About Myself
I am a Ph.D. student at Tri-Institutional Computational Biology & Medicine (hosted by Cornell University & MSKCC & Rockefeller University), advised by Prof. Christina Leslie.
I received my Bachelor’s degree with honors from Zhili College, Tsinghua University. During my undergraduate years, I was honored to be advised by Prof. Stephen Shing-Toung Yau from Department of Mathematical Sciences and Prof. Bryan Wei from School of Life Sciences. Previously, I was also a visiting scholar at Stanford University through UGVR program, advised by Prof. Bo Wang.
For contact: Email (rur4004@med.cornell.edu).
Research Overview
I am currently a Ph.D. student with a focus on computational biology, bioinformatics, and the application of deep learning to biological research. My work spans several interdisciplinary projects that leverage advanced computational methods, including machine learning, natural language processing, and mathematical modeling, to address biological challenges.
In my research on AI for Biology, I have contributed to several projects that integrate machine learning with genomic analysis. Notably, I developed kmer2vec, a novel approach for comparing DNA sequences using NLP methods, which was applied to phylogenetic analysis and SARS-CoV-2 typing. Additionally, I constructed a deep learning model CAPE for prokaryotic promoter evolution that was successfully validated through biological experiments.
My research aims to bridge computational techniques with biological discovery, improving our understanding of genomic evolution, gene regulation, developmental biology, and disease mechanisms through innovative models and software tools.
Selected Publications
[1] Ruohan Ren, et al. “CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution.” Briefings in Bioinformatics 25.5 (2024): bbae398.
[2] Ruohan Ren, Changchuan Yin, and Stephen S.-T. Yau. “kmer2vec: A novel method for comparing DNA sequences by word2vec embedding.” Journal of Computational Biology 29.9 (2022): 1001-1021.
[3] Hongyu Yu*, Nan Sun*, Ruohan Ren*, et al. “The grand biological universe: A comprehensive geometric construction of genome space.” The Innovation (2025).
[4] Erin Haus*, Anthony Santella*, Yichi Xu, Ruohan Ren, Dali Wang, Zhirong Bao. “A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics.” Cell Reports Methods (2026).
[5] Zixuan Bian*, Ruohan Ren*, Yue Yang, Chris Callison-Burch. “HOLODECK 2.0: Vision-Language-Guided 3D World Generation with Editing.” ArXiv Preprint (2025).
* Co-first authors
Experience
2024/09 - Present: Ph.D. Student, Weill Cornell Medicine & MSKCC & Rockefeller University, New York
2024/03 - 2024/07: Research Intern, Microsoft Research Asia, Beijing
2023/06 - 2023/10: Summer Research, Bioengineering Department, Stanford University, California
2020/09 - 2024/07: Bachelor of Science with Honors, Zhili College, Tsinghua University, Beijing
Selected Awards and Honors
• “Tsinghua University Future Scholar” PI (with up to 150,000 CNY funding per year)
• Comprehensive Excellence Scholarship/Jiang Nanxiang Scholarship in Tsinghua University
• Baosteel Scholarship
• Selected to Spark Program at Tsinghua University
• Best Research Award, XueTang Program, Tsinghua University
• Zhili College Dean’s List (7/219)
• Best Software Nomination Award & Silver Medal of International Genetically Engineered Machine (iGEM) Competition
• Gold Medal of China National Biology Olympiad (CNBO)
• First Prize of National Olympiad in Informatics in Provinces (NOIP)
Miscellaneous
• Presented a poster, “Interpretable motif-mediated gene regulation modeling from single-cell multiomics with SCARlink+,” at the IGVF (Impact of Genomic Variation on Function) Consortium Annual Meeting 2026, St. Louis, MO
• Gave a 30-minute talk at the 5th TSIMF (Tsinghua Sanya International Mathematics Forum) Conference on Computational and Mathematical Bioinformatics and Biophysics, Sanya, 2023
• Gave a 20-minute talk at the HKUST-Tsinghua Joint Workshop, Hong Kong, 2023
• Participated in the International Congress of Chinese Mathematicians (ICCM) 2022
• Participated in the EuroSpark Study Tour in France, Germany, and Switzerland, 2022
• Volunteered at the Beijing Winter Olympics 2022