Ye Zheng, PHD

Peer-Reviewed Articles

1. Lubna Rehman, Wenting Song, Abdur Rehman, Kamini Singh, Shiv Govind Rawat, Faezeh Darbaniyan, Cao Cuong Le, Federico Mario Aletti, Jinsheng Weng, Jingwei Liu, Xiayoun Cheng, Yongfu Tang, Sridevi Patchva,, Matthew D. Richard,, Fuliang Chu, Jingjing Cao, Christopher R. Flowers, Elizabeth J. Shpall, Mark R. Tanner, Johannes Fahrmann, Eran Elinav,, Christoph K. Stein-Thoeringer, Michael D. Jain, Robert R. Jenq, Abhinav Jain,, Sattva S. Neelapu, Ye Zheng, Neeraj Y Saini. Microbial valerate is associated with CAR T dysbiosis and its supplementation enhances CAR T function in B-cell lymphoma. e-Pub 2026.
2. Ni X, Han W, Kunta N, Goswami M, Burks J, Zheng Y, Kim Y, Duvic M. Dissecting Immune Determinants in Lesional Skin of Cutaneous T-Cell Lymphoma During Mogamulizumab Therapy. Cancers, 2026. e-Pub 2026.
3. Liu Z, Niu Y, Le T, Chen D, Su Y, Zheng Y. Single-cell Tree-based Model for Genomic-Disease Association. bioRxiv, 2026. e-Pub 2026.
4. Zheng, Y, Caron, DP, Kim, JY, Jun, SH, Tian, Y, Mair, F, Stuart, KD, Sims, PA, Gottardo, R. ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets. Nature communications 16(1), 2025. e-Pub 2025. PMID: 40595741.
5. Zheng Y, Ahmad K, Henikoff S. Total whole-arm chromosome losses predict malignancy in human cancer. PNAS, 2025. e-Pub 2025. PMID: 40314975.
6. Henikoff S, Zheng Y, Paranal RM, Xu Y, Greene JE, Henikoff JG, Russell ZR, Szulzewsky F, Thirimanne N, Kugel S, Holland EC, Ahmad K. RNA polymerase II at histone genes predicts outcome in human cancer. Science 387(6735):737 - 743, 2025. e-Pub 2025. PMID: 39946483.
7. 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 AC. Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nature Communications, 2024. e-Pub 2024. PMID: 39333103.
8. Zheng Y, Shen S, Keleş S. Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Genome Biology 23(1), 2022. e-Pub 2022. PMID: 36253828.
9. Shen S, Zheng Y, Keleş S. scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinformatics 38(14):3642-3644, 2022. e-Pub 2022. PMID: 35652733.
10. Cheng J, Clayton JS, Acemel RD, Zheng Y, Taylor RL, Keleş S, Franke M, Boackle SA, Harley JB, Quail E, Gomez-Skarmeta JL, Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Frontiers in Immunology 13, 2022. e-Pub 2022. PMID: 35769482.
11. Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur H, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene C, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nature Biotechnology, 2021. e-Pub 2021. PMID: 33846646.
12. Zheng Y, Zhou P, Keleş S. FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection. Methods, 2021. e-Pub 2021. PMID: 32663510.
13. Vitanza N, Biery MC, Myers C, Ferguson E, Zheng Y, Girard EJ, Przystal JM, Park G, Noll A, Pakiam F, Winter CA, Morris SM, Sarthy J, Cole BL, S Leary SE, Crane C, P Lieberman NA, Mueller S, Nazarian J, Gottardo R, Brusniak M, Mhyre AJ, Olson JM. Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models. NEURO-ONCOLOGY, 2021. e-Pub 2021. PMID: 33130903.
14. Huang K, Wu Y, Shin J, Zheng Y, Siahpirani AF, Lin Y, Ni Z, Chen J, You J, Keles S, Wang D, Roy S, Lu Q. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLoS Genetics, 2021. e-Pub 2021. PMID: 33539344.
15. Consortium EP, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang X, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry J, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 2020. e-Pub 2020. PMID: 32728249.
16. Consortium EP, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry J, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Perspectives on ENCODE. Nature, 2020. e-Pub 2020. PMID: 32728248.
17. Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Report, 2020. e-Pub 2020. PMID: 32610133.
18. Germanos AA, Arora S, Zheng Y, Goddard ET, Coleman IM, Ku AT, Wilkinson S, Song H, Brady NJ, Amezquita RA, Zager M, Long A, Yang YC, Bielas JH, Gottardo R, Rickman DS, Huang FW, Ghajar CM, Nelson PS, Sowalsky AG, Setty M, Hsieh AC. Defining cellular population dynamics at single-cell resolution during prostate cancer progression. eLife 11, 2019. e-Pub 2019. PMID: 36511483.
19. Zheng Y, Keles S. FreeHi-C simulates high fidelity Hi-C data for benchmarking and data augmentation. Nature Methods, 2019. e-Pub 2019. PMID: 31712779.
20. Zheng Y, Ay F, Keles S. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. eLife, 2019. e-Pub 2019. PMID: 30702424.
21. Soukup AA, Zheng Y, Mehta C, Wu J, Liu P, Cao M, Hofmann I, Zhou Y, Zhang J, Johnson KD, Choi K, Keles S, Bresnick EH. Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer. Journal of clinical investigation, 2019. e-Pub 2019. PMID: 30620726.
22. Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keles S, Xu J, Coon JJ, Bresnick EH. GATA/heme multi-omics reveals a trace metal-dependent cellular differentiation mechanism. Developmental cell, 2018. e-Pub 2018. PMID: 30122630.
23. Zheng Y, Aris-Brosou S. Approximate Bayesian Computation Algorithms for Estimating Network Model Parameters. BioRxiv. e-Pub 2017.
24. Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Perm-seq: mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping. PLOS Computational Biology, 2015. e-Pub 2015. PMID: 26484757.

Review Articles

1. Ahmad K, Brahma S, Janssens D, Kind J, Khyzha N, Meers M, Ramachandran S, Zheng Y, Henikoff S. Enzyme tethering for in situ epigenomics. Nat Rev Methods Primers, 2026. e-Pub 2026.

Abstracts

1. Fiorenza S, Zheng Y, Sarthy J, Sheih A, Kimble EL, Kirchmeier D, Janssens D, Phi T, Gauthier J, Hirayama AV, Wu Q, Gottardo R, Riddell SR, Maloney DG, Henikoff S, Turtle CJ. Histone Methylation Mark Analyses Distinguish Carts Manufactured from Distinct Sources and Uncover Novel Transcription Factors Associated with In Vivo Function of Carts after Infusion into DLBCL Patients That Are Not Identified By RNA-Seq. Blood, 2023. e-Pub 2023.
2. Chour T, Hirayama A, Zheng Y, Sheih A, Zhuang S, Wilson A, Wu V, Gottardo R, Turtle C, Gardner R, Newell E. Cellular profiling of leukapheresis and infusion products of patients enrolled in CD19 CAR T cell therapy identifies biomarkers associated with clinical outcomes. Cancer Research, 2022. e-Pub 2022.
3. Hirayama AV, Zheng Y, Dowling MR, Sheih A, Phi T, Kirchmeier DR, Chucka AW, Gauthier J, Maloney DG, Gottardo R, Turtle CJ. Long-term follow-up and single-cell multiomics characteristics of infusion products in patients with chronic lymphocytic leukemia treated with CD19 CAR-T cells. Blood, 2021. e-Pub 2021.

Book Chapters

1. https://hutchdatascienceorg/Choosing_Genomics_Tools/about-the-authorshtml. Choosing Genomics Tools. https://hutchdatascience.org/Choosing_Genomics_Tools/index.html, 2024.

Web Publications

1. Zheng Y, Ahmad K, Henikoff S. CUT&Tag Data Processing and Analysis Tutorial.