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View article: BACH1 as a key driver in rheumatoid arthritis fibroblast-like synoviocytes identified through gene network analysis
BACH1 as a key driver in rheumatoid arthritis fibroblast-like synoviocytes identified through gene network analysis Open
RNA-sequencing and differential gene expression studies have significantly advanced our understanding of pathogenic pathways underlying rheumatoid arthritis (RA). Yet, little is known about cell-specific regulatory networks and their contr…
View article: Lessons learned from the IMMREP23 TCR-epitope prediction challenge
Lessons learned from the IMMREP23 TCR-epitope prediction challenge Open
International audience
View article: Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues
Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues Open
Rheumatoid arthritis (RA) is a common autoimmune and inflammatory disease characterized by inflammation and hyperplasia of the synovial tissues. RA pathogenesis involves multiple cell types, genes, transcription factors (TFs) and networks.…
View article: T-cell receptor binding prediction: A machine learning revolution
T-cell receptor binding prediction: A machine learning revolution Open
Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenge…
View article: Do domain-specific protein language models outperform general models on immunology-related tasks?
Do domain-specific protein language models outperform general models on immunology-related tasks? Open
Deciphering the antigen recognition capabilities by T-cell and B-cell receptors (antibodies) is essential for advancing our understanding of adaptive immune system responses. In recent years, the development of protein language models (PLM…
View article: Cell-Specific Gene Networks and Drivers in Rheumatoid Arthritis Synovial Tissues
Cell-Specific Gene Networks and Drivers in Rheumatoid Arthritis Synovial Tissues Open
Rheumatoid arthritis (RA) is a common autoimmune and inflammatory disease characterized by inflammation and hyperplasia of the synovial tissues. RA pathogenesis involves multiple cell types, genes, transcription factors (TFs) and networks.…
View article: Gene Network Analyses Identify Co-regulated Transcription Factors and BACH1 as a Key Driver in Rheumatoid Arthritis Fibroblast-like Synoviocytes
Gene Network Analyses Identify Co-regulated Transcription Factors and BACH1 as a Key Driver in Rheumatoid Arthritis Fibroblast-like Synoviocytes Open
RNA-sequencing and differential gene expression studies have significantly advanced our understanding of pathogenic pathways underlying Rheumatoid Arthritis (RA). Yet, little is known about cell-specific regulatory networks and their contr…
View article: T cell receptor binding prediction: A machine learning revolution
T cell receptor binding prediction: A machine learning revolution Open
Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenge…
View article: Do Domain-Specific Protein Language Models Outperform General Models on Immunology-Related Tasks?
Do Domain-Specific Protein Language Models Outperform General Models on Immunology-Related Tasks? Open
Deciphering the antigen recognition capabilities by T cell and B cell receptors (antibodies) is essential for advancing our understanding of adaptive immune system responses. In recent years, the development of protein language models (PLM…
View article: Convergent evolution and B-cell recirculation in germinal centers in a human lymph node
Convergent evolution and B-cell recirculation in germinal centers in a human lymph node Open
Germinal centers (GCs) play a central role in generating an effective immune response against infectious pathogens, and failures in their regulating mechanisms can lead to the development of autoimmune diseases and cancer. Although previou…
View article: Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires
Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires Open
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation …
View article: Quantifying B-cell Clonal Diversity In Repertoire Data
Quantifying B-cell Clonal Diversity In Repertoire Data Open
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation …
View article: Practical and scalable simulations of non-Markovian stochastic processes and temporal networks with individual node properties
Practical and scalable simulations of non-Markovian stochastic processes and temporal networks with individual node properties Open
Discrete stochastic processes are prevalent in natural systems, with applications in physics, biochemistry, epidemiology, sociology, and finance. While analytic solutions often cannot be derived, existing simulation frameworks can generate…
View article: Convergent Evolution and B-Cell Recirculation in Germinal Centers in a Human Lymph Node
Convergent Evolution and B-Cell Recirculation in Germinal Centers in a Human Lymph Node Open
Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. They play a central role in…
View article: Understanding repertoire sequencing data through a multiscale computational model of the germinal center
Understanding repertoire sequencing data through a multiscale computational model of the germinal center Open
Sequencing of B cell and T cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes and their frequencies. Generally, additional time-consuming or expe…
View article: Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts
Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts Open
Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. Through the GC lifespan, in…
View article: Beyond the Nucleus: Cytoplasmic Dominance in Follicular Thyroid Carcinoma Detection Using Single-Cell Raman Imaging Across Multiple Devices
Beyond the Nucleus: Cytoplasmic Dominance in Follicular Thyroid Carcinoma Detection Using Single-Cell Raman Imaging Across Multiple Devices Open
Cytological diagnosis of follicular thyroid carcinoma (FTC) is one of major challenges in the field of endocrine oncology due to absence of evident morphological indicators. Morphological abnormalities in the nucleus are typically key indi…
View article: Coupling of a single active nanoparticle to a polymer-based photonic structure
Coupling of a single active nanoparticle to a polymer-based photonic structure Open
The engineered coupling between a guest moiety (molecule, nanoparticle) and the host photonic nanostructure may provide a great enhancement of the guest optical response, leading to many attractive applications. In this article, we describ…