Yiyan Yang

Yiyan Yang, PhD
Contact: yiyanyang0728@gmail.com

Welcome! Currently, I am a postdoctoral research fellow at Brigham and Women's Hospital and Harvard Medical School. Before this, I worked at National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH).

I completed my undergraduate (Outstanding Graduate Thesis Award) and PhD studies (Outstanding Graduates Awards and National Scholarship of PhD candidate) at Tongji University, Shanghai, China (2010-2019). I identify myself as a bioinformatician with a focus on leveraging computational techniques to solve complex biological challenges.

My primary interests are in comparative genomics and evolutionary biology, especially their applications in microbiology and virology. I studied the evolution of influenza virus and ammonia-oxidizing archaea during my PhD study. My current focus is to leverage genomic and metagenomic data to understand the adaptive mechanisms that pathogenic or commensal microbes employ during interactions with their hosts. In the future, I hope to contribute to understanding the role of microbes in the diagnosis, treatment, and progression of human diseases.

Research interests: Host-microbe interactions, Microbiome, Microbiology, Virology, Evolutionary biology, Comparative Genomics.

Hobbies

When I'm not working in the lab, I often go running outside or do powerlifting at the gym. I played softball in national competitions during my college years and also used to run half marathons, winning awards both at university and in Shanghai city. While I've tried CrossFit, I find that powerlifting is my favorite, and I've won some national awards in it. In 2019, I also obtained a personal trainer certification from the American Council on Exercise (but it has expired since I didn't renew it. So sad). As a huge fan of anime, you can also find me binge-watching animations or reading comics if I'm not lifting weights or running algorithms.

Education & Experience

Postdoctoral Fellow (2024 - Present)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA

Advisor: Professor Yang-Yu Liu

Research direction: microbiome, virome, deep learning

Postdoctoral Fellow (2020 - 2024)

National Library of Medicine, National Institutes of Health, Bethesda, MD

Advisor: Dr. Xiaofang Jiang

Research direction: microbial genomics, microbial evolution and host-microbe interactions

Ph.D. in Biology (2014 - 2019)

Tongji University, Shanghai, China

Advisor: Professor Zhiwei Cao

Thesis: “Computational study of microbial adaptive evolution to the environments”

BA in Biotechnology (2010 - 2014)

Tongji University, Shanghai, China

Advisor: Professor Zhiwei Cao

Thesis: “An evolutionary model for the antigenic sites of A/H3N2 influenza virus hemagglutinin”

Publications

Published 8 (co)first-authored papers and 20 papers in total. A list of my publications can be found here.

Softwares

I enjoy coding and communicating with computers. I developed several bioinformatic tools which are listed here.

Awards

I've obtained several awards since I've been doing science:

Excellent Student of Tongji University (2011-2012)
Learning Scholarship of Tongji University, Second Class (2011-2013)
PetroChina Tarim Scholarship of Tongji University (2012)
Guanghua Scholarship of Tongji University (2013)
Outstanding Graduate Thesis Award (2014)
Academical Cultural Festival Award of Tongji University (2017)
National Scholarship of PhD candidate of Tongji University (2018)
Outstanding Graduates Awards of Tongji University (2019)
NIH Postdoctoral Visiting Program Award (2020-2023)
Poster Honorable mentions in EvolCompGen of 2022 International Conference on Intelligent Systems for Molecular Biology (ISMB) (2022)

Skills

Skilled in analyzing data from Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS)
Skilled in genomic and metagenomic analysis
Proficiency in comparative genomics and understanding of evolutionary biology
Knowledge and practical application of deep learning and machine learning techniques
Familiarity with high-performance computing and optimization
Experience in software development with an emphasis on bioinformatics tools
Proficient in Python and R programming languages
Capability in analyzing and interpreting Protein 3D structure
Capability in network analysis related to biological systems
Experience in web server configuration/building

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