Yuval Elhanati

Computational identification of responding T cell clones from longitudinal repertoire sequencing

This paper introduces CloneSearch, a method to identify expanding and contracting T cell clones from longitudinal TCR sequencing without requiring antigen-specific information.

Neoantigen-reactive CD8+ T cell engagement marks exceptional survivors of pancreatic cancer

The paper identifies TIE CD8+ T cell clonotypes associated with prolonged survival in pancreatic cancer patients and links resistance to stromal and immune barriers.

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

The paper introduces enFoldX, a structure-based method for predicting TCR:pMHC binding using AlphaFold3 ensembles, achieving high accuracy for cognate vs. non-cognate classification.

Ecological determinants of disease and immunity in myelodysplastic syndromes

This study uses spatial transcriptomics and single-cell analysis to reveal how MDS bone marrow microenvironments are altered, showing TGFβ dysregulation in malignant cells and immune escape mechanisms.

TCRi: Information theoretic metrics for single cell RNA and TCR sequencing in cancer

This paper introduces TCRi, an information theoretic framework to analyze TCR and gene expression data from cancer patients, showing improved characterization of clonotypes and their phenotypic changes post-therapy.

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

OLGA calculates amino acid sequence generation probabilities for B- and T-cell receptors using dynamic programming, showing agreement with published data and potential for vaccine design.

repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data

repgenHMM infers immune receptor rearrangement rules from sequence data using a Hidden Markov Model and Baum-Welch algorithm, accurately reconstructing parameters from synthetic and real T cell receptor sequences.

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

The paper shows that fetal T-cell receptor clones persist into adulthood, contributing to the public TCR repertoire and decaying slowly with age.

Inferring processes underlying B-cell repertoire diversity.

The paper quantifies VDJ recombination and somatic hypermutation in human B-cells using probabilistic methods on DNA sequence data, revealing diversity patterns and mutation distribution.

Quantifying selection in immune receptor repertoires

The paper quantifies selection factors in human T-cell receptor repertoires using probabilistic maximum likelihood analysis of high-throughput sequence data.