| Bioinformatics methods for mass spectrometry-based proteomics data analysis C Chen, J Hou, JJ Tanner, J Cheng International journal of molecular sciences 21 (8), 2873, 2020 | 231 | 2020 |
| Multiomics profiling establishes the polypharmacology of FDA-approved CDK4/6 inhibitors and the potential for differential clinical activity M Hafner, CE Mills, K Subramanian, C Chen, M Chung, SA Boswell, ... Cell chemical biology 26 (8), 1067-1080. e8, 2019 | 194 | 2019 |
| DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks C Chen, J Hou, X Shi, H Yang, JA Birchler, J Cheng BMC bioinformatics 22, 1-18, 2021 | 67 | 2021 |
| Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa J Hou, X Shi, C Chen, MS Islam, AF Johnson, T Kanno, B Huettel, MR Yen, ... Proceedings of the National Academy of Sciences 115 (48), E11321-E11330, 2018 | 60 | 2018 |
| Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction C Chen, T Wu, Z Guo, J Cheng Proteins: Structure, Function, and Bioinformatics 89 (6), 697-707, 2021 | 37 | 2021 |
| Geometric transformers for protein interface contact prediction A Morehead, C Chen, J Cheng arXiv preprint arXiv:2110.02423, 2021 | 31 | 2021 |
| Berberine reverses abnormal expression of L-type pyruvate kinase by DNA demethylation and histone acetylation in the livers of the non-alcoholic fatty disease rat Y Zhang, X Chang, X Song, C Chen, H Chen, Z Lu, X Gao, D Lu International journal of clinical and experimental medicine 8 (5), 7535, 2015 | 29 | 2015 |
| Genomic imbalance determines positive and negative modulation of gene expression in diploid maize X Shi, H Yang, C Chen, J Hou, KM Hanson, PS Albert, T Ji, J Cheng, ... The Plant Cell 33 (4), 917-939, 2021 | 27 | 2021 |
| Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15 J Liu, Z Guo, T Wu, RS Roy, F Quadir, C Chen, J Cheng Communications biology 6 (1), 1140, 2023 | 26 | 2023 |
| 3D-equivariant graph neural networks for protein model quality assessment C Chen, X Chen, A Morehead, T Wu, J Cheng Bioinformatics 39 (1), btad030, 2023 | 26 | 2023 |
| Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize H Yang, X Shi, C Chen, J Hou, T Ji, J Cheng, JA Birchler The Plant Cell 33 (4), 901-916, 2021 | 24 | 2021 |
| Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii N Zhang, EM Mattoon, W McHargue, B Venn, D Zimmer, K Pecani, ... Communications biology 5 (1), 460, 2022 | 23 | 2022 |
| Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance AF Johnson, J Hou, H Yang, X Shi, C Chen, MS Islam, T Ji, J Cheng, ... Journal of genetics and genomics 47 (2), 93-103, 2020 | 18 | 2020 |
| Dips-plus: The enhanced database of interacting protein structures for interface prediction A Morehead, C Chen, A Sedova, J Cheng Scientific data 10 (1), 509, 2023 | 16 | 2023 |
| The gene balance hypothesis: epigenetics and dosage effects in plants X Shi, C Chen, H Yang, J Hou, T Ji, J Cheng, RA Veitia, JA Birchler Plant epigenetics and epigenomics: methods and protocols, 161-171, 2020 | 15 | 2020 |
| Interpretable attention model in transcription factor binding site prediction with deep neural networks C Chen, J Hou, X Shi, H Yang, JA Birchler, J Cheng bioRxiv, 648691, 2019 | 13 | 2019 |
| Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15 J Liu, Z Guo, T Wu, RS Roy, C Chen, J Cheng Communications chemistry 6 (1), 188, 2023 | 12 | 2023 |
| Effect of aneuploidy of a non‐essential chromosome on gene expression in maize X Shi, H Yang, C Chen, J Hou, T Ji, J Cheng, JA Birchler The Plant Journal 110 (1), 193-211, 2022 | 12 | 2022 |
| High-performance deep learning toolbox for genome-scale prediction of protein structure and function M Gao, P Lund-Andersen, A Morehead, S Mahmud, C Chen, X Chen, ... 2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing …, 2021 | 12 | 2021 |
| Traumatic brain injury recapitulates developmental changes of axons H Song, C Chen, B Kelley, A Tomasevich, H Lee, JP Dolle, J Cheng, ... Progress in neurobiology 217, 102332, 2022 | 10 | 2022 |
