🌈 We are looking for new Postdocs and PhD students (CBD or MLD) to work on Comp Bio + ML.

I am the Ray and Stephanie Lane Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University. I also have an Affiliated Faculty appointment in Machine Learning. Our group was established at the University of Illinois at Urbana-Champaign in August 2009 and later moved to Carnegie Mellon in January 2016. I have been fortunate to receive several awards, including, among others, being named "Tomorrow's PI" by Genome Technology (2011), a National Science Foundation CAREER award (2011), and a Guggenheim Fellowship (2020). I am an elected Fellow of AIMBE and AAAS. I served as the Program Chair for RECOMB 2024. I am also a member of the Scientific Advisory Board of the Chan Zuckerberg Biohub Chicago and the RECOMB Steering Committee.

The primary focus of our ongoing research is the development of AI/ML methods to study the structure and function of the human genome and cellular organization, with implications for health and disease. Recent interests include nuclear organization, single-cell epigenomics, spatial omics, and complex molecular interactions. These goals are often pursued through the development of probabilistic models and advanced deep learning techniques, particularly graph-based representation learning, with the aim of driving discovery and guiding experimentation. We are also exploring large language models to uncover gene regulatory mechanisms and the intricate connections among cellular components at various scales in complex tissues. Ultimately, our goal is to learn the language of cells through innovation in AI/ML.

Our lab is leading a UM1 Center in the NIH 4D Nucleome (4DN) Program [CMU News]. I am also serving as Co-Chair of the Steering Committee of the NIH 4DN Program. In addition, our lab is involved in the NIH SenNet Consortium and the IGVF Consortium.

We recently launched the Center for AI-Driven Biomedical Research (AI4BIO) [CMU News], which will be a catalyst for innovations at the intersection of AI and biomedicine across the School of Computer Science and campus.