| DEEPre: sequence-based enzyme EC number prediction by deep learning Y Li, S Wang, R Umarov, B Xie, M Fan, L Li, X Gao Bioinformatics 34 (5), 760-769, 2018 | 268 | 2018 |
| Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks RK Umarov, VV Solovyev PloS one 12 (2), e0171410, 2017 | 235 | 2017 |
| TSSPlant: a new tool for prediction of plant Pol II promoters IA Shahmuradov, RK Umarov, VV Solovyev Nucleic acids research 45 (8), e65-e65, 2017 | 121 | 2017 |
| Promoter analysis and prediction in the human genome using sequence-based deep learning models R Umarov, H Kuwahara, Y Li, X Gao, V Solovyev Bioinformatics 35 (16), 2730-2737, 2019 | 97 | 2019 |
| RNA secondary structure prediction by learning unrolled algorithms X Chen, Y Li, R Umarov, X Gao, L Song arXiv preprint arXiv:2002.05810, 2020 | 93 | 2020 |
| A deep learning framework to predict binding preference of RNA constituents on protein surface JH Lam, Y Li, L Zhu, R Umarov, H Jiang, A Héliou, FK Sheong, T Liu, ... Nature communications 10 (1), 4941, 2019 | 84 | 2019 |
| Sequence2vec: a novel embedding approach for modeling transcription factor binding affinity landscape H Dai, R Umarov, H Kuwahara, Y Li, L Song, X Gao Bioinformatics 33 (22), 3575-3583, 2017 | 58 | 2017 |
| Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics S Maddirevula, H Kuwahara, N Ewida, HE Shamseldin, N Patel, ... Genome biology 21, 1-21, 2020 | 57 | 2020 |
| HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes Y Li, Z Xu, W Han, H Cao, R Umarov, A Yan, M Fan, H Chen, CM Duarte, ... Microbiome 9, 1-12, 2021 | 56 | 2021 |
| ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation R Umarov, Y Li, T Arakawa, S Takizawa, X Gao, E Arner PLOS Computational Biology 17, 1-18, 2021 | 10 | 2021 |
| DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment R Umarov, Y Li, E Arner PLoS Computational Biology 17 (10), e1009465, 2021 | 9 | 2021 |
| SBOLme: a repository of SBOL parts for metabolic engineering H Kuwahara, X Cui, R Umarov, R Grunberg, CJ Myers, X Gao ACS Synthetic Biology 6 (4), 732-736, 2017 | 8 | 2017 |
| ACRE: Absolute concentration robustness exploration in module-based combinatorial networks H Kuwahara, R Umarov, I Almasri, X Gao Synthetic Biology 2 (1), ysx001, 2017 | 4 | 2017 |
| System and method for promoter prediction in human genome X Gao, R Umarov US Patent App. 17/297,233, 2021 | 2 | 2021 |
| Novel computational methods for promoter identification and analysis R Umarov | 2 | 2020 |
| HMD-ARG: Identifying antibiotic resistance genes through machine learning Y Li, Z Xu, W Han, H Cao, R Umarov, A Yan, M Fan, H Chen, C Duarte, ... | 1 | 2021 |
| NNfold: RNA secondary structure prediction by deep learning with an architecture imposing contextual constraining C Van Neste, R Umarov, Y Li, A Salhi, H Kuwahara, X Gao Available at SSRN 3813288, 2021 | 1 | 2021 |
| A DeepFake framework for prediction of cell type specific transcriptional states induced by drug treatment R Umarov, E Arner bioRxiv, 2020.12. 14.422792, 2020 | 1 | 2020 |
| Enhancer target prediction: state-of-the-art approaches and future prospects R Umarov, CC Hon Biochemical Society Transactions 51 (5), 1975-1988, 2023 | | 2023 |
| NNfold: RNA secondary structure prediction by deep learning R Umarov, Y Li, C Van Neste | | 2020 |
