Sebastian Deorowicz
@sdeorowicz.bsky.social
Head of Department of Algorithmics and Software,
Silesian University of Technology
bioinformatician, computer scientist
Silesian University of Technology
bioinformatician, computer scientist
MDCompress (www.biorxiv.org/content/10.6...) is our recent proposal for storing molecular dynamics simulations. Try if you feel that your XTC files are too big or need random access features. Great collaboration with Travis Wheeler's lab.
MDCompress: better, faster compression of molecular dynamics simulation trajectories
Motivation: Molecular dynamics (MD) simulations model the physical movements of atoms in biomolecular systems over time, providing atomic-resolution insight into conformational changes, binding events...
www.biorxiv.org
December 23, 2025 at 9:02 AM
MDCompress (www.biorxiv.org/content/10.6...) is our recent proposal for storing molecular dynamics simulations. Try if you feel that your XTC files are too big or need random access features. Great collaboration with Travis Wheeler's lab.
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
Reposted by Sebastian Deorowicz
Vclust generates fast and accurate estimation of average nucleotide identity (ANI) for viral genomes, scaling clustering to millions of genomes. @sdeorowicz.bsky.social @bedutilh.bsky.social @prozwalak.bsky.social
@uni-jena.de @microverse.bsky.social
www.nature.com/articles/s41...
@uni-jena.de @microverse.bsky.social
www.nature.com/articles/s41...
May 15, 2025 at 4:30 PM
Vclust generates fast and accurate estimation of average nucleotide identity (ANI) for viral genomes, scaling clustering to millions of genomes. @sdeorowicz.bsky.social @bedutilh.bsky.social @prozwalak.bsky.social
@uni-jena.de @microverse.bsky.social
www.nature.com/articles/s41...
@uni-jena.de @microverse.bsky.social
www.nature.com/articles/s41...
Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods
Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.
www.nature.com
May 15, 2025 at 9:31 AM
Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
Recently, our SPLASH paper (www.nature.com/articles/s41...) was published in NatBiotech. Now, we release its extended version, sc-SPLASH (www.biorxiv.org/content/10.1...), which allows reference-free analysis of single-cell data. It was a great experience to work with our collaborators on that!
Scalable and unsupervised discovery from raw sequencing reads using SPLASH2 - Nature Biotechnology
SPLASH2 speeds up analysis of sequence variation in massive datasets.
www.nature.com
December 26, 2024 at 6:41 PM
Recently, our SPLASH paper (www.nature.com/articles/s41...) was published in NatBiotech. Now, we release its extended version, sc-SPLASH (www.biorxiv.org/content/10.1...), which allows reference-free analysis of single-cell data. It was a great experience to work with our collaborators on that!
First post here. :-) AGC 3.2 (assembled genome compressor) has been released. Better speed, better ratio (at least for bacteria genomes), optional low-memory decompression.
github.com/refresh-bio/...
github.com/refresh-bio/...
GitHub - refresh-bio/agc: Assembled Genomes Compressor
Assembled Genomes Compressor. Contribute to refresh-bio/agc development by creating an account on GitHub.
github.com
November 25, 2024 at 7:37 AM
First post here. :-) AGC 3.2 (assembled genome compressor) has been released. Better speed, better ratio (at least for bacteria genomes), optional low-memory decompression.
github.com/refresh-bio/...
github.com/refresh-bio/...