Track topics on Twitter Track topics that are important to you
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 analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single, paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation, and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis such as germline gene annotation, diversity, and overlap estimation, sequence similarity, network architecture, clustering analysis, and machine learning methods for motif detection.
This article was published in the following journal.
Name: Bioinformatics (Oxford, England)
Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid metho...
Multivalent nanoparticles that target a cell surface receptor that is overexpressed by cancer cells are a promising delivery system for cancer therapy. However, the impact of receptor density and nano...
T cells and T cell receptors (TCRs) play pivotal roles in adaptive immune responses against tumors. The development of next-generation sequencing technologies has enabled the analysis of the TCRβ rep...
Extensive characterization of B cell receptor repertoires across six immune-mediated diseases reveals novel insights into disease pathogenesis.
Universal immune receptors represent a rapidly emerging form of adoptive T cell therapy with the potential to overcome safety and antigen escape challenges faced by conventional chimeric antigen recep...
[Development of diagnosis algorism for paroxysmal arrhythmia using ultra-thin resistive membrane: a pilot study] Comparison of blood pressure via tunable crack sensor and invasive pressure...
This is the prospective randomized parallel groups trial with two participating centers (Department of Urology, Saint Petersburg State University Clinic of advanced medical technologies n....
The purpose of this trial is to assess device performance against participants in an overnight study to ensure the product meets user and clinical requirements
High fidelity simulation provide educational skills but the simulation of critical events could eventually provide anxiety among participants. The anxiety could raise before the simulatio...
Rapid technological advances in the last 20 years have led to the exponential adoption of simulation-based learning in nursing education.
A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
A computer simulation developed to study the motion of molecules over a period of time.
A family of GLYCOSYLPHOSPHATIDYLINOSITOL-anchored cell surface receptors that are specific for GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTORS. They form a multi-component receptor complex with PROTO-ONCOGENE PROTEIN C-RET and regulate a variety of intracellular SIGNAL TRANSDUCTION PATHWAYS in conjunction with c-ret protein.
An inhibitory T-lymphocyte receptor that has specificity for CD274 ANTIGEN and PROGRAMMED CELL DEATH 1 LIGAND 2 PROTEIN. Signaling by the receptor limits T cell proliferation and INTERFERON GAMMA synthesis. The receptor also may play an essential role in the regulatory pathway that induces PERIPHERAL TOLERANCE.
A cell surface protein-tyrosine kinase receptor that is found to be overexpressed in a significant number of adenocarcinomas. It has extensive homology to and can heterodimerize with the EGF receptor (RECEPTOR, EPIDERMAL GROWTH FACTOR), the erbB-3 receptor (RECEPTOR, ERBB-3) and the erbB-4 receptor. Activation of the erbB-2 receptor occurs during heterodimer formation with a ligand-bound erbB receptor family members.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...