Qian Zhu, Ph.D.
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Qian Zhu, Ph.D.
Assistant Professor
Positions
- Assistant Professor
-
Lester and Sue Smith Breast Center
Department of Molecular Genetics
Baylor College of Medicine
Houston, US
Addresses
- BCM Jewish Building (Office)
-
Room 644D
Houston, TX 77030
United States
qian.zhu@bcm.edu
Zhu Lab Webpage
Education
- BSc from University of Ottawa
- Ottawa, Ontario Canada
- PhD from Princeton University
- Princeton, New Jersey United States
- Postdoctoral Training at Dana-Farber Cancer Institute/Harvard Medical School
- Boston, Massachusetts United States
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.Websites
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
- Nan Liu*, Victoria V Hargreaves*, Qian Zhu*, Jesse V Kurland, Jiyoung Hong, Woojin Kim, Falak Sher, Claudio Macias-Trevino, Julia M Rogers, Ryo Kurita, Yukio Nakamura, Guo-Cheng Yuan, Daniel E Bauer, Jian Xu, Martha L Bulyk, Stuart H Orkin "Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch." Cell. 2018;173(2):430-442. Pubmed PMID: 29606353
- Qian Zhu, Xavier Tekpli, Olga G Troyanskaya, Vessela N Kristensen "Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations." Bioinformatics. 2019;36(4):994-999. Pubmed PMID: 31529022
Memberships
- Intelligent Systems for Molecular Biology Conference
- American Association for Cancer Research
Funding
- Recruitment of First-Time, Tenure-Track Faculty Members CPRIT
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