Zong-Yan Liu (劉宗晏)

Hi, my name is

Zong-Yan Liu.

I teach machines to read plant genomes

Ph.D. candidate at Cornell University in the Buckler Lab. I build DNA foundation models that annotate plant genomes directly from sequence — including GeneCAD, the first foundation-model workflow to assemble complete gene models without RNA-seq or proteomics.

Curriculum Vitae

About Me

I am a Ph.D. candidate 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.

My current research applies DNA foundation models to plant genome annotation — teaching large sequence models to read genomes and predict gene structures at single-nucleotide resolution, across both diploid and polyploid species. I also work on genomic prediction and statistical modeling 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).

Cornell International Services Advisory Board - Cornell

Spring 2025 - present

As a member of the Cornell International Services Advisory Board, I contribute to enhancing the support and resources available to international students. In my role as Secretary for the Cornell Diversity and International Students Committee (DISC), I am responsible for coordinating communication, and assisting in the development of initiatives that promote diversity and inclusion.

President - Synapsis

Aug 2024 - present

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

Majoring in Agronomy with 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

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.

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.

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

ASPB Ambassador

I am honored to be competitively selected as an ASPB Ambassador for the American Society of Plant Biologists, the premier international professional society for plant scientists. In this role, I represent the global plant biology community by promoting scientific outreach, fostering professional development for early-career researchers, and enhancing the visibility of plant research through international networking and engagement initiatives.

Exemplary Leadership Award

I am honored to receive the Exemplary Leadership Award from OISE and the Graduate and Professional Diversity Council for my dedicated service to the Cornell graduate and professional student community. This recognition highlights my commitment to promoting diversity, inclusion, and student engagement through leadership, advocacy, and support of graduate student organizations.

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.

Honorary Membership

In 2020, I was inducted as a member of The Phi Tau Phi Scholastic Honor Society of the Republic of China, a prestigious recognition of academic excellence and outstanding scholastic achievements. This honor reflects my commitment to academic rigor and my contributions to research in my field.

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.