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Molecular Artificial Intelligence & Digital Biochemistry
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Computational Structural Biology & Machine Learning for Biomolecules
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Molecular Machine Learning & Chemoinformatics for Drug Discovery
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Computational Structure-based Drug Discovery
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Molecular Modeling & Molecular Dynamics Simulation for Biomolecules

ABOUT

Hello, I'm Bundit, a Ph.D. candidate in Information Science and Technology at Natural Language Processing and Representation Learning Lab (NRL), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand. I received a B.Sc. degree in Chemistry from Prince of Songkla University, Thailand and an M.S. degree in Biochemistry from Kasetsart University, Thailand.

Bundit Boonyarit

" SUCCESS DOES NOT COME FROM SMARTNESS

BUT IT'S CAUSED BY THE IMPLEMENTATION. "

MY ACHIEVEMENTS

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  • 2024

    Remarkable Ranking in the Top 20 (17th Place Out of 79 Participating Teams) for the Tox24 Challenge and The Solution has been Invited to be Published in Chemical Research in Toxicology (ChemResTox), ACS

  • 2024

    Best Oral Presentation in Computational Biology Session, The 27th International Annual Symposium on Computational Science and Engineering (ANSCSE27)

  • 2023

    JSTP Mentor for High School Student and Received Long-term Scholarship, National Science and Technology Development Agency (NSTDA)

  • 2023

    Research Advisor for Genius Olympiad Finalists and Received Honorable Mention Award in Science, Genius Olympiad 2023

  • 2023

    Research Advisor for ISEF Finalists and Received Fourth Place Award in Computational Biology and Bioinformatics, Regeneron ISEF 2023

  • 2023

    Research Advisor for High School Students and Received Top Award and First Award of Thailand in Interdisciplinary Fields (Computational Biology & Bioinformatics), and Second Award of Thailand in Computer Science, Young Scientist Competition (YSC) 2023

  • 2022

    Research Advisor for Genius Olympiad Finalists and Received Bronze Medal in Science, Genius Olympiad 2022

  • 2022

    Research Advisor for ISEF Finalists and Received First Place Award in Computational Biology and Bioinformatics, Regeneron ISEF 2022

  • 2022

    Research Advisor for High School Students and Received Top Award, First Award, and Second Award of Thailand in Interdisciplinary Fields (Computational Biology & Bioinformatics), Young Scientist Competition (YSC) 2022

  • 2021

    Research Advisor for Genius Olympiad Finalists and Received Gold Medal in Science, Genius Olympiad 2021

  • 2021

    Research Advisor for ISEF Finalists and Received First Place Award in Computational Biology and Bioinformatics, Regeneron ISEF 2021

  • 2021

    Research Advisor for High School Students and Received Championship of Thailand in Computer Science, Young Scientist Competition (YSC) 2021

  • 2020

    Research Advisor for High School Students and Received Championship of Thailand in Computer Science, Young Scientist Competition (YSC) 2020

  • 2018

    Ph.D. scholarship from Vidyasirimedhi Institute of Science and Technology and PTT Group, and SCB

  • 2015

    Academic Activist and Person who made reputation for Faculty of Science, Prince of Songkla University, Hatyai Campus, Thailand

  • 2015

    Young Thai Science Ambassador 2014, National Science Museum, Thailand

  • 2014

    The 11th True Young Webmaster Camp

  • 2013

    Intermediate level (Band 4 of 6) in the PSU English Test

  • 2012

    JSTP scholarship student, National Science and Technology Development Agency, Thailand

  • 2008 – 2010

    Computer Olympiad Camp (POSN), 1st & 2nd camps, Walailak University, Thailand

EXPERIENCES

Recent Invited Talks

  • Talk 99 – Poster Preparation for Science Project Presentation Workshop

    EECi Young Innovator Contest 2024
    Organized by Kamnoetvidya Science Academy (KVIS)

    Venue: Kamnoetvidya Science Academy, Rayong
    Date: Aug 24, 2024

  • Talk 98 – Fun with Food

    Fun Thinking with Science Around You Camp
    for Grade 6 students of Anuban Ubonratchathani School, Ubon Ratchathani
    Organized by National Science and Technology Development Agency (NSTDA)

    Venue: Sirindhorn Science Home, Science Park, Pathum Thani
    Date: Jul 11, 2024

  • Talk 97 – Jump-start Science Project & Scientist Invents Dough

    Jump Start Science Camp
    for Grade 9 students of Horwang Pathumthani School, Pathum Thani
    Organized by National Science and Technology Development Agency (NSTDA)

    Venue: Sirindhorn Science Home, Thailand Science Park, Pathum Thani
    Date: Jul 4–5, 2024

Outstanding Extracurricular Activities

  • Regeneron International Science and Engineering Fair 2024 (Regeneron ISEF 2024)

    Staff and Research Mentor
    Fair: THA002 – Young Scientist Competition
    Year: 2024

  • Regeneron International Science and Engineering Fair 2022 (Regeneron ISEF 2022)

    Thai Interpreter
    Year: 2022

  • Thailand Machine Learning for Chemistry Competition (TMLCC)

    Organizer and Speaker
    Lecture: Machine Learning for Molecular Chemistry in a Nutshell
    Year: 2021

  • The White Room Enterprise Co., Ltd.

    Co-founder
    Science camps for students interested in science and education and charity camps for students underprivileged in science education
    Year: 2012 – Present

  • 12th Young Webmaster Camp, Thailand Webmaster Association

    Organizer
    Year: 2015

Research Experience

  • Artificial Intelligence-driven Prediction of Molecular Properties and Bioactivity for Cancer Therapeutics Using Graph Neural Networks

    Mentors: Assoc. Prof. Dr. Sarana Nutanong, and Assoc. Prof. Dr. Thanyada Rungrotmongkol
    Year: 2018 – Now

  • Computational Screening of Tripeptides Against Kinase-Domain for Human Epidermal Growth Factor Receptor 2 (HER2)

    Research Experience at NSTDA, Thailand (JSTP Scholarship)

    Mentors: Assoc. Prof. Dr. Kiattawee Choowongkomon, Dr. Sissades Tongsima
    Year: 2014 – 2017

  • Characterization of Gelatin From Silver Carp Skin As Influenced by Acid Pretreatment

    Research Experience at Fac. Agro-Industry, PSU, Thailand (JSTP Scholarship)

    Mentor: Prof. Dr. Soottawat Benjakul
    Year: 2011 – 2012

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RESEARCH INTERESTS

The research focuses on exploring new frontiers in Molecular Property & Interaction, Molecular Design & Discovery, and Molecular Representation & Learning, aiming to revolutionize the understanding and application that contribute significant strides for (bio)molecular science by integrating cutting-edge computational techniques and interdisciplinary knowledge from Biochemistry, Chemistry, Pharmaceutical Sciences, and Computer Science.

The current research themes, collectively termed “CompMol3D – Computational Molecular Discovery, Design, and Development”, encompass the following areas:

  • Molecular Property & Interaction

    Elucidate relationships between (bio)molecular structures, properties, and interactions, informing predictions and facilitating new discoveries.

  • Molecular Design & Discovery

    Utilize structural analysis to innovate in the discovery, design, and understanding of (bio)molecular phenomena, creating new pathways for molecular development and applications.

  • Molecular Representation & Learning

    Develop advanced model architectures and feature engineering strategies, enhancing machine learning and deep learning model performance in (bio)molecular science.

Current Research Projects

  • Molecular Representation Learning for Drug Design & Discovery

    This project focuses on developing advanced molecular representation learning techniques, utilizing deep learning models (i.e. graph neural networks) to enhance cancer drug discovery processes. The goal is to improve the prediction of molecular properties and interactions, contributing to more efficient drug design and development.

  • Multimodal Deep Learning Based-on Multi-Omics for Drug Response Prediction and Biomarker Discovery

    This project focuses on developing multimodal deep learning models integrated with multi-omics data (i.e. genomics, transcriptomics, and proteomics), aiming to predict cancer drug responses and discover novel cancer biomarkers. This approach leverages the power of machine learning to uncover complex relationships between various biological data types, enhancing personalized medicine strategies.

  • Machine Learning and Computational Biology for Drug Design & Discovery, Enzyme Engineering, and Structural Biology

    This project integrates machine learning and computational biology to address challenges in drug discovery, enzyme engineering, and structural biology. By leveraging advanced techniques, the project aims to predict and design novel molecules for cancer protein targets, optimize enzymes for applications such as PET degradation, and explore the structural biology of proteins, including Asgard archaea and chitin degradation proteins. This holistic approach enhances the understanding of complex biological systems and promotes the development of innovative biotechnological solutions.

Future Research Projects

  • Machine Learning and Computational Biology for Peptide- and Nucleotide-Based Therapeutics

    This project will focus on leveraging machine learning and computational biology to design and optimize peptide- and nucleotide-based therapeutics, including cyclic peptides, etc. These therapeutic modalities are gaining traction in treating various diseases, and advanced computational methods will accelerate their discovery and development.

  • Deep Learning for Epitranscriptomics

    This project aims to develop deep learning models to explore the emerging field of epitranscriptomics, which studies chemical modifications on RNA molecules. This approach will facilitate the identification of these modifications and their role in disease mechanisms, opening new avenues for therapeutic interventions.

Research Publications

  • Boonyarit, B., Yamprasert, N. , Kaewnuratchadasorn, P., Kinchakawat, J., Prommin, C., Rungrotmongkol, T., & Nutanong, S., (2024). GraphEGFR: Multi-task and Transfer Learning Based on Molecular Graph Attention Mechanism and Fingerprints Improving Inhibitor Bioactivity Prediction for EGFR Family Proteins on Data Scarcity. Journal of Computational Chemistry, 45(23), 2001-2023.

  • Phengsakun, G., Boonyarit, B., Rungrotmongkol, T., & Suginta, W. (2023). Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: classical and machine learning scoring functions, and molecular dynamics simulations. Computational Biology and Chemistry, 107856.

  • Phengsakun, G., Boonyarit, B., & Suginta, W. (2021). Docking-based virtual screening and pharmacophore analysis of novel GH-20 β-N-acetylglucosaminidase inhibitors. 7th International Conference on Biochemistry and Molecular Biology (BMB2021).

  • Virakarin, P., Saengnil, N., Boonyarit, B., Kinchagawat, J., Laotaew, R., Saeteng, T., Nilsu, T., Suvannang, N., Rungrotmongkol, T. & Nutanong, S. (2020). LigEGFR: Spatial graph embedding and molecular descriptors assisted bioactivity prediction of ligand molecules for epidermal growth factor receptor on a cell line-based dataset. bioRxiv.

  • Seetaha, S., Boonyarit, B., Tongsima, S., Songtawee, N., & Choowongkomon, K. (2020). Potential tripeptides against the tyrosine kinase domain of human epidermal growth factor receptor (HER) 2 through computational and kinase assay approaches. Journal of Molecular Graphics and Modelling, 97, 107564.

  • Boonyarit B, Mokmak W, Tongsima S, & Choowongkomon K. (2016). Computational screening of tripeptides against kinase-domain for human epidermal growth factor receptor 2 (HER2). The 42nd Congress on Science and Technology of Thailand (STT42), 495-504.

Research Collaborations

  • Prof. Robert (Bob) Charles Robinson

    - School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong, Thailand
    - Research Institute of Interdisciplinary Science, Okayama University, Japan

  • Prof. Dr. Wipa Suginta

    School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong, Thailand

  • Assoc. Prof. Dr. Thanyada Rungrotmongkol

    Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathum Wan, Bangkok, Thailand

  • Dr. Chayanon Ngambenjawong

    School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong, Thailand

RESEARCH ADVISEMENT

Students: 1. Phongsakorn Sriwicha
Advisors: Bundit Boonyarit
School: Sakolraj Wittayanukul School
Year: 2024 – 2024

Students: 1. Panuwat Wongpattanawut, 2. Phurivet Methmaolee
Advisors: Theerawut Chantapan and Bundit Boonyarit
School: Princess Chulabhorn Science High School Mukdahan
Year: 2022 – 2023

Students: 1. Tisorn Na phattalung, 2. Matin Kositchutima, 3. Kittiphat Pongarunotai
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2022 – 2023

Students: 1. Tisorn Na phattalung, 2. Surapa Panjaphakdee, 3. Matin Kositchutima
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Pawit Kaewnuratchadasorn, 2. Wutthipong Chongchareansanti, 3. Nattawin Yamprasert
Advisors: Dr. Sarote Boonseng and Bundit Boonyarit
School: Mahidol Wittayanusorn School (MWIT)
Year: 2021 – 2022

Students: 1. Thiranich Sawatdipap, 2. Phanfa Laohasinnuruk
Advisors: Dr. Tanawan Leeboonngam and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Theeradon Sakpetch, 2. Phandej Soisamuth
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2021 – 2022

Students: 1. Parajaree Ungudonpakdee, 2. Thanasan Kumdee
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Theeradon Sakpetch, 2. Phandej Soisamuth
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Natthakan Saeng-nil, 2. Puri Virakarin
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2020 – 2021

Students: 1. Natthakan Saeng-nil, 2. Puri Virakarin
Advisors: Dr. Thanasan Nilsu and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2019 – 2020

Students: 1. Chawapon Tritipchatsakun, 2. Thanis Prucksikanont
Advisors: Pimsiri Danphitsanuparn and Bundit Boonyarit
School: Kamnoetvidya Science Academy (KVIS)
Year: 2018 – 2019

BioXcepTion

BioXcepTion is a high school student research team with a particular emphasis on Computational Biology, Computational Chemistry, and Artificial Intelligence.

(Click arrow for more information about our student research team)

PERSONAL

I also have other interests including graphics design, presentation design, web design, online learning design, and server administration.

Graphics & Presentation Design

I have been interested in graphics and presentation design since I was an undergraduate student. I am most good a PR media design such as posters, brochures, and book covers. I have also been invited to lecture on the design for research presentation to school students and researchers.

Online Learning Design

I got an excellent chance from the Department of Chemistry, Faculty of Science Chulalongkorn University to build online learning for  Stereochemistry Lecture Series. This lesson is used in organic chemistry classes for undergraduate students. The instructional material includes videos and interactive activities.

Server Administration

I also have been interested in server administration for computational science research. In basic, I have used CentOS operating system and Slurm job scheduler for operation and management. For more detail, you can visit my GitHub for the setup instruction.

CONTACT

Bundit Boonyarit
Email: [email protected]

Natural Language Processing and Representation Learning Lab (NRL)
School of Information Science and Technology (IST)
Vidyasirimedhi Institute of Science and Technology (VISTEC)

555 Moo 1, Pa Yup Nai, Wang Chan, Rayong 21210, THAILAND