Skip to main content

People


Principal Investigator

Jian Ma

Ray and Stephanie Lane Professor of Computational Biology (Professor 07/2021-08/2021; Associate Professor 01/2016-06/2021) and Affiliated Faculty of Machine Learning, School of Computer Science, Carnegie Mellon University

Associate Professor with tenure (08/2015-12/2015) and Assistant Professor (08/2009-07/2015), Bioengineering; Faculty Member, Carl R. Woese Institute for Genomic Biology; Faculty Member, Biophysics and Computational Biology; Affiliate Faculty, Computer Science; University of Illinois at Urbana-Champaign

Postdoc, 01/2007-07/2009, UC Santa Cruz (with David Haussler)
Ph.D. (12/2006) in Computer Science, Penn State University (with Webb Miller)
M.S. (2003) and B.S. (2000) in Computer Science, Fudan University, Shanghai, China


Project Scientist

Yang Zhang

Project Manager of the NIH 4DN UM1 Center Project
PhD in BioE, University of Illinois at Urbana-Champaign (2017)
Yee Memorial Fund Fellowship (2014)
CZI napari Ecosystem Grant (2022)
Interests: 3D epigenomics, comparative genomics

Postdocs / Research Associate

Shaoheng Liang

Lane Fellow
PhD in Computer Science, Rice University (2022)
BS in EE, Tsinghua University (2017)
Interests: machine learning for spatial omics

Spencer Krieger

Lane Fellow
PhD in Computer Science, University of Arizona (2022)
BS in Biochemistry, Brigham Young University (2016)
Interests: spatial omics, gene regulation

PhD Students

Shahul Alam

PhD student, CBD/SCS, CMU
BS in Computer Science, Massachusetts Institute of Technology (2020)
CPCB NIH T32 Trainee (2023-2024)
Interests: machine learning for spatial omics

Xue Er Ding

PhD student, CBD/SCS, CMU
BS in Computer Science, McGill University (2023)
Interests: machine learning for single-cell data

Ellie Haber

PhD student, MLD/SCS, CMU
BS in Computer Science, New York University (2022)
Interests: LLMs for single-cell data

Nicholas Ho

PhD student, CBD/SCS, CMU
BS in Math & CS, Arizona State University (2023)
NSF Graduate Research Fellowship (2024-2027)
Joint with Eric Xing
Interests: LLMs for genome sequences

Xinyue Lu

PhD student, CBD/SCS, CMU
MS, CBD/SCS, CMU (2023)
BS, Zhiyuan Honor Program, Shanghai Jiao Tong University (2021)
Interests: 3D epigenomics and gene regulation

Akanksha Sachan

PhD student, CBD/SCS, CMU
BS in Chemical Engineering, Indian Institute of Technology Bombay (2022)
Interests: 3D epigenomics and gene regulation

Shike Wang

PhD student, CBD/SCS, CMU
MS in Computer Science, ShanghaiTech (2023)
BS in Computer Science, East China U of Sci & Tech (2020)
Interests: complex biomolecular interactome

Wendy Yang

PhD student, CBD/SCS, CMU
BS in Computer Science, Carnegie Mellon University (2019)
Interests: 3D epigenomics and gene regulation

Tianming Zhou

PhD student, CBD/SCS, CMU
BS, Yao Class, Tsinghua University (2018)
CBD Outstanding Research Accomplishment Award (2023)
Honorable Mention, CBD Outstanding Research Accomplishment Award (2021, 2022)
Interests: machine learning for 3D epigenomics and spatial omics

MS Students

Wenduo Cheng

MS student, MSCB, CMU
BS, Genomics, Duke Kunshan University (2022)

Yun-Shuo Chou

MS student, MSCB, CMU
BS, Computer Science, Tsinghua University (2022)

Recent PhD Graduates [2020 - ]

Kyle Xiong

PhD, CBD/SCS, CMU (2023)
BS in BME, Johns Hopkins University (2016)
PhD Dissertation: Application of machine learning algorithms to reveal 3D genome compartmentalization patterns.
CPCB NIH T32 Trainee (2017-2019)
Current Position: Data Scientist at Benevolence Med LLC

Ruochi Zhang

PhD, CBD/SCS, CMU (2022)
BS in Automation, Tsinghua University (2017)
PhD Dissertation: Charting the landscape of 3D genome organization with graph representation learning.
CBD PhD Program Outstanding Research Accomplishment (2020)
Current Position: Eric and Wendy Schmidt Center Fellow at the Broad Institute (mentors: Bonnie Berger and Jason Buenrostro)

Yuchuan Wang

PhD, CBD/SCS, CMU (2021)
BS in Biology, Tsinghua University (2014)
PhD Dissertation: Computational methods for integrative analysis of nuclear genome compartmentalization.
Current Position: Scientist at Illumina AI Lab

Yang Yang

PhD, CBD/SCS, CMU (2020)
BS and MS in Automation, Tsinghua University (2015)
PhD Dissertation: Computational methods for multi-species comparison of 3D genome organization and function.
CBD PhD Program Outstanding Research Accomplishment (2018)
EECS Rising Stars (2019)
Current Position: Postdoc with Dana Pe'er