Hi, my name is

Zong-Yan Liu.

I build things for the plants

A dedicated PhD student at Cornell University, I leverage machine learning techniques to unravel the complexities of plant genomes and their evolutionary history.

About Me

I am a third-year Ph.D. student at Cornell University in the Buckler Lab with a passion for computational biology and genetics. My background bridges computer science and plant genetics, and I’m deeply interested in how data science can advance our understanding of crop genomes. Currently, I am conducting research in maize genetics, focusing on genomic prediction and statistical modeling to improve crop resilience.

I am working on a project that utilizes advanced computational techniques to enhance genomic analysis in maize, aiming to contribute to sustainable agriculture and food security.

Here are a few technologies I've been working with recently:
  • Python
  • R
  • Machine Learning
  • Database

Experience

Cornell Biological Sciences Representative - GPSA
Aug 2024 - present
I represent the Biological Sciences in Cornell’s Graduate and Professional Student Assembly (GPSA), where I advocate for the interests and well-being of graduate students in the biological sciences. Additionally, I have served as the Secretary for the Cornell Diversity and International Students Committee (DISC).
President - Synapsis
Aug 2024 - present

I serve as the President of Synapsis, where I lead initiatives to build a supportive community and enhance the professional and academic experiences of graduate students in Cornell Plant Breeding and integrative plant sciences.

  • Lead and coordinate 10 different committees.
  • Organize and manage events and workshops that promote professional development.
President - CTSA
Jun 2023 - Jun 2024

I serve as the President of the Cornell Taiwanese Student Association (CTSA), where I lead initiatives to foster community and cultural exchange, organize events and resources to support Taiwanese and international students, and advocate for their needs and interests within the Cornell University environment.

  • Collaborate with government agencies and companies to establish strong connections between academia and industry.
  • Plan and execute cultural events, workshops, and networking opportunities that enhance the academic and social experiences.
Graduate Research Assistant - Academia Sinica
Jul 2021 - Aug 2022

I am a Graduate Research Assistant at Academia Sinica’s Institute of Information Science, where I focus on studying extrachromosomal circular DNA (eccDNA) for cancer prediction. Additionally, I am responsible for maintaining our lab’s database, ensuring data integrity and accessibility to support ongoing research initiatives.

  • Develop and apply computational methods to analyze eccDNA.
  • Maintain server clusters and manage databases to support research operations.
Graduate Research Assistant - NTU
Jul 2020 - Jul 2022
I am a Graduate Research Assistant at the National Taiwan University Institute of Plant Biology and Department of Biomechatronics Engineering, where I leverage machine learning techniques to predict plant microRNA target genes, enhancing our understanding of gene regulation in plants.

Education

2022 - NOW
Doctor of Philosophy in Plant Breeding and Genetics
Cornell University

Focuses on developing advanced computational models to accurately predict gene structures and protein abundance in plants, enhancing our understanding of plant genomics and providing valuable insights into crop biology and evolution.

  • Gene Structure Prediction: Utilize large language models to predict plant gene structures, aiming to improve the accuracy and performance of genome annotation tools compared to traditional methods.
  • Protein Abundance Modeling: Extends to modeling the protein abundance of highly expressed genes, incorporating evolutionary insights to predict protein levels across diverse plant species, with a special focus on agriculturally important crops.
2018 - 2020
Master of Science in Plant Biology
National Taiwan University
GPA: 4.09 out of 4.3

Analysis of IbHypSys-mediated MicroRNAs upon Wounding in Sweet Potato (Ipomoea batatas cv. Tainung 57)

  • Target Gene Development: Design and implement algorithms to accurately identify and predict plant microRNA target genes from sequencing data.
  • Experimental Validation: Clone microRNA precursors and target genes into vectors and perform transgenic over-expression to evaluate the inhibitory effects of microRNAs on target gene expression.
2014 - 2018
Bachelor of Science in Agronomy
National Chung Hsing University
GPA: 4.04 out of 4.3

I have a double minor in Management Information Systems and Applied Economics.

  • Management Information Systems: Gained expertise in data management, systems analysis, and information technology strategies to optimize business processes.
  • Applied Economics: Developed strong analytical skills through economic modeling, data analysis, and the application of economic theories to real-world scenarios.

Research in Agronomy

  • Experimental Design and Implementation: Conducted controlled experiments to assess the impact of various hydrolysis salts on the osmoregulation of rice seedlings under stress conditions.
  • Data Analysis and Interpretation: Analyzed experimental data to determine the effectiveness of hydrolysis salts in mitigating osmosis stress, contributing to improved agronomic practices for rice cultivation.

Projects

Gene Annotation
Caduceus Transformer Large Language Model
Gene Annotation
Advancements in genome sequencing have greatly facilitated the study of organisms, yet understanding genomic variation remains complex, particularly in genome annotation which models genetic transcription and translation.
Identify Storage Proteins
ProtTrans Large Language Model
Identify Storage Proteins
Seed storage proteins, crucial for plant development and as a food source, are abundantly found in crops like wheat and maize. However, their diversity in different plant species is not fully understood. We used the ProtTrans tool and a support vector machine classifier to analyze their physicochemical properties, aiming to identify new storage proteins in the UniProt database and Andropogoneae genomes, enhancing our knowledge of these essential proteins.
Identifying Targets of MicroRNA by Deep Learning
microRNA mirScore biLSTM
Identifying Targets of MicroRNA by Deep Learning
A tool to collate microRNA with transcriptome data. The output files are concurrent with MirTarSite obligatory input format. Conflate the sequencing data and deep-learning method to predict microRNA target.

Achievements

Fellowships
I have been honored to receive the Government Scholarships for Overseas Study and the Pilot Projects on Scholarship for Taiwanese Studying in Focused Fields at Top Foreign Universities from Taiwan. These highly competitive fellowships recognize my academic excellence and have enabled me to advance my research in plant genetics at Cornell University, fostering international collaboration and innovation.
Outstanding Performance Award
I was honored with the Outstanding Performance in Moral and Intellectual Aspects award from National Chung Hsing University, recognizing my exemplary academic achievements and strong ethical leadership. This award highlights my dedication to both scholarly excellence and personal integrity.
Young Elite Representative
I was selected as a Young Elite Representative by the China Youth Corps, recognizing my leadership potential and contributions to the community. This honor underscores my commitment to youth engagement, cultural exchange, and leadership development.
National Energy Science & Technology Creative Design Contest Award
I received the National Energy Science & Technology Creative Design Contest Award from the Ministry of Education, R.O.C., in recognition of my innovative contributions to energy-related technology and design. This award highlights my ability to apply creative problem-solving to important challenges in the field of energy science.

Get in Touch

My inbox is always open. Whether you have a question or just want to say hi, I’ll try my best to get back to you!