Sebastian Deorowicz
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Explore the profile of Sebastian Deorowicz including associated specialties, affiliations and a list of published articles.
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44
Citations
820
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Recent Articles
1.
Dehghannasiri R, Kokot M, Starr A, Maziarz J, Gordon T, Tan S, et al.
bioRxiv
. 2025 Jan;
PMID: 39763839
Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by...
2.
Beeloo R, Zomer A, Deorowicz S, Dutilh B
NAR Genom Bioinform
. 2024 Oct;
6(4):lqae142.
PMID: 39445080
The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database...
3.
Kokot M, Dehghannasiri R, Baharav T, Salzman J, Deorowicz S
Nat Biotechnol
. 2024 Sep;
PMID: 39313645
We introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach for regulated sequence variation detection in massive datasets from a wide range of sequencing...
4.
Deorowicz S, Gudys A
Bioinformatics
. 2024 Jul;
40(7).
PMID: 38984796
Motivation: The introduction of Deep Minds' Alpha Fold 2 enabled the prediction of protein structures at an unprecedented scale. AlphaFold Protein Structure Database and ESM Metagenomic Atlas contain hundreds of...
5.
Meyer E, Saldivar E, Kokot M, Xue B, Deorowicz S, Rhee S, et al.
bioRxiv
. 2024 Jun;
PMID: 38826472
Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data....
6.
Dlugosz M, Deorowicz S
Sci Rep
. 2024 Jan;
14(1):2232.
PMID: 38278837
The paper focuses on the correction of Illumina WGS sequencing reads. We provide an extensive evaluation of the existing correctors. To this end, we measure an impact of the correction...
7.
Santus L, Garriga E, Deorowicz S, Gudys A, Notredame C
Curr Opin Struct Biol
. 2023 Apr;
80:102577.
PMID: 37012200
Large-scale genomics requires highly scalable and accurate multiple sequence alignment methods. Results collected over this last decade suggest accuracy loss when scaling up over a few thousand sequences. This issue...
8.
Kokot M, Dehghannasiri R, Baharav T, Salzman J, Deorowicz S
bioRxiv
. 2023 Mar;
PMID: 36993432
SPLASH is an unsupervised, reference-free, and unifying algorithm that discovers regulated sequence variation through statistical analysis of -mer composition, subsuming many application-specific methods. Here, we introduce SPLASH2, a fast, scalable...
9.
Deorowicz S, Danek A, Li H
Bioinformatics
. 2023 Mar;
39(3).
PMID: 36864624
Motivation: High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Each project...
10.
Khan J, Kokot M, Deorowicz S, Patro R
Genome Biol
. 2022 Sep;
23(1):190.
PMID: 36076275
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic...