The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Nature microbiology 5 (4), 536-544, 2020 | 8358* | 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 | 74 | 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 | 69 | 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 | 46 | 2020 |
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 | 44 | 2019 |
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 | 28 | 2018 |
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 | 12 | 2019 |
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 | 10 | 2023 |
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 | 4 | 2022 |
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods N Null, S Jain, C Bakolitsa, SE Brenner, P Radivojac, J Moult, S Repo, ... Genome Biology 25 (1), 1-46, 2024 | 3 | 2024 |
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, 485085, 2019 | 3 | 2019 |
Evaluation and optimization of sequence-based gene regulatory deep learning models AM Rafi, D Nogina, D Penzar, D Lee, D Lee, N Kim, S Kim, D Kim, Y Shin, ... bioRxiv, 2023 | 2 | 2023 |
PQ, a new program for phylogeny reconstruction D Penzar, M Krivozubov, S Spirin BMC bioinformatics 19, 1-14, 2018 | 2 | 2018 |
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 | | 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, 2024.02. 24.581671, 2024 | | 2024 |
PhyloBench: a Benchmark for Evaluating Phylogenetic Programs S Spirin, A Sigorskikh, A Efremov, D Penzar, A Karyagina | | 2023 |
LegNet: a novel approach to modeling regulatory sequences with deep convolutional networks MCCMB'2023 https://mccmb.belozersky.msu.ru/2023/thesis/MCCMB.utf8.html, 2023 | | 2023 |
NogiNet: repurposing EfficientNetV2 for accurate promoter sequence-to-expression modeling D Penzar https://www.iscb.org/rsgdream2022-schedule/programme/dream-challenges, 2022 | | 2022 |
PhyloBench, a benchmark for evaluation of phylogenetic programs A Sigorskih, A Efremov, D Penzar, A Karyagina, S Spirin Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB …, 2022 | | 2022 |
PREDICTION OF REGULATORY SEQUENCE VARIANTS USING DATA FROM MULTIPLE PARALLEL REPORTER ASSAYS DD Penzar, AO Zinkevich, IE Vorontsov, VV Sitnik, AV Favorov, ... VII Съезд Вавиловского общества генетиков и селекционеров, посвященный 100 …, 2019 | | 2019 |