Related papers: Using B cell receptor lineage structures to predic…
Personalized cancer treatment requires a thorough understanding of complex interactions between drugs and cancer cell lines in varying genetic and molecular contexts. To address this, high-throughput screening has been used to generate…
The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these…
There is a growing awareness of the important roles that microbial communities play in complex biological processes. Modern investigation of these often uses next generation sequencing of metagenomic samples to determine community…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Single-cell RNA sequencing (scRNA-seq) enables the study of cellular diversity at single cell level. It provides a global view of cell-type specification during the onset of biological mechanisms such as developmental processes and human…
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning methods excel at learning antigen binding patterns from known…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing…
Artificial intelligence (AI) is accelerating progress in modeling T and B cell receptors by enabling predictive and generative frameworks grounded in sequence data and immune context. This chapter surveys recent advances in the use of…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
Recent advances in immunomics have shown that T-cell receptor (TCR) signatures can accurately predict active or recent infection by leveraging the high specificity of TCR binding to disease antigens. However, the extreme diversity of the…
Accurate prediction of antibody-binding sites (epitopes) on antigens is crucial for vaccine design, immunodiagnostics, therapeutic antibody development, antibody engineering, research into autoimmune and allergic diseases, and advancing our…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…