| The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Nature microbiology 5 (4), 536-544, 2020 | 8819* | 2020 |
| H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 histone tags suggest distinct regulatory evolution of open and condensed chromatin landmarks AA Igolkina, A Zinkevich, KO Karandasheva, AA Popov, MV Selifanova, ... Cells 8 (9), 1034, 2019 | 99 | 2019 |
| Landscape of allele-specific transcription factor binding in the human genome S Abramov, A Boytsov, D Bykova, DD Penzar, I Yevshin, SK Kolmykov, ... Nature communications 12 (1), 2751, 2021 | 89 | 2021 |
| Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study PB Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol ... Genome Biology 21, 2020 | 65 | 2020 |
| GENA-LM: a family of open-source foundational DNA language models for long sequences V Fishman, Y Kuratov, A Shmelev, M Petrov, D Penzar, D Shepelin, ... Nucleic Acids Research 53 (2), gkae1310, 2025 | 64* | 2025 |
| Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay D Shigaki, O Adato, AN Adhikari, S Dong, A Hawkins‐Hooker, F Inoue, ... Human mutation 40 (9), 1280-1291, 2019 | 58 | 2019 |
| Massively parallel characterization of transcriptional regulatory elements V Agarwal, F Inoue, M Schubach, D Penzar, BK Martin, PM Dash, ... Nature, 1-10, 2025 | 42* | 2025 |
| Profiling of human molecular pathways affected by retrotransposons at the level of regulation by transcription factor proteins D Nikitin, D Penzar, A Garazha, M Sorokin, V Tkachev, N Borisov, ... Frontiers in Immunology 9, 30, 2018 | 34 | 2018 |
| CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Genome biology 25 (1), 53, 2024 | 32 | 2024 |
| LegNet: a best-in-class deep learning model for short DNA regulatory regions IVK Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich ... Bioinformatics 39 (8), 2023 | 26 | 2023 |
| Retroelement—linked transcription factor binding patterns point to quickly developing molecular pathways in human evolution D Nikitin, A Garazha, M Sorokin, D Penzar, V Tkachev, A Markov, ... Cells 8 (2), 130, 2019 | 19 | 2019 |
| A community effort to optimize sequence-based deep learning models of gene regulation AM Rafi, D Nogina, D Penzar, D Lee, D Lee, N Kim, S Kim, D Kim, Y Shin, ... Nature biotechnology, 1-11, 2024 | 11* | 2024 |
| Ribonanza: deep learning of RNA structure through dual crowdsourcing S He, R Huang, J Townley, RC Kretsch, TG Karagianes, DBT Cox, H Blair, ... bioRxiv, 2024 | 11 | 2024 |
| Investigation of the role of PUFA metabolism in breast cancer using a rank-based random forest algorithm MV Guryleva, DD Penzar, DV Chistyakov, AA Mironov, AV Favorov, ... Cancers 14 (19), 4663, 2022 | 6 | 2022 |
| What do neighbors tell about you: the local context of cis-regulatory modules complicates prediction of regulatory variants DD Penzar, AO Zinkevich, IE Vorontsov, VV Sitnik, AV Favorov, ... Frontiers in Genetics 10, 1078, 2019 | 5 | 2019 |
| Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors IE Vorontsov, I Kozin, S Abramov, A Boytsov, A Jolma, M Albu, ... bioRxiv, 2024.11. 11.619379, 2024 | 4 | 2024 |
| PQ, a new program for phylogeny reconstruction D Penzar, M Krivozubov, S Spirin BMC bioinformatics 19, 1-14, 2018 | 3 | 2018 |
| PhyloBench: A benchmark for evaluating phylogenetic programs S Spirin, A Sigorskikh, A Efremov, D Penzar, A Karyagina Molecular Biology and Evolution 41 (6), msae084, 2024 | 2 | 2024 |
| GENA-web-genomic annotations web inference using DNA language models A Shmelev, M Petrov, D Penzar, N Akhmetyanov, M Tavritskiy, ... bioRxiv, 2024.04. 26.591391, 2024 | 2 | 2024 |
| A generative framework for enhanced cell-type specificity in rationally designed mRNAs M Khoroshkin, A Zinkevich, E Aristova, H Yousefi, SB Lee, T Mittmann, ... bioRxiv, 2024.12. 31.630783, 2024 | | 2024 |
