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General Information
| Full Name | Hao Yuan |
| Position | Postdoctoral Fellow, Department of Molecular Biosciences, University of Texas at Austin |
| hao.yuan@austin.utexas.edu | |
| Phone | (517) 402-1770 |
| Languages | English, Chinese |
Education
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2021-2026 PhD in Genetics and Genome Sciences & Ecology, Evolution and Behavior
Michigan State University, MI, USA - Topic
- Contextualizing Biological Associations Across Genes, Cell Types, Species, and Evolution
- Advisor
- Ingo Braasch
- Arjun Krishnan
- Topic
-
2016-2019 MS in Biology
Shanghai Ocean University, Shanghai, China - Topic
- Assembly and Filtering of Enriched Data from Exon Capture Across Species
- Advisor
- Chenhong Li
- Topic
-
2012-2016 BS in Marine Biology
Shanghai Ocean University, Shanghai, China - Advisor
- Chenhong Li
- Advisor
Experience
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2026- Postdoctoral Fellow
Marcotte Lab, University of Texas at Austin -
2021-2026 Graduate Assistant
Braasch Lab & Krishnan Lab, Michigan State University -
2020-2021 Bioinformatician
Shanghai Amplicongene Bioscience Co. LTD. -
2019 Bioinformatician
Genergy Biotechnology Co. LTD
Open Source Projects
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2026 ICePop
- Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop
-
2024 txt2onto2.0
- Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata
-
2023 CONE
- CONE: COntext-specific Network Embedding via Contextualized Graph Attention
-
2018-2019 Assexon
- Assexon: Assembling Exon Using Gene Capture Data
Skills
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Computational Background and Skills
- Well-versed with Python, R, Linux command line and version control using GitHub
- Experience with Python package development
- Experience working with high-performance computing resources
-
Computational Genomics, Network Modeling, and Text Mining Skills
- Well-versed with genomic data analysis including genomic sequences, bulk and single-cell transcriptomics
- Experience with graph learning methods using protein-protein interaction networks and integrated analysis with omic data
- Experience with statistical modeling using single cell omic data
- Experience with using large language models for large-scale text mining and metadata analysis
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Statistics, Data Science, and Machine Learning
- Data wrangling and visualization in Python with pandas, matplotlib, and seaborn
- Statistical modeling and machine learning in Python with numpy, numba, statsmodels, scipy, scikit-learn and PyTorch
Honors and Awards
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2026 - Genetics and Genome Sciences Program Outstanding Student Award
-
2023 - Summer College of Natural Science Outstanding Scholar Fellowship
Talks
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Sep 2024 CONE: COntext-specific Network Embedding via Contextualized Graph Attention
Machine Learning in Computational Biology 2024, Seattle, WA -
Mar 2024 Discovering context-specific functionally equivalent genes in research organisms using cross species transcriptome-based machine learning
The Allied Genetics Conference 2024, Metro Washington, DC -
Dec 2022 An ML framework for precision medicine: from patient-specific gene networks to translational animal models
Rocky 2022 Bioinformatics Conference, Snowmass, CO -
Oct 2016 Genome-wide detection of sites under selection using a modified method of evolutionary probability - a case study on adaptive evolution of Homo species
23rd Academic Annual Meeting of China Zoological Society, Wuhan, China -
Oct 2024 Annotating public omics samples and studies using interpretable modeling of unstructured metadata by txt2onto 2.0
Genetics and Genome Sciences Forum, Michigan State University -
Feb 2024 An ML framework for precision medicine: from patient-specific gene networks to translational research organisms
Genetics and Genome Sciences Forum, Michigan State University -
Oct 2023 Reconstruct patient-specific gene networks from transcriptomic data
Genetics and Genome Sciences Forum, Michigan State University -
Oct 2022 An ML framework for precision medicine: from patient-specific gene networks to translational animal models
Computational Biology Forum, Michigan State University
Posters
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2025 Evolutionary Implications of the Teleost Genome Duplication Revealed by Cross-Species Single-Cell Transcriptomic Comparison
American Society for Biochemistry and Molecular Biology 2025: Evolution and Core Processes in Gene Expression, Kansas City, MO -
2025 ICePop: Identifying Disease-Affected Cell Types Through Network-Based Analysis of Gene Module Overexpression in Single-Cell Data
Network Biology 2025, Cold Spring Harbor, NY -
2024 ICePop: Identifying Disease-Affected Cell Types Through Network-Based Analysis of Gene Module Overexpression in Single-Cell Data
Biological Data Science 2024, Cold Spring Harbor, NY -
2024 Tracking dynamic regulatory changes in rare diseases using single sample networks
Annual Meeting of American Society of Human Genetics 2024, Denver, CO -
2024 CONE: COntext-specific Network Embedding via Contextualized Graph Attention
Machine Learning in Computational Biology 2024, Seattle, WA -
2023 Interpretable text-based machine learning for inferring systematic tissue and disease annotations of public transcriptome samples
Genome Informatics 2023, Cold Spring Harbor, NY -
2023 An ML framework for precision medicine: from patient-specific gene networks to translational animal models
Network Biology 2023, Cold Spring Harbor, NY -
2022 An ML framework for precision medicine: from patient-specific gene networks to translational animal models
Rocky 2022 Bioinformatics Conference, Snowmass, CO -
2022 Cross-species transcriptome-based regression to discover equivalents of human samples and genes in biomedical research organisms
30th Conference on Intelligent Systems for Molecular Biology, Madison, WI -
2018 EXpipe: An Assembly Pipeline for Exon Capture Data Across Large Scales of Divergence
1st AsiaEvo Conference, Shenzhen, China
Teaching and Mentoring
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Teaching
- 2023: IBIO341 Fundamental Genetics, Teaching Assistant
-
Mentoring (Post-baccalaureate)
- 2023-2025: Lydia Valtadoros, Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus
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Mentoring (Junior Graduate Student)
- 2023-2026: Parker Hicks, Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus
Professional Service
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Reviewing Service
- 2026: G3: Genes, Genomes, Genetics (2 manuscripts)
- 2025: G3: Genes, Genomes, Genetics (1 manuscript)
- 2024: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution (1 manuscript, co-review with Dr. Ingo Braasch)
- 2023: Genome Biology (1 manuscript, co-review with Dr. Arjun Krishnan)
- 2022: Genome Research (1 manuscript, co-review with Dr. Arjun Krishnan)
-
Community Service
- 2023-2025: Genetics and Genome Sciences Program Seminar Coordinator
- 2023-2025: Genetics and Genome Sciences Program Graduate Student Organization
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Career Development Activities
- Jan 2023: Graduate Student Career Forum
- Apr 2022: APIDA Virtual Career Panel: Careers in Data, Analytics, Technology, & Engineering
- Apr 2022: Boost your professional power skills
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STEM Outreach
- Dec 2023: AP Biology DeWitt High School Visit Day
Academic Interests
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Biomedicine
- Heterogeneity of complex diseases
- Gene network analysis of complex diseases
- Statistical modeling of single cell data
-
Evolution
- Cross-species knowledge transfer between research organism and human
- Cell type evolution
Other Interests
- Hobbies: Cooking, Video Game