| Convolutional neural network based on SMILES representation of compounds for detecting chemical motif M Hirohara, Y Saito, Y Koda, K Sato, Y Sakakibara BMC bioinformatics 19, 83-94, 2018 | 224 | 2018 |
| Machine-learning-guided mutagenesis for directed evolution of fluorescent proteins Y Saito, M Oikawa, H Nakazawa, T Niide, T Kameda, K Tsuda, M Umetsu ACS synthetic biology 7 (9), 2014-2022, 2018 | 154 | 2018 |
| Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions Y Saito, J Tsuji, T Mituyama Nucleic acids research 42 (6), e45-e45, 2014 | 77 | 2014 |
| Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration Y Saito, M Oikawa, T Sato, H Nakazawa, T Ito, T Kameda, K Tsuda, ... Acs Catalysis 11 (23), 14615-14624, 2021 | 53 | 2021 |
| Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model Y Miyazaki, T Oda, Y Inagaki, H Kushige, Y Saito, N Mori, Y Takayama, ... Scientific reports 11 (1), 4690, 2021 | 50 | 2021 |
| Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells R Nakato, Y Wada, R Nakaki, G Nagae, Y Katou, S Tsutsumi, N Nakajima, ... Epigenetics & Chromatin 12, 1-16, 2019 | 37 | 2019 |
| An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds M Nakamura, T Hachiya, Y Saito, K Sato, Y Sakakibara BMC bioinformatics 13, 1-12, 2012 | 33 | 2012 |
| Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria Y Saito, W Kitagawa, T Kumagai, N Tajima, Y Nishimiya, K Tamano, ... Scientific reports 9 (1), 8338, 2019 | 30 | 2019 |
| Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures Y Saito, K Sato, Y Sakakibara BMC bioinformatics 12, 1-8, 2011 | 25 | 2011 |
| Predicting antibody affinity changes upon mutations by combining multiple predictors Y Kurumida, Y Saito, T Kameda Scientific reports 10 (1), 19533, 2020 | 21 | 2020 |
| Ribosome incorporation into somatic cells promotes lineage transdifferentiation towards multipotency N Ito, K Katoh, H Kushige, Y Saito, T Umemoto, Y Matsuzaki, H Kiyonari, ... Scientific reports 8 (1), 1634, 2018 | 19 | 2018 |
| Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins H Yamaguchi, Y Saito Briefings in Bioinformatics 22 (6), bbab234, 2021 | 17 | 2021 |
| Existence and possible roles of independent non-CpG methylation in the mammalian brain JH Lee, Y Saito, SJ Park, K Nakai DNA Research 27 (4), dsaa020, 2020 | 17 | 2020 |
| Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans K Morita, Y Saito, K Sato, K Oka, K Hotta, Y Sakakibara Nucleic acids research 37 (3), 999-1009, 2009 | 16 | 2009 |
| Brief exposure to small molecules allows induction of mouse embryonic fibroblasts into neural crest‐like precursors Y Takayama, T Wakabayashi, H Kushige, Y Saito, Y Shibuya, S Shibata, ... FEBS letters 591 (4), 590-602, 2017 | 14 | 2017 |
| Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions Y Saito, T Mituyama BMC genomics 16, 1-10, 2015 | 12 | 2015 |
| Methylome, transcriptome, and PPARγ cistrome analyses reveal two epigenetic transitions in fat cells H Takada, Y Saito, T Mituyama, Z Wei, E Yoshihara, S Jacinto, M Downes, ... Epigenetics 9 (9), 1195-1206, 2014 | 12 | 2014 |
| Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning T Ito, TD Nguyen, Y Saito, Y Kurumida, H Nakazawa, S Kawada, H Nishi, ... MAbs 15 (1), 2168470, 2023 | 10 | 2023 |
| Engineering the substrate specificity of toluene degrading enzyme XylM using biosensor XylS and machine learning Y Ogawa, Y Saito, H Yamaguchi, Y Katsuyama, Y Ohnishi ACS Synthetic Biology 12 (2), 572-582, 2023 | 9 | 2023 |
| AI and computational chemistry-accelerated development of an alotaketal analogue with conventional PKC selectivity J Maki, A Oshimura, C Tsukano, RC Yanagita, Y Saito, Y Sakakibara, ... Chemical Communications 58 (47), 6693-6696, 2022 | 9 | 2022 |
