| Algorithm for optimized mRNA design improves stability and immunogenicity H Zhang, L Zhang, A Lin, C Xu, Z Li, K Liu, B Liu, X Ma, F Zhao, H Jiang, ... Nature 621, 396–403, 2023 | 192 | 2023 |
| LinearFold: linear-time approximate RNA folding by 5'-to-3'dynamic programming and beam search L Huang, H Zhang, D Deng, K Zhao, K Liu, DA Hendrix, DH Mathews Bioinformatics 35 (14), i295-i304, 2019 | 145 | 2019 |
| LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities H Zhang, L Zhang, DH Mathews, L Huang Bioinformatics 36 (Supplement_1), i258-i267, 2020 | 71 | 2020 |
| CoV-Seq, a new tool for SARS-CoV-2 genome analysis and visualization: Development and usability study B Liu, K Liu, H Zhang, L Zhang, Y Bian, L Huang Journal of medical Internet research 22 (10), e22299, 2020 | 33* | 2020 |
| LinearTurboFold: linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2 S Li, H Zhang, L Zhang, K Liu, B Liu, DH Mathews, L Huang Proceedings of the National Academy of Sciences 118 (52), e2116269118, 2021 | 25 | 2021 |
| Using relative lines of code to guide automated test generation for python J Holmes, I Ahmed, C Brindescu, R Gopinath, H Zhang, A Groce ACM Transactions on Software Engineering and Methodology (TOSEM) 29 (4), 1-38, 2020 | 17 | 2020 |
| ThreshKnot: Thresholded ProbKnot for improved RNA secondary structure prediction L Zhang, H Zhang, DH Mathews, L Huang arXiv preprint arXiv:1912.12796, 2019 | 15 | 2019 |
| LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2 H Zhang, S Li, L Zhang, DH Mathews, L Huang Nucleic Acids Research 51 (2), e7-e7, 2022 | 8* | 2022 |
| Learning to fold RNAs in linear time FA Rezaur Rahman Chowdhury, H Zhang, L Huang bioRxiv, 852871, 2019 | 6 | 2019 |
| Linear-time algorithms for RNA structure prediction H Zhang, L Zhang, K Liu, S Li, DH Mathews, L Huang RNA Structure Prediction, 15-34, 2022 | 4 | 2022 |
| LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules H Zhang, S Li, N Dai, L Zhang, DH Mathews, L Huang Nucleic Acids Research 51 (18), e94-e94, 2023 | 3 | 2023 |
| LinearAlifold: Linear-time consensus structure prediction for RNA alignments A Malik, L Zhang, M Gautam, N Dai, S Li, H Zhang, DH Mathews, L Huang Journal of Molecular Biology, 168694, 2024 | 1 | 2024 |
| Deep generative models generate mRNA sequences with enhanced translation capacity and stability H Zhang, H Liu, Y Xu, Y Liu, J Wang, Y Qin, H Wang, L Ma, Z Xun, TK Lu, ... bioRxiv, 2024.06. 20.599727, 2024 | | 2024 |
| LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs S Li, N Dai, H Zhang, A Malik, DH Mathews, L Huang arXiv preprint arXiv:2307.09580, 2023 | | 2023 |
