Author

Fedor A. Kolpakov

Sirius University of Science and Technology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:DNA methylation· 4 Research Focus:gene regulatory network inference· 4 Organism:human· 4 Approach:experimental assay· 3 Assay:ChIP-seq· 2 Research Focus:differential expression· 2 Research Focus:protein structure prediction· 2 Approach:benchmark study· 1

Frequent Co-Authors

Arttu JolmaiD· 4 shared Bart DeplanckeiD· 4 shared Dmitry PenzariD· 4 shared Ilya E. VorontsoviD· 4 shared Ivan KoziniD· 4 shared Ivan V. KulakovskiyiD· 4 shared Ivo GroßeiD· 4 shared Jan GrauiD· 4 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersGenomics

Arttu JolmaORCID

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Author profile →

4 papers

Recent·Most cited

Inferring binding specificities of human transcription factors with the wisdom of crowds

Nikita Gryzunov, Dmitry Penzar, Vasilii Kamenets, Valery Vyaltsev, Ivan Kozin, Irina A. Eliseeva, Vladimir Nozdrin, Ilya E. Vorontsov, Sergey Bushuev, Vadim V. Strekalovskikh, Arsenii O. Zinkevich, Gregory Andrews, Matwej Bedarew, Ido Blass, Dmitry Frolov, , Ivan V. Kulakovskiy

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

Cell Reports · Oct 1, 2026Peer-reviewedBioinformatics

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

Antoni J. Gralak, Kateřina Faltejsková, Ally W. H. Yang, Clemence Steiner, Julie Russeil, Nadia Grenningloh, Sachi Inukai, Mustafa Demir, Riccardo Dainese, C. C. Owen, Eugenia V. Pankevich, Philipp Bücher, Oriol Fornés, Jan Grau, Ivo Große, , Bart Deplancke

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

Nature Communications · Aug 5, 2026Peer-reviewedGenomics

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

Arttu Jolma, Aldo Hernández-Corchado, Ally W. H. Yang, Ali Fathi, Kaitlin U. Laverty, Alexander V. Brechalov, Rozita Razavi, Mihai Albu, Hong Zheng, Philipp Bücher, Bart Deplancke, Oriol Fornés, Jan Grau, Ivo Große, Fedor A. Kolpakov, , Timothy Hughes

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

Nature Methods · Aug 5, 2026Peer-reviewedGenomics

Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors

Arttu Jolma, Kaitlin U. Laverty, Ali Fathi, Ally W. H. Yang, Isaac Yellan, Ilya E. Vorontsov, Sachi Inukai, Judith F. Kribelbauer-Swietek, Antoni J. Gralak, Rozita Razavi, Mihai Albu, Alexander V. Brechalov, Zain M. Patel, Vladimir Nozdrin, Georgy Meshcheryakov, , Xiaoting Chen

The paper systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

bioRxiv · Nov 11, 2024 · PreprintGenomics