Related papers: Diversity in immunogenomics: the value and the cha…
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
The diverse repertoire of T-cell receptors (TCR) plays a key role in the adaptive immune response to infections. Previous studies show that secondary responses to the yellow fever vaccine - the model for acute infection in humans - are…
Item Response Theory (IRT) is a ubiquitous model for understanding humans based on their responses to questions, used in fields as diverse as education, medicine and psychology. Large modern datasets offer opportunities to capture more…
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of…
Response-adaptive randomisation (RAR) can considerably improve the chances of a successful treatment outcome for patients in a clinical trial by skewing the allocation probability towards better performing treatments as data accumulates.…
Therapeutic antibody development has become an increasingly popular approach for drug development. To date, antibody therapeutics are largely developed using large scale experimental screens of antibody libraries containing hundreds of…
The adaptive immune system of vertebrates can detect, respond to, and memorize diverse pathogens from past experience. While the clonal selection of T helper (Th) cells is the simple and established mechanism to better recognize new…
Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…
Cancer is a complex disease driven by genomic alterations, and tumor sequencing is becoming a mainstay of clinical care for cancer patients. The emergence of multi-institution sequencing data presents a powerful resource for learning…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
The human immune system has numerous properties that make it ripe for exploitation in the computational domain, such as robustness and fault tolerance, and many different algorithms, collectively termed Artificial Immune Systems (AIS), have…
Replicability and reproducibility of experimental results are primary concerns in all the areas of science and IR is not an exception. Besides the problem of moving the field towards more reproducible experimental practices and protocols,…
The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses…
Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new…
Users prefer diverse recommendations over homogeneous ones. However, most previous work on Sequential Recommenders does not consider diversity, and strives for maximum accuracy, resulting in homogeneous recommendations. In this paper, we…
Retrieval-augmented generation (RAG) has evolved into a family of paradigms with distinct performance profiles and resource demands, turning paradigm selection into a multi-criteria, context-dependent decision problem. Nevertheless,…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…