Email

qian.zhu2@bcm.edu

Positions

Assistant Professor

Lester and Sue Smith Breast Center
Department of Molecular Genetics
Baylor College of Medicine
Houston, US

Education

PhD from Princeton University

Princeton, New Jersey United States

Postdoctoral Training at Dana-Farber Cancer Institute

Boston, Massachusetts United States

BSc from University of Ottawa

Ottawa, Ontario Canada

Professional Interests

• Bioinformatics
• Computational genomics
• Cancer biology

Professional Statement

Dr. Qian Zhu is interested in the development of computational methods for genomic technologies that are being applied in cancer research. His previous works include: smfishHMRF, a hidden-Markov random field model for single-molecule FISH; Giotto, a comprehensive package for spatial transcriptomic analyses; CUT&RUNTools, a tool for CUT&RUN data processing and motif footprinting prediction. These tools are being applied to data to better understand the sources of intra-tumor heterogeneity, tumor-immune cross-talk, and reveal novel image-based and genomic biomarkers that are predictive of clinical outcomes. He works closely with experimental collaborators and contributes in a collaborative team to understand mechanisms underlying tumor progression and therapy resistance. Recently, he is interested in developing methods in the area of spatial transcriptomics, and working on improving the integration of machine learning algorithms in histopathology imaging analyses. He is also interested in large-scale data visualization approaches and developing databases/portals to improve the access of genomics information for patients and clinicians.

Selected Publications

• Ruben Dries*, Qian Zhu*, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao, Rani E. George, Nico Pierson, Long Cai & Guo-Cheng Yuan "Giotto, a toolbox for integrative analysis and visualization of spatial expression data." Genome Biol.. 2021; Pubmed PMID: 33685491
• Qian Zhu, Nan Liu, Stuart H Orkin, Guo-Cheng Yuan "CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.." Genome Biol.. 2019; Pubmed PMID: 31500663
• Qian Zhu, Sheel Shah, Ruben Dries, Long Cai, Guo-Cheng Yuan "Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data." Nat Biotechnol.. 2018;36:1183-1190. Pubmed PMID: 30371680
• Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, Ran Zhang, David C Corney, Casey S Greene, Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, and Olga G. Troyanskaya "Targeted exploration and analysis of large cross-platform human transcriptomic compendia." Nat Methods. 2015;12(3):211-214. Pubmed PMID: 25581801

Memberships

Intelligent Systems for Molecular Biology Conference

American Association for Cancer Research

Funding

Recruitment of First-Time, Tenure-Track Faculty Members

CPRIT