Nika Abdollahi

Ancestra simulates B-cell receptor repertoires with known lineage histories to benchmark clonal grouping and lineage reconstruction methods.

UnivAIRRse introduces a unified framework to organize and compare AIRR-seq simulators, identifying limitations and providing a tool for dynamic comparison.

The paper introduces new automated and scalable tools for immune locus analysis, enhancing genomic data access, repertoire analysis, and peptide-MHC prediction through FAIR data principles.

The paper identifies TCR-V gene usage patterns in T cells sorted by anti-TCR mAbs using single-cell RNAseq and finds enriched ERV1-family LTR expression in specific TRBV regions.

The paper examines T cell changes in mammary glands during pregnancy and lactation, finding an expansion of T effector cells and similarities to intestinal T cells.

ClonalTree reconstructs B cell lineage trees using genotype abundances and minimum spanning trees, outperforming existing methods in speed and accuracy for high-throughput BCR sequencing data.

This paper introduces a multi-objective clustering method for identifying clonally-related sequences in B cell repertoire data, showing improved accuracy and efficiency compared to existing tools.

The paper introduces a method to generate high-precision ground truth data for evaluating clonal grouping methods in B-cell populations using real repertoires and V(D)J annotations.