Saito Lab

Bioinformatics for Bioengineering

We seek to reveal the principles of life through large-scale data analysis based on machine-learning and bioinformatics approaches, and to use these rules for designing and controlling biomolecules. We are also interested in laboratory automation using experiment robots.

Topics

Recruiting graduate students! [Join us]

2024.08.02
Our paper "Protein-compound interaction prediction using microbial chemical communication network" received IPSJ Yamashita Research Award 2024. [Link]

2024.06.24
Deguchi gives presentation in IUPAB 2024. [Conference Link]

2024.06.03

Nur Syatila Binti Ab Ghani (Project Assistant Professor, Kitasato University) joined our lab. [Member]
2024.05.09

Shen's research received Best Presentation in IPSJ SIGBIO 76. [Conference Link]
2024.05.01

Takuma Matsushita (Project Assistant Professor, Kitasato University) joined our lab. [Member]
2024.04.30

Our paper "Protein-compound interaction prediction using microbial chemical communication network" was accepted in IPSJ Transactions on Bioinformatics. [Journal Link]
2024.04.18

Our paper "Functional enhancement of flavin-containing monooxygenase through machine learning methodology" was accepted in ACS Catalysis. [Journal Link]
2024.01.04

Our paper "Extensive antibody search with whole spectrum black-box optimization" was accepted in Scientific Reports. [Journal Link]
2024.01.04

Adrien Mialland (postdoc researcher, AIST) joined our lab. [Member]
2023.11.20

Our paper "VeloPro: A pipeline integrating Ribo-seq and AlphaFold deciphers association patterns between translation velocity and protein structure features" was accepted in iMeta. [Journal Link]
2023.11.14

Deguchi gives presentation in BSJ 2023. [Conference Link]
2023.11.12

Bian gives presentation in InCoB 2023. [Conference Link]
2023.11.03

Wang Yicheng gives presentation in Bioimaging 32. [Conference Link]
2023.10.04

Our grant proposals for JST GteX was accepted.
2023.09.19

Our grant proposals for JST CREST and ACT-X were accepted.
2023.09.09

Jin received Best Poster Presentation in IIBMP 2023. [Conference Link]
2023.09.07

Bian, Zhang, Wang Yicheng, Jin, Deguchi, Oniduka, Katsuki and Syatila give presentation in IIBMP 2023. [Conference Link]
2023.05.17

Our grant proposal for NEDO was accepted.
2023.04.21

Our paper "A multiomics atlas of brown adipose tissue development over time" was accepted in Endocrinology. [Journal Link]
2023.04.01

Our grant proposal for JSPS KAKENHI was accepted.
2023.04.01

Iida, Kurumida (Assistant Professor, Kitasato University), Noguchi (JSPS Research Fellow, PD), Dong, Wang, Jin, Deguchi (graduate student, The University of Tokyo) joined our lab. [Member]
2023.02.04

Our paper "Engineering the substrate specificity of toluene degrading enzyme XylM using biosensor XylS and machine learning" was accepted in ACS Synthetic Biology. [Journal Link]
2023.01.23

Our paper "Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning" was accepted in mAbs. [Journal Link]
2023.01.20

Gonzalo Molpeceres (student internship, Spanish National Research Council (CSIC)) joined our lab. [Member]
2022.12.02

Our paper "EvoOpt: an MSA-guided, fully unsupervised sequence optimization pipeline for protein design" was accepted in Machine Learning in Structural Biology Workshop, NeurIPS2022. [Conference Link] [Paper PDF]
2022.10.13

We are hiring a postdoc researcher. [JREC-IN Portal Link]
2022.10.03

Nur Syatila Binti Ab Ghani (postdoc researcher, AIST) joined our lab. [Member]
2022.09.15

Yamaguchi received Best Poster Presentation in IIBMP 2022. [Conference Link]
2022.09.13

Yamaguchi, Bian, Shen, Wang and Toki give presentation in IIBMP 2022. [Conference Link]
2022.09.03

Wang gives presentation in The 31st Annual Meeting of The Bioimaging Society. [Conference Link]
2022.08.22

Matsushita (student internship, University of Shizuoka) joined our lab. [Member]
2022.08.08

Katsuki (student internship, The University of Electro-Communications) joined our lab. [Member]
2022.07.29

Saito received Oxford Journals JSBi Prize 2022. [Link]
2022.05.20

Saito received JACI Prize for Encouraging Young Researcher 2022. [Link]
2022.05.18

Our paper "AI and computational chemistry-accelerated development of an alotaketal analogue with conventional PKC selectivity" was accepted in Chemical Communications. [Journal Link]
2022.04.29

We are hiring a postdoc researcher. [JREC-IN Portal Link]
2022.04.26

Zhang gives presentation in APBC 2022. [Conference Link]
2022.04.01

Noguchi (postdoc researcher, AIST) and Oniduka (graduate student, The University of Tokyo) joined our lab. [Member]
2022.02.28

Our grant proposals for JSPS KAKENHI were accepted in KIBAN-B and KIBAN-A tracks.
2022.02.15

Toki (student internship, The University of Tokyo) joined our lab. [Member]
2021.12.06

Our lab web site was renewed!
2021.11.19

Our paper "Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration" was accepted and selected as Cover Art in ACS Catalysis. [Journal Link] [Cover Art]
2021.10.01

Bian and Jiang (graduate student, The University of Tokyo) joined our lab. [Member]
2021.09.27

Yamaguchi, Fukunaga and Oniduka give presentation in IIBMP 2021. [Conference Link]
2021.07.31

Yamaguchi received Best Talk Award (First Prize) in ISMB / ECCB 2021, Special Session: Representation learning in biology. [Conference Link]
2021.07.25

Yamaguchi gives presentation in ISMB / ECCB 2021. [Conference Link]
2021.07.22

Our paper "Machine learning approach for discrimination of genotypes based on bright-field cellular images" was accepted in npj Systems Biology and Applications. [Journal Link]
2021.06.29

Our paper "Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins" was accepted in Briefings in Bioinformatics. This is the first paper first-authored by our student! [Journal Link]
2021.06.18

Yamaguchi received Best Poster Presentation in PSSJ 2021. [Conference Link]
2021.06.16

Yamaguchi gives presentation in PSSJ 2021. [Conference Link]
2021.05.28

Our paper "Comparative analysis of the relationship between translation efficiency and sequence features of endogenous proteins in multiple organisms" was accepted in Genomics. [Journal Link]
2021.05.21

Our grant proposal for AMED was accepted.
2021.04.06

Our paper "Rational thermostabilisation of four-helix bundle dimeric de novo proteins" was accepted in Scientific Reports. [Journal Link]
2021.04.01

Shen and Wang (graduate student, The University of Tokyo) joined our lab. [Member]
2021.02.25

Our paper "Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model" was accepted in Scientific Reports. [Journal Link]

Past Topics