Related papers: IGoR: a tool for high-throughput immune repertoire…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
Summary: We present a new tool to correct sequencing errors in Illumina data produced from high-coverage whole-genome shotgun resequencing. It uses a non-greedy algorithm and shows comparable performance and higher accuracy in an evaluation…
Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions…
Reconstructing high-fidelity magnetic resonance (MR) images from under-sampled k-space is a commonly used strategy to reduce scan time. The posterior sampling of diffusion models based on the real measurement data holds significant promise…
Generative Recommendation (GR) has emerged as a promising paradigm by formulating item recommendation as a sequence-to-sequence generation task over item identifiers. Recent studies have incorporated multimodal signals to provide richer…
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…
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…
The study of immune cellular composition has been of great scientific interest in immunology because of the generation of multiple large-scale data. From the statistical point of view, such immune cellular data should be treated as…
We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the…
Background: Radiogenomics allows identification of radiological biomarkers for genomic phenotypes. In glioblastoma, these biomarkers could potentially complement patient stratification strategies. We aim to develop and analytically validate…
In contemporary age, Computational Intelligence (CI) performs an essential role in the interpretation of big biological data considering that it could provide all of the molecular biology and DNA sequencing computations. For this purpose,…
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…
Retrieval-Augmented Generation (RAG) has emerged as a powerful paradigm for enhancing the capabilities of large language models. However, existing RAG evaluation predominantly focuses on text retrieval and relies on opaque, end-to-end…
Benchmarking the performance of information retrieval (IR) is mostly conducted with a fixed set of documents (static corpora). However, in realistic scenarios, this is rarely the case and the documents to be retrieved are constantly updated…
Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major…
Generative Retrieval (GR) is an emerging paradigm in information retrieval that leverages generative models to directly map queries to relevant document identifiers (DocIDs) without the need for traditional query processing or document…
Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a…
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…
Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model…
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic…