Marek Kokot
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Explore the profile of Marek Kokot including associated specialties, affiliations and a list of published articles.
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15
Citations
406
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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.
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...
3.
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....
4.
Aurivillius M, Bednarczyk A, Kokot M, Madriaga J, Mei J, Collison K, et al.
Pulm Pharmacol Ther
. 2023 Aug;
83:102245.
PMID: 37607661
Introduction: The climate crisis poses an immediate threat to human health and well-being, demanding urgent adaptions across sectors, including healthcare. The development of pressurized metered dose inhalers (MDIs) with greater...
5.
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...
6.
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...
7.
Dufresne Y, Lemane T, Marijon P, Peterlongo P, Rahman A, Kokot M, et al.
Bioinformatics
. 2022 Jul;
38(18):4423-4425.
PMID: 35904548
Summary: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a...
8.
Kokot M, Gudys A, Li H, Deorowicz S
Nat Methods
. 2022 Mar;
19(4):441-444.
PMID: 35347321
The cost of maintaining exabytes of data produced by sequencing experiments every year has become a major issue in today's genomic research. In spite of the increasing popularity of third-generation...
9.
Deorowicz S, Danek A, Kokot M
Bioinformatics
. 2021 Mar;
37(19):3358-3360.
PMID: 33787870
Summary: Variant Call Format (VCF) files with results of sequencing projects take a lot of space. We propose the VCFShark, which is able to compress VCF files up to an...
10.
Olaszek P, Wyczalek I, Sala D, Kokot M, Swiercz A
Sensors (Basel)
. 2020 May;
20(10).
PMID: 32408682
In the case of the monitoring of bridges, the determination of vertical displacements is one of the most important issues. A new measuring system has been developed and implemented for...