Author

Maksim M. Kholmatov

European Molecular Biology LaboratoryORCID 0000-0002-4201-8124Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genomics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Research Focus:gene regulatory network inference· 2 Assay:scRNA-seq· 2 Assay:ATAC-seq· 1

Frequent Co-Authors

Judith B. ZauggiD· 3 shared Borhane GuezgueziD· 2 shared Eva Hellström‐LindbergiD· 2 shared Karin D. PrummeliD· 2 shared Pedro Luís MouraiD· 2 shared Anatolii ZaikovskiiiD· 1 shared Annique ClaringbouldiD· 1 shared Armando Reyes‐PalomaresiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersBioinformatics

Judith B. ZauggORCID

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Author profile →

4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintSep 22, 2025

SpliceUp: Predicting SF3B1 mutations in individual cells via aberrant splice site activation from scRNA-seq data

Maksim M. Kholmatov, Karin D. Prummel, Borhane Guezguez…·Judith B. Zaugg

SpliceUp detects SF3B1-mutant cells in scRNA-seq data by analyzing aberrant splicing signatures, improving detection from low-coverage datasets.

3 citations

Molecular BiologybioRxivPreprintNov 27, 2024

Inflammatory Mesenchymal Stromal Cells and IFN-responsive T cells are key mediators of human bone marrow niche remodeling in CHIP and MDS

Karin D. Prummel, Kevin Woods, Maksim M. Kholmatov…·Borhane Guezguez

DOI 10.1101/2024.11.27.625734

GenomicsbioRxivPreprintDec 18, 2021

GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages

Aryan Kamal, Christian Arnold, Annique Claringbould…·Judith B. Zaugg

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.

12 citations

BioinformaticsJournal of CheminformaticsPeer-reviewedMay 23, 2018

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules.

Ilia O. Korvigo, Maksim M. Kholmatov, Anatolii Zaikovskii, Mikhail Y. Skoblov

The paper develops a deep CNN-RNN model for chemical named entity recognition without hand-crafted rules, achieving near human-level performance on the CHEMDNER corpus.

53 citations

deep learningbenchmarking