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Bioinformatics (Oxford, England)|April 12, 2026
MDCompress: better, faster compression of molecular dynamics simulation trajectoriesMarek Kokot, Amitava Roy, Travis J Wheeler, et al.Bioinformatics (Oxford, England)|March 31, 2021
VCFShark: how to squeeze a VCF fileSebastian Deorowicz, Agnieszka Danek, Marek KokotBioinformatics (Oxford, England)|May 5, 2017
KMC 3: counting and manipulating k-mer statisticsMarek Kokot, Maciej Dlugosz, Sebastian DeorowiczGenome Biology|September 8, 2022
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2Jamshed Khan, Marek Kokot, Sebastian Deorowicz, et al.Bioinformatics (Oxford, England)|January 23, 2015
KMC 2: fast and resource-frugal k-mer countingSebastian Deorowicz, Marek Kokot, Szymon Grabowski, et al.Biorxiv : the Preprint Server for Biology|March 30, 2023
SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing readsMarek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, et al.Bioinformatics (Oxford, England)|July 10, 2018
Kmer-db: instant evolutionary distance estimationSebastian Deorowicz, Adam Gudys, Maciej Dlugosz, et al.Nature Biotechnology|September 23, 2024
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2Marek Kokot, Roozbeh Dehghannasiri, Tavor Baharav, et al.Plant Direct|April 13, 2026
A Reference-Free Algorithm Discovers Regulation in the Plant TranscriptomeElisabeth Meyer, Evan V Saldivar, Marek Kokot, et al.Pageof 17