| ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index T Obayashi, Y Aoki, S Tadaka, Y Kagaya, K Kinoshita Plant and Cell Physiology 59 (1), e3-e3, 2018 | 289 | 2018 |
| COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference T Obayashi, Y Kagaya, Y Aoki, S Tadaka, K Kinoshita Nucleic acids research 47 (D1), D55-D62, 2019 | 143 | 2019 |
| ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components T Obayashi, H Hibara, Y Kagaya, Y Aoki, K Kinoshita Plant and Cell Physiology 63 (6), 869-881, 2022 | 50 | 2022 |
| Real-time structure search and structure classification for AlphaFold protein models T Aderinwale, V Bharadwaj, C Christoffer, G Terashi, Z Zhang, ... Communications Biology 5 (1), 316, 2022 | 39 | 2022 |
| Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction A Jain, G Terashi, Y Kagaya, SR Maddhuri Venkata Subramaniya, ... Scientific Reports 11 (1), 7574, 2021 | 21 | 2021 |
| Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment MF Lensink, G Brysbaert, N Raouraoua, PA Bates, M Giulini, RV Honorato, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1658-1683, 2023 | 15 | 2023 |
| COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations T Obayashi, S Kodate, H Hibara, Y Kagaya, K Kinoshita Nucleic Acids Research 51 (D1), D80-D87, 2023 | 13 | 2023 |
| MAINMASTseg: automated map segmentation method for cryo-EM density maps with symmetry G Terashi, Y Kagaya, D Kihara Journal of chemical information and modeling 60 (5), 2634-2643, 2020 | 13 | 2020 |
| Protein contact map refinement for improving structure prediction using generative adversarial networks SR Maddhuri Venkata Subramaniya, G Terashi, A Jain, Y Kagaya, ... Bioinformatics 37 (19), 3168-3174, 2021 | 9* | 2021 |
| ContactPFP: protein function prediction using predicted contact information Y Kagaya, ST Flannery, A Jain, D Kihara Frontiers in bioinformatics 2, 896295, 2022 | 8 | 2022 |
| Domain-PFP allows protein function prediction using function-aware domain embedding representations N Ibtehaz, Y Kagaya, D Kihara Communications Biology 6 (1), 1103, 2023 | 3* | 2023 |
| A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams (Lutraria rhynchaena) OTP Kim, Y Kagaya, HS Tran, R Minei, TTH Tran, HTT Duong, BTN Le, ... Archives of virology 165, 2921-2926, 2020 | 3 | 2020 |
| Metagenome sequences from the environment of diseased otter clams, Lutraria rhynchaena, from a Farm in Vietnam Y Kagaya, R Minei, HTT Duong, BTN Le, LT Dang, TTH Tran, HT Nguyen, ... Microbiology Resource Announcements 9 (2), 10.1128/mra. 01068-19, 2020 | 2 | 2020 |
| NuFold: A Novel Tertiary RNA Structure Prediction Method Using Deep Learning with Flexible Nucleobase Center Representation Y Kagaya, Z Zhang, N Ibtehaz, X Wang, T Nakamura, D Huang, D Kihara bioRxiv, 2023 | 1 | 2023 |
| Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints Y Zhang, Z Zhang, Y Kagaya, G Terashi, B Zhao, Y Xiong, D Kihara bioRxiv, 2023.12. 01.569498, 2023 | 1 | 2023 |
| AttentiveDist: Protein Inter-Residue Distance Prediction Using Deep Learning with Attention on Quadruple Multiple Sequence Alignments A Jain, G Terashi, Y Kagaya, SR Maddhuri Venkata Subramaniya, ... bioRxiv, 2020.11. 24.396770, 2020 | 1 | 2020 |
| Improved Peptide Docking with Privileged Knowledge Distillation using Deep Learning Z Zhang, J Verburgt, Y Kagaya, C Christoffer, D Kihara bioRxiv, 2023.12. 01.569671, 2023 | | 2023 |
Kinoshita KengoTohoku UVahvistettu sähköpostiosoite verkkotunnuksessa ecei.tohoku.ac.jp
