Publications

Group highlights

(For a full list of publications see below)

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2

A Gudyś, A Zielezinski, C Notredame, S Deorowicz

Nature Biotechnology, https://doi.org/10.1038/s41587-026-03095-3 (2026)

Ultrafast and accurate sequence alignment and clustering of viral genomes

A Zielezinski, A Gudys, J Barylski, K Siminski, P Rozwalak, BE Dutilh, S Deorowicz

Nature Methods, 22(6), 1191-1194 (2025)

AGC: Compact representation of assembled genomes with fast queries and updates

High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. AGC is a utility allowing to represent collections of genome sequences obtained in pangenome projects in a very compact form. It also allows to access any contig (or its part) in a fraction of a second.

S Deorowicz, A Danek, H Li

Bioinformatics 39, btad094 (2023)

CoLoRd: Compressing long reads

M Kokot, A Gudys, H Li, S Deorowicz

Nature Methods 19, 441–444 (2022)

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences

A Zielezinski, S Deorowicz, A Gudys

Bioinformatics 38, 1447–1449 (2022)

KMC 3: counting and manipulating k-mer statistics

M Kokot, M Dlugosz, S Deorowicz

Bioinformatics 33, 2759–2761 (2017)

Full List of publications

A Gudyś, A Zielezinski, C Notredame, S Deorowicz, Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2, Nature Biotechnology, https://doi.org/10.1038/s41587-026-03095-3 (2026) [Citations]
DJ Cotter, M-C Harrison, A Rustagi, PL Wang, M Kokot, AF Carey, S Deorowicz, J Salzman, FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning, bioRxiv, 2026.04.04.715981 (2026) [Citations]
M Kokot, A Roy, TJ Wheeler, S Deorowicz, MDCompress: better, faster compression of molecular dynamics simulation trajectories, Bioinformatics 42 (4), btag176 (2026) [Citations]
E Meyer, EV Saldivar, M Kokot, B Xue, S Deorowicz, SY Rhee, J Salzman, A Reference‐Free Algorithm Discovers Regulation in the Plant Transcriptome, Plant Direct 10 (4), e70061 (2026) [Citations]
L Mboning, M Dlugosz, M Kokot, J Chen, EK Costa, M-R Wu, S Wang, L-S Bouchard, S Deorowicz, M Pellegrini, MKMC enables reference-free transcriptomic analysis using k-mer representations, bioRxiv, 2026.07.06.73686 (2026) [Citations]
C Lood, et al., First community challenge for automated virus taxonomy, bioRxiv, 2026.07.04.736517 (2026) [Citations]
L Santus, J Espinosa-Carrasco, L Rauschning, J Mir-Pedrol, I Trujnara, A Vignoli, L Mansouri, A Baltzis, EW Floden, P Di Tommaso, E Garriga, A Gudys, S Deorowicz, C Gilchrist, M Steinegger, C Notredame, An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study, NAR genomics and bioinformatics 7 (3), lqaf104 (2025) [Citations]
A Zielezinski, A Gudys, J Barylski, K Siminski, P Rozwalak, BE Dutilh, S Deorowicz, Ultrafast and accurate sequence alignment and clustering of viral genomes, Nature Methods, 22(6), 1191-1194 (2025) [Citations]
R Beeloo, AL Zomer, S Deorowicz, BE Dutilh, Graphite: painting genomes using a colored de Bruijn graph, NAR Genomic and Bioinformatics, lqae142 (2024) [Citations]
M Kokot, R Dehghannasiri, T. Baharav, J. Salzman, S Deorowicz, Scalable and unsupervised discovery from raw sequencing reads using SPLASH2, Nature Biotechnology (2024) [Citations]
S Deorowicz, A Gudys, Efficient protein structure archiving using ProteStAr, Bioinformatics, btae428 (2024) [Citations]
A Zielezinski, A Gudys, J Barylski, K Siminski, P Rozwalak, BE Dutilh, S Deorowicz, Ultrafast and accurate sequence alignment and clustering of viral genomes, bioRxiv.org (2024) [Citations]
E Meyer, EV Saldivar, M Kokot, B Xue, S Deorowicz, SY Rhee, J Salzman, A reference-free algorithm discovers regulation in the plant transcriptome, bioRxiv.org (2024) [Citations]
M Dlugosz, S Deorowicz, Illumina reads correction - evaluation and improvements, Scientific Reports 14, 2232 (2024) [Citations]
G Henderson, A Gudys, T Baharav, P. Sundaramurthy, M Kokot, PL Wang, S Deorowicz, AF Carey, J Salzman, Ultra-efficient, unified discovery from microbial sequencing with SPLASH and precise statistical assembly, bioRxiv.org (2024) [Citations]
L Santus, E Garriga, S Deorowicz, A Gudys, C Notredame, Towards the accurate alignment of over a million protein sequences: Current state of the art, Current Opinion in Structural Biology 80, 102577 (2023) [Citations]
S Deorowicz, A Danek, H Li, AGC: Compact representation of assembled genomes with fast queries and updates, Bioinformatics 39, btad094 (2023) [Citations]
J Khan, M Kokot, S Deorowicz, R Patro, Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2, Genome Biology 23, 190 (2022) [Citations]
M Kokot, A Gudys, H Li, S Deorowicz, CoLoRd: Compressing long reads, Nature Methods 19, 441–444 (2022) [Citations]
A Zielezinski, S Deorowicz, A Gudys, PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences, Bioinformatics 38, 1447–1449 (2022) [Citations]
S Deorowicz, A Danek, M Kokot, VCFShark: how to squeeze a VCF file, Bioinformatics 37, 3358–3360 (2021) [Citations]
S Deorowicz, A Gudys, Whisper 2: indel-sensitive short read mapping, SoftwareX 14, 100692 (2021) [Citations]
S Deorowicz, FQSqueezer: k-mer-based compression of sequencing data, Scientific Reports 10, 578 (2020) [Citations]
S Deorowicz, A Debudaj-Grabysz, A Gudys, Sz Grabowski, Whisper: read sorting allows robust robust mapping of DNA sequencing data, Bioinformatics 35, 2043–2050 (2019) [Citations]
S Deorowicz, A Danek, GTShark: Genotype compression in large projects, Bioinformatics 35, 4791–4793 (2019) [Citations]
S Deorowicz, A Gudys, M Dlugosz, M Kokot, A Danek, Kmer-db: instant evolutionary distance estimation, Bioinformatics 35, 133–136 (2019) [Citations]
S Deorowicz, J Walczyszyn, A Debudaj-Grabysz, CoMSA: compression of protein multiple sequence alignment files, Bioinformatics 35, 227–234 (2019) [Citations]
J Kawulok, M Kawulok, S Deorowicz, Environmental metagenome classification for constructing a microbiome fingerprint, Biology Direct 14, 20 (2019) [Citations]
A Danek, S Deorowicz, GTC: how to maintain huge genotype collections in a compressed form, Bioinformatics 34, 1834–1840 (2018) [Citations]
L Roguski, I Ochoa, M Hernaez, S Deorowicz, FaStore—a space-saving solution for raw sequencing data, Bioinformatics 34, 2748–2756 (2018) [Citations]
A Gudys, S Deorowicz, QuickProbs 2: towards rapid construction of high-quality alignments of large protein families, Scientific Reports 7, 41553 (2017) [Citations]
M Długosz, S Deorowicz, RECKONER: read error corrector based on KMC, Bioinformatics 33, 1086–1089 (2017) [Citations]
M Kokot, M Dlugosz, S Deorowicz, KMC 3: counting and manipulating k-mer statistics, Bioinformatics 33, 2759–2761 (2017) [Citations]
M Kokot, S Deorowicz, A Debudaj-Grabysz, Sorting Data on Ultra-Large Scale with RADULS: New Incarnation of Radix Sort, Chapter in book Beyond Databases, Architectures, and Structures 5, 235–245 (2017) [Citations]
M Długosz, S Deorowicz, M Kokot, Improvements in DNA Reads Correction, Chapter in book Man-Machine Interactions 5, 115–124 (2017) [Citations]
S Deorowicz, A Debudaj-Grabysz, A Gudys, FAMSA: Fast and accurate multiple sequence alignment of huge protein families, Scientific Reports 6, 33964 (2016) [Citations]
S Deorowicz, Sz Grabowski, I Ochoa, M Hernaez, T Weissman, Comment on: ERGC: An efficient referential genome compression algorithm, Bioinformatics 32, 1115–1117 (2016) [Citations]
S Deorowicz, M Kokot, A Debudaj-Grabysz, Sz Grabowski, KMC 2: Fast and resource-frugal k-mer counting, Bioinformatics 31, 1569–1576 (2015) [Citations]
J Kawulok, S Deorowicz, CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE 10, e0121453 (2015) [Citations]
T Kowalski, Sz Grabowski, S Deorowicz, Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE 10, 0133198 (2015) [Citations]
M Kabza, MR Kubiak, A Danek, W Rosikiewicz, S Deorowicz, A Polanski, I Makałowska, Inter-population Differences in Retrogene Loss and Expression in Humans, PLOS Genetics 11, e1005579 (2015) [Citations]
S Deorowicz, A Danek, M Niemiec, GDC 2: Compression of large collections of genomes, Scientific Reports 5, 11565 (2015) [Citations]
Sz Grabowski, S Deorowicz, L Roguski, Disk-based compression of data from genome sequencing, Bioinformatics 31, 1389–1395 (2014) [Citations]
A Danek, S Deorowicz, Sz Grabowski, Indexes of Large Genome Collections on a PC, PLOS ONE 9, 0109384 (2014) [Citations]
A Gudys, S Deorowicz, QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors, PLOS ONE 9, e88901 (2014) [Citations]
L Roguski, S Deorowicz, DSRC 2: Industry-oriented compression of FASTQ files, Bioinformatics 30, 2213–2215 (2014) [Citations]
J Kawulok, S Deorowicz, An Improved Algorithm for Fast and Accurate Classification of Sequences, Chapter in book Man-Machine Interactions 31, 495–502 (2014) [Citations]
S Deorowicz, Sz Grabowski, Data compression for sequencing data, Algorithms for Molecular Biology 8, 25 (2013) [Citations]
A Gudys, MW Szczesniak, M Sikora, I Makalowska, HuntMi: an efficient and taxon-specific approach in pre-miRNA identification, BMC Bioinformatics 14, 83 (2013) [Citations]
MW Szczesniak, M Kabza, R Pokrzywa, A Gudys, I Makalowska, ERISdb: A Database of Plant Splice Sites and Splicing Signals, Plant and Cell Physiology 54, e10 (2013) [Citations]
S Deorowicz, A Danek, A, Sz Grabowski, Genome compression: a novel approach for large collection, Bioinformatics 29, 2572–2578 (2013) [Citations]
S Deorowicz, A Debudaj-Grabysz, Sz Grabowski, Disk-based k-mer counting on a PC, BMC Bioinformatics 14, 160 (2013) [Citations]
MW Szczesniak, S Deorowicz, J Gapski, L Kaczynski, I Makalowska, miRNEST database: an integrative approach in microRNA search and annotation, Nucleic Acids Research 40(D1), D198–D204 (2012) [Citations]
S Deorowicz, Sz Grabowski, Robust relative compression of genomes with random access, Bioinformatics 27, 2979–2986 (2011) [Citations]
S Deorowicz, Sz Grabowski, Compression of DNA sequence reads in FASTQ format, Bioinformatics 27, 860–862 (2011) [Citations]