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Article
Open AccessTransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry
Small molecule identification is a crucial task in analytical chemistry and life sciences. One of the most commonly used technologies to elucidate small molecule structures is mass spectrometry. Spectral libra...
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Article
Open AccessFragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use kno...
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Article
Open AccessPersistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients
A large proportion of HIV-coinfected visceral leishmaniasis (VL-HIV) patients exhibit chronic disease with frequent VL recurrence. However, knowledge on immunological determinants underlying the disease course...
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Article
Open AccessA new Plasmodium vivax reference genome for South American isolates
Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) ...
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Article
The pitfalls of negative data bias for the T-cell epitope specificity challenge
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Article
Open AccessHow deep learning influences workflows and roles in virtual surgical planning
Deep learning (DL) has the potential to transform surgical practice, altering workflows and changing the roles of practitioners involved. However, studies have shown that introducing such change requires user ...
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Article
Open AccessA global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional recor...
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Protocol
Clustering and Annotation of T Cell Receptor Repertoires
Immunological protection against a wide variety of pathogens is largely mediated by the diverse and dynamic T cell receptor (TCR) repertoire, a crucial component of the adaptive immune system. An encounter wit...
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Article
Open AccessBlood transcriptomics to facilitate diagnosis and stratification in pediatric rheumatic diseases – a proof of concept study
Transcriptome profiling of blood cells is an efficient tool to study the gene expression signatures of rheumatic diseases. This study aims to improve the early diagnosis of pediatric rheumatic diseases by inve...
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Article
Open AccessA treatment recommender clinical decision support system for personalized medicine: method development and proof-of-concept for drug resistant tuberculosis
Personalized medicine tailors care based on the patient’s or pathogen’s genotypic and phenotypic characteristics. An automated Clinical Decision Support System (CDSS) could help translate the genotypic and phe...
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Article
MoMAC: Multi-objective optimization to combine multiple association rules into an interpretable classification
A crucial characteristic of machine learning models in various domains (such as medical diagnosis, financial analysis, or real-time process monitoring) is the interpretability. The interpretation supports huma...
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Article
Open AccessA targeted multi-omics approach reveals paraoxonase-1 as a determinant of obesity-associated fatty liver disease
The multifactorial nature of non-alcoholic fatty liver disease cannot be explained solely by genetic factors. Recent evidence revealed that DNA methylation changes take place at proximal promoters within susce...
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Article
Clustering association rules to build beliefs and discover unexpected patterns
Interesting pattern discovery is an important topic in data mining research. Many different definitions have been proposed to describe whether a pattern is interesting. Among these many definitions, unexpected...
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Protocol
Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires
Recognition of cancer epitopes by T cells is fundamental for the activation of targeted antitumor responses. As such, the identification and study of epitope-specific T cells has been instrumental in our under...
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Article
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance...
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Article
Open AccessDiagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture?
Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated ...
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Article
Memory CD4+ T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus
Pathogens of past and current infections have been identified directly by means of PCR or indirectly by measuring a specific immune response (e.g., antibody titration). Using a novel approach, Emerson and coll...
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Article
In vitro assessment of hepatotoxicity by metabolomics: a review
Omics technologies, and in particular metabolomics, have received an increasing attention during the assessment of hepatotoxicity in vitro. However, at present, a consensus on good metabolomics practices has y...
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Article
Open AccessGras** frequent subgraph mining for bioinformatics applications
Searching for interesting common subgraphs in graph data is a well-studied problem in data mining. Subgraph mining techniques focus on the discovery of patterns in graphs that exhibit a specific network struct...
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Article
Increased herpes zoster risk associated with poor HLA-A immediate early 62 protein (IE62) affinity
Around 30% of individuals will develop herpes zoster (HZ), caused by the varicella zoster virus (VZV), during their life. While several risk factors for HZ, such as immunosuppressive therapy, are well known, t...
