Author

Daniil M. Nikitin

Institute of Molecular BiologyORCID 0000-0003-1029-1174Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Assay:bulk RNA-seq· 3 Approach:statistical model· 3 Research Focus:batch correction / integration· 2 Assay:ChIP-seq· 2 Research Focus:differential expression· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Arsen ArakelyaniD· 2 shared Alexander A. NesmeloviD· 1 shared Alexander BagaeviD· 1 shared Alexandr Zaitsev· 1 shared Anatoly S. BobeiD· 1 shared Andrey KravetsiD· 1 shared Maria SavchenkoiD· 1 shared Mark MeersoniD· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Arsen ArakelyanORCID

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4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 15, 2026

2,234 attempts to harmonize a multi-platform B-cell lymphoma bulk transcriptomic dataset: ComBat is superior by cross-batch prediction quality

Daniil M. Nikitin, Arsen Arakelyan

The paper benchmarks 2,234 transcriptomic harmonization approaches on B-cell lymphoma data, finding ComBat excels in cross-batch prediction quality.

DOI 10.64898/2026.10.08.757652

humanbulk RNA-seq

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Cancer BiologybioRxivPreprintSep 17, 2026

✦ In-depth digest

Benchmarking of bulk transcriptomic harmonization tools in a multi-platform B-cell lymphoma cohort identifies feature-specific quantile normalization and surrogate variable analysis as top-performing methods

Daniil M. Nikitin, Nikolay Borisov, Maria Savchenko…·Arsen Arakelyan

Across 7,174 multi-platform lymphoma transcriptomes, only surrogate variable analysis and feature-specific quantile normalization corrected batch effects while keeping subtype and normal B-cell differences; top-scoring MNN erased biomarker correlations.

1 citation

humanbulk RNA-seq

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GenomicsRoyal Society Open SciencePeer-reviewedAug 26, 2026

Transposable element-host genome evolutionary arms race revealed by multi-modal epigenomic profiling in a telomere-to-telomere human genome reference

Daniil M. Nikitin

The paper analyzes epigenomic data from twelve human cell lines to reveal how transposable elements evolve in response to host defense mechanisms across different chromatin states.

1 citation

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BioinformaticsbioRxivPreprintSep 24, 2025

Joint analysis of human retroelements-linked histone modification profiles reveals quickly evolving molecular processes connected with cancer

Daniil M. Nikitin

The paper analyzes histone modification profiles linked to human retroelements to identify regulatory impacts on genes associated with cancer and immune responses.

1 citation

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