Marek Kokot

This study identifies age-associated k-mer signals in canine buccal and cell-free DNA using alignment-free k-mer analysis and ridge regression models.

MKMC enables reference-free transcriptomic analysis using k-mer representations, detecting isoform-specific events and matching alignment-based methods in differential expression and age prediction.

FLASH predicts phenotype from sequence using deep learning, achieving high accuracy on unseen variants and identifying new virulence predictors across microbes.

MDCompress introduces a new trajectory compression format and software that reduces file size and improves compression/decompression speed for molecular dynamics simulations.

The paper introduces SPLASH, a reference-free algorithm for detecting sequence variation from RNA-seq data, and applies it to discover novel regulatory mechanisms in plant transcriptomes.

sc-SPLASH enables reference-free discovery in scRNA-seq and spatial transcriptomics, uncovering novel transcriptomic features like V(D)J recombination and secreted repeat proteins.

The paper introduces SPLASH and compactors to efficiently discover microbial genetic elements and perform strain typing without reference genomes.

SPLASH2 is an efficient, scalable algorithm for discovering regulated sequence variation in RNA-seq data, revealing new biology in single-cell and bulk datasets without parameter tuning.

The paper introduces Cuttlefish 2, a tool that significantly speeds up and reduces memory usage for constructing compacted de Bruijn graphs from large genomic datasets.

CoLoRd compresses third-generation sequencing data by an order of magnitude without affecting downstream analysis accuracy.

VCFShark compresses VCF files more efficiently than standard methods, reducing their size by up to an order of magnitude.

Kmer-db estimates evolutionary distances between pathogens using k-mers, achieving 44x faster performance than Mash on a modern workstation.