Faraz Hach

The paper analyzes segmental duplications in 117 vertebrate genomes and starfish, revealing species-specific patterns and rapid evolution of duplication landscapes.

The paper investigates how AR-bound CREs influence gene expression through epigenetic changes and chromatin looping, finding that contact frequency with promoters drives expression.

TKSM simulates transcriptomic long-read sequencing data by modularly combining steps, enabling customizable and scalable benchmarking of sequencing tools.

This study develops snpSTARRseq, a high-throughput method to test non-coding variants from GWAS, showing 37% of prostate cancer risk loci alter enhancer activity.

Freddie detects and discovers transcriptomic alternative splicing isoforms without relying on existing annotations, outperforming other tools in recall and identifying a novel Androgen Receptor isoform in prostate cancer.

The paper introduces CWAS, a method linking genetic variation to chromatin states, identifying novel prostate cancer risk loci and regulatory mechanisms not detectable by eQTLs.

scTagger matches cellular barcodes from long- and short-reads in single-cell RNA-seq experiments, showing improved accuracy and speed over existing methods.

The paper introduces a heuristic method for finding high-scoring local alignments of DNA queries to pangenome graphs and demonstrates its scalability and effectiveness.

HASLR is a hybrid assembler that combines second and third generation sequencing reads to generate fast and accurate genome assemblies, outperforming other assemblers in speed and misassembly count.

PhISCS integrates single-cell and bulk sequencing data to reconstruct sub-perfect tumor phylogenies by minimizing false negatives, false positives, and ISA violations.

The paper introduces a computational framework integrating genomic, transcriptomic, and proteomic data to identify and interpret translated fusions and micro structural variations in cancer, finding many novel peptides and private aberrations in breast cancer.