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Fiorenza S+, Zheng Y+, Sarthy J, Sheih AS, Wu Q, Hirayama AV, Kimble EL, Kirchmeier D, Gottardo R, Henikoff S, Turtle CJ (2022). High-throughput, high sensitivity mapping of human T cell and CAR-T cell epigenomic landscapes underscores the role of H3K27me3 in subset differences and therapeutic outcomes. Manuscript in preparation.

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Zheng Y, Seong-Hwan J, Conn D, Kim J, Tian Y, Florian M, Gottardo R (2022). Robust Normalization and Integration of Single-cell Protein Expression across CITE-seq Datasets. bioRxiv.

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Shen S, Zheng Y++, Keleş S++ (2022). scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinformatics.

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Zheng Y+, Shen S+, Keleş S (2022). Normalization and De-noising of Single-cell Hi-C Data with BandNorm and scVI-3D. Accepted by Genome Biology.

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Hirayama AV, Zheng Y, Dowling MR, Sheih A, Phi TD, Kirchmeier DR, Chucka AW, Gauthier J, Maloney DG, Gottardo R, Turtle CJ (2021). 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.

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Zheng Y++, Zhou P, Keleş S++ (2021). FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection. Methods.

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Liao R+, Zheng Y+, Liu X, Zhang Y, Seim G, Tanimura N, Wilson G, Hematti P, Coon J, Fan J, Xu J, Keleş S++, Bresnick E++ (2020). Discovering How Heme Controls Genome Function Through Heme-omics. Cell Reports. Cell Reports.

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Zheng Y, Keleş S (2019). FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. Nature Methods.

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Zheng Y, Ay F, Keleş S (2019). Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies. eLife.

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