PREPRINT 2026
Steering Conformational Sampling in Boltz-2 via Pair Representation Scaling
S. Suzuki, T. Amagasa
bioRxiv
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Ph.D. Student
Graduate School of Systems and Information Engineering
University of Tsukuba
About
I am a Ph.D. student in Computer Science at the University of Tsukuba. My research focuses on protein dynamics and design, genomic language models, and deep learning for biology. I am particularly interested in conformational sampling, de novo binder design, and transformer-based approaches to biological sequence analysis.
Education
Ph.D. in Computer Science
University of Tsukuba · 2025.04 - 2028.03 (expected)
M.S. in Agro-Bioresources Science
University of Tsukuba · 2023.04 - 2025.03
B.S. in Agro-Biological Resource Sciences
University of Tsukuba · 2019.04 - 2023.03
Funding & Computing
JSPS DC2
日本学術振興会 特別研究員 DC2
2026.04 - 2028.03
JST SPRING
次世代研究者挑戦的研究プログラム
2025.04 - 2026.03
Osaka Univ. D3 Center SQUID
世界と伍する学生育成特設枠
2026.04 - 2027.03
Research Assistant
National Institute of Advanced Industrial Science and Technology (AIST)
2024.09 - Present
National Institute of Genetics (NIG)
2025.04 - Present
National Agriculture and Food Research Organization (NARO)
2022.04 - 2024.08
Research
Protein Dynamics & Design
Conformational sampling in protein structure prediction models, dynamics-driven de novo binder design, and latent space manipulation for exploring protein conformational landscapes.
Conformational Sampling Binder Design Protein Dynamics Generative AI
Genomic Language Models
Developing transformer-based models for plant genome annotation and regulatory element prediction with novel k-mer tokenization strategies.
NLP Genomics Transformers Gene Annotation
Deep Learning for Biology
Applying modern deep learning techniques to diverse biological problems, bridging computational methods with experimental validation.
Deep Learning Bioinformatics Structure Prediction
Publications
PAPER 2025
Genomic language models with k-mer tokenization strategies for plant genome annotation and regulatory element strength prediction
S. Suzuki, K. Horie, T. Amagasa, N. Fukuda
Plant Molecular Biology
Conferences
Pacific Symposium on Biocomputing (PSB) 2026
Jan 2026Poster · Hawaii, USA
The 48th Annual Meeting of the Molecular Biology Society of Japan
Dec 2025Poster / Forum · Yokohama, Japan
Awards
Protein Design Competition (NiG)
ONGOINGAdaptyv Bio - Selected for Expert Review & Wet Lab Validation
MBSJ-EMBO Poster Award
The 48th Annual Meeting of the Molecular Biology Society of Japan
Top 3% (51 selected from 1,599 entries)
8th Place, Protein Design Competition (EGFR)
Adaptyv Bio
Top 10 out of 130+ participants worldwide
Japan Biology Olympiad - Excellence Award
158th place out of 4,189 competitors
Top 3%