative survival of 50%, partly because markers of early-stage disease are not available in current clinical diagnostics. The aim of the present study was to investigate whether EOC is associat…
View article: Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor
Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor Open
Previous studies have indicated a synergistic effect between radiotherapy and immunotherapy. A better understanding of how this combination affects the immune system can help to clarify its role in the treatment of metastatic cancer. We pe…
View article: In silico proof of principle of machine learning-based antibody design at unconstrained scale
In silico proof of principle of machine learning-based antibody design at unconstrained scale Open
Generative machine learning (ML) has been postulated to be a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of t…
View article: Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction
Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for real-world antibody specificity prediction Open
Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: The lack of a unified ML f…
View article: Individualized VDJ recombination predisposes the available Ig sequence space
Individualized VDJ recombination predisposes the available Ig sequence space Open
The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual’s naïve Ig repertoire, and consequently (auto)antigen recognition. VDJ recombination follows proba…
View article: A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding Open
Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo antibody and (neo-)epitope design. A fundamental pre…
View article: immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires Open
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns rende…
View article: A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding Open
Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo antibody and (neo-)epitope design. A fundamental pre…
View article: 9. Signals of Death—Post-Diagnostic Single Gene ExpressionTrajectories in Breast Cancer—A Proof of Concept
9. Signals of Death—Post-Diagnostic Single Gene ExpressionTrajectories in Breast Cancer—A Proof of Concept Open
Using the time-dependent dynamics of gene expression from immune cells in blood, we aimed to explore single gene expression trajectories as biomarkers for death after a diagnosis of breast cancer introducing a new statistical method denote…
View article: immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking Open
Summary B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire anal…
View article: immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking Open
Summary B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire anal…
View article: Each pregnancy linearly changes immune gene expression in the blood of healthy women compared with breast cancer patients
Each pregnancy linearly changes immune gene expression in the blood of healthy women compared with breast cancer patients Open
We found marked differences in gene expression and enrichment profiles of immunologic gene sets between BC cases and healthy controls, suggesting an important protective effect of the immune system on BC risk.
View article: Inhibition of chemerin/CMKLR1 axis in neuroblastoma cells reduces clonogenicity and cell viability <i>in vitro</i> and impairs tumor growth <i>in vivo</i>
Inhibition of chemerin/CMKLR1 axis in neuroblastoma cells reduces clonogenicity and cell viability <i>in vitro</i> and impairs tumor growth <i>in vivo</i> Open
Pro-inflammatory cells, cytokines, and chemokines are essential in promoting a tumor supporting microenvironment. Chemerin is a chemotactic protein and a natural ligand for the receptors CMKLR1, GPR1, and CCRL2. The chemerin/CMKLR1 axis is…
View article: The role of inflammatory pathways in neuroblastoma tumorigenesis
The role of inflammatory pathways in neuroblastoma tumorigenesis Open
Neuroblastoma er en type nervecellekreft hos barn. Den har en svært kompleks biologisk heterogenisitet og er i noen tilfeller resistent mot cellegift. Den aggressive varianten av neuroblastoma er vanskelig å behandle, og dødeligheten er re…
View article: FITC Conjugation Markedly Enhances Hepatic Clearance of N-Formyl Peptides
FITC Conjugation Markedly Enhances Hepatic Clearance of N-Formyl Peptides Open
In both septic and aseptic inflammation, N-formyl peptides may enter the circulation and induce a systemic inflammatory response syndrome similar to that observed during septic shock. The inflammatory response is brought about by the bindi…