Related papers: Using B cell receptor lineage structures to predic…
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs…
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique…
Approximate Bayesian Computation (ABC) is a popular inference method when likelihoods are hard to come by. Practical bottlenecks of ABC applications include selecting statistics that summarize the data without losing too much information or…
T-cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
We propose a novel transfer learning approach for orphan screening called corresponding projections. In orphan screening the learning task is to predict the binding affinities of compounds to an orphan protein, i.e., one for which no…
We analyze the interactions between division, mutation and selection in a simplified evolutionary model, assuming that the population observed can be classified into fitness levels. The construction of our mathematical framework is…
In this letter, a novel method for change detection is proposed using neighborhood structure correlation. Because structure features are insensitive to the intensity differences between bi-temporal images, we perform the correlation…
Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform…
Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
The clonal selection principle explains the basic features of an adaptive immune response to a antigenic stimulus. It established the idea that only those cells that recognize the antigens are selected to proliferate and differentiate. This…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
We consider the problem of antibody sequence design given 3D structural information. Building on previous work, we propose a fine-tuned inverse folding model that is specifically optimised for antibody structures and outperforms generic…
The repertoire of lymphocyte receptors in the adaptive immune system protects organisms from diverse pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the cost of infections. We develop a general…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…