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| Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning J Zheng, X Zhang, X Zhao, X Tong, X Hong, J Xie, S Liu Scientific reports 8 (1), 15264, 2018 | 51 | 2018 |
| Template-based modeling of protein-RNA interactions J Zheng, PJ Kundrotas, IA Vakser, S Liu PLoS computational biology 12 (9), e1005120, 2016 | 33 | 2016 |
| The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes J Zheng, LW Meinhardt, R Goenaga, D Zhang, Y Yin Horticulture Research 8, 2021 | 30 | 2021 |
| eCAMI: simultaneous classification and motif identification for enzyme annotation J Xu, H Zhang, J Zheng, P Dovoedo, Y Yin Bioinformatics 36 (7), 2068-2075, 2020 | 30 | 2020 |
| dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes J Zheng, B Hu, X Zhang, Q Ge, Y Yan, J Akresi, V Piyush, L Huang, Y Yin Nucleic Acids Research 51 (D1), D557-D563, 2023 | 26 | 2023 |
| Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution X Feng, J Zheng, I Irisarri, H Yu, B Zheng, Z Ali, S de Vries, J Keller, ... bioRxiv, 2023 | 24 | 2023 |
| P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking J Zheng, X Hong, J Xie, X Tong, S Liu Bioinformatics 36 (1), 96-103, 2020 | 20 | 2020 |
| RMalign: an RNA structural alignment tool based on a novel scoring function RMscore J Zheng, J Xie, X Hong, S Liu BMC genomics 20, 1-10, 2019 | 20 | 2019 |
| Rabies viruses leader RNA interacts with host Hsc70 and inhibits virus replication R Zhang, C Liu, Y Cao, M Jamal, X Chen, J Zheng, L Li, J You, Q Zhu, ... Oncotarget 8 (27), 43822, 2017 | 18 | 2017 |
| PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction J Xie, J Zheng, X Hong, X Tong, S Liu Communications biology 3 (1), 384, 2020 | 13 | 2020 |
| Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. bioRxiv X Feng, J Zheng, I Irisarri, H Yu, B Zheng, Z Ali, S de Vries, J Keller, ... | 5 | 2023 |
| dbAPIS: a database of anti-prokaryotic immune system genes Y Yan, J Zheng, X Zhang, Y Yin Nucleic acids research 52 (D1), D419-D425, 2024 | 4 | 2024 |
| Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2–6 X Cheng, B Yang, J Zheng, H Wei, X Feng, Y Yin Computational and Structural Biotechnology Journal 19, 5678-5687, 2021 | 4 | 2021 |
| AcaFinder: Genome mining for anti-CRISPR-associated genes B Yang, J Zheng, Y Yin Msystems 7 (6), e00817-22, 2022 | 3 | 2022 |
| The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes J Zheng, LW Meinhardt, R Goenaga, T Matsumoto, D Zhang, Y Yin Horticulture Research 9, uhac014, 2022 | 3 | 2022 |
| RR3DD: an RNA global structure-based RNA three-dimensional structural classification database X Hong, J Zheng, J Xie, X Tong, X Liu, Q Song, S Liu, S Liu RNA biology 18 (sup2), 738-746, 2021 | 3 | 2021 |
| Protein-DNA complex structure modeling based on structural template J Xie, J Zheng, X Hong, X Tong, X Liu, Q Song, S Liu, S Liu Biochemical and Biophysical Research Communications 577, 152-157, 2021 | 3 | 2021 |
| Homeobox transcription factor HbxA influences expression of over one thousand genes in the model fungus Aspergillus nidulans SS Pandit, J Zheng, Y Yin, S Lorber, O Puel, S Dhingra, EA Espeso, ... PLoS One 18 (7), e0286271, 2023 | 2 | 2023 |
