Tomasz Gambin

nf-rare-var-assoc: a comprehensive genetic association pipeline with rich QC

The paper presents a Nextflow-based pipeline for genetic association analysis of exome sequencing data, designed to simplify and standardize the process for small cohorts.

polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets

polars-bio provides fast, scalable, and out-of-core operations for genomic interval datasets, outperforming existing libraries in speed and memory efficiency.

Meta-analysis of RNA-seq gene fusion detection tools: performance and variability across benchmarks

This study evaluates ten gene fusion detection tools using RNA-seq benchmarks, identifying performance metrics and benchmarking practices, and recommends improvements for future evaluations.

playOmics: A multi-omics pipeline for interpretable predictions and biomarker discovery

playOmics is an open-source R package for multi-omics analysis that enables biomarker discovery and interpretable predictions through logistic regression models and visualization tools.

The impact of the Turkish (TK) population variome on the genomic architecture of rare disease traits

The paper analyzes the Turkish population's variome to understand its impact on rare disease traits, finding that long ROHs and inbreeding contribute to recessive diseases.

Cloud-native distributed genomic pileup operations

The paper presents a distributed pileup algorithm for genomic analysis that improves speed and memory efficiency in cloud environments.

The Thousand Polish Genomes Project- a national database of Polish variant allele frequencies

The paper describes the creation of a national database of Polish genomic variant allele frequencies using 1,079 whole genomes, identifying rare variants and confirming allele frequencies for known pathogenic variants.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

Integrated Sequencing & Array Comparative Genomic Hybridization in Familial Parkinson’s Disease

The paper combines exome sequencing and array-based comparative genomic hybridization to identify genetic risk factors in familial Parkinson’s disease, finding novel SNVs and CNVs.

SeQuiLa-cov: A fast and scalable library for depth of coverage calculations

SeQuiLa-cov provides a fast and scalable tool for depth of coverage calculations, achieving over 100x speedup compared to existing methods.

Clustering-based optimization method of reference set selection for improved CNV callers performance

This paper evaluates reference set selection methods for CNV callers using WES data and finds that clustering-based approaches improve detection performance and efficiency.