Zheng Laboratory
Ye Zheng, Ph.D.
Principal Investigator
- Departments, Labs and Institutes
- Labs
- Zheng Laboratory
Areas of Research
- Bioinformatics
- Cancer Biology
- Chromatin
- Computational Biology
- Epigenetics
- Proteomics
- Single-Cell Genomics
- Transcriptional Regulation
The Zheng Laboratory is a dynamic hybrid research team combining computational and experimental approaches. Our computational dry lab specializes in addressing biologically and clinically significant challenges through innovative statistical models, traditional and modern computational methods and integrative multiomics data analysis. Our research spans diverse topics leveraging rich bulk, single-cell and spatial multimodal data, including epigenomics, 3D genomics, proteomics and their applications in cancer studies and other disease systems. The wet lab focuses on epigenomic profiling of formalin-fixed, paraffin-embedded (FFPE) samples, unraveling gene regulation mechanisms across human cancers.
Funding
Our research is supported by:
Pathway to Independence Award (K99/R00)
August 2023–August 2024, $237,438 (K99 Phase)
September 2024–August 2027, $747,000 (R00 Phase)
PI: Ye Zheng, Ph.D.
Title: Bridging the gap: joint modeling of single-cell 1D and 3D genomics
Sponsoring agency: NIH/NHGRI
New Faculty Award (P01)
January 2026–June 2026, $50,000
PI: Ye Zheng, Ph.D.
Sponsoring agency: NCI
UT System Rising STARs Award
September 2024–December 2025, $125,000
PI: Ye Zheng, Ph.D.
Sponsoring agency: The University of Texas
Recent Publications
Henikoff S*, Zheng Y*, Paranal R, Xu Y, Greene J, Henikoff J, Russell Z, Szulzewsky F, Thirimanne H, Kugel S, Holland E, Ahmad K. RNA polymerase II at histone genes predicts outcome in human cancer. Science. 2025 Jan 2;387(6735):737-743. doi: 10.1126/science.ads2169. Epub 2025 Feb 13. PMID: 39946483; PMCID: PMC12184985.
Zheng Y*, Caron D*, Kim J, Jun S, Tian Y, Florian M, Stuart K, Sims P, Gottardo R. ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets. Nat Commun. 2025 Jul 1;16(1):5852. doi: 10.1038/s41467-025-61023-6. PMID: 40595741; PMCID: PMC12218154.
Fiorenza S*, Zheng Y*, Purushe J, Bock T, Sarthy J, Janssens D, Sheih A, Kimble E, Kirchmeier D, Phi T, Gauthier J, Hirayama A, Riddell S, Wu Q, Gottardo R, Maloney D, Yang J, Henikoff S, Turtle C. Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nat Commun. 2024 Sep 27;15(1):8309. doi: 10.1038/s41467-024-52503-2. PMID: 39333103; PMCID: PMC11436946.
Zheng Y*, Shen S*, Keleş S. Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Genome Biol. 2022 Oct 17;23(1):222. doi: 10.1186/s13059-022-02774-z. PMID: 36253828; PMCID: PMC9575231.
Zheng Y, Keleş S. FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. Nat Methods. 2020 Jan;17(1):37-40. doi: 10.1038/s41592-019-0624-3. Epub 2019 Nov 11. PMID: 31712779; PMCID: PMC8136837.
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Research Areas
Find out about the four types of research taking place at UT MD Anderson.