Publications

Zheng Y , Caron D, Kim J, Jun S, Tian Y, Florian M, Stuart K, Sims P, Gottardo R (2025). ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets. Nature Communications.

Code Project DOI Preprint

Zheng Y , Ahmad K, Henikoff S (2025). Total whole-arm chromosome losses predict malignancy in human cancer. PNAS.

DOI Paper

Henikoff S, Zheng Y , Paranal R, Xu Y, Greene J, Henikoff J, Russell Z, Szulzewsky F, Thirimanne H, Kugel S, Holland E, Ahmad K (2025). ⭐⭐⭐RNA Polymerase II at histone genes predicts outcome in human cancer⭐⭐⭐. Science.

PDF Project DOI Science

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 (2024). Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nature Communications.

Project DOI Paper

Fiorenza S, Zheng Y , Sarthy J, Sheih A, Kimble E, Kirchmeier D, Janssens D, Phi T, Gauthier J, Hirayama A, Wu Q, Gottardo R, Riddell S, Maloney D, Henikoff S, Turtle C (2023). 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.

Project DOI Paper

Savonen C, Zheng Y , Henikoff S, Ahmad K (2023). CUT&RUN and CUT&Tag. Choosing Genomics Tools.

Project Chapter Authors

Germanos AA, Arora S, Zheng Y , Goddard ET, Coleman IM, Ku AT, Wilkinson S, Amezquita RA, Zager M, Long A, Yang YC, Bielas J, Gottardo R, Ghajar C, Nelson P, Sowalsky A, Setty M, Hsieh A (2022). Defining cellular population dynamics at single cell resolution during prostate cancer progression. eLife.

Project DOI Paper

Chour T, Hirayama A, Zheng Y , Sheih A, Zhuang S, Wilson A, Wu V, Gottardo R, Turtle C, Gardner R, Newell E (2022). Cellular profiling of leukapheresis and infusion products of patients enrolled in CD19 CAR T cell therapy identifies biomarkers associated with clinical outcomes. Cancer Research.

Project Paper

Cheng J, Clayton J, Acemel R, Zheng Y , Taylor R, Keles S, Harley J, Quail E, Gómez-Skarmeta J, Ulgiati D (2022). Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells. Frontiers in Immunology.

Project DOI Paper

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

Project DOI Paper

Zheng Y , Shen S, Keles S (2022). Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Genome Biology.

Project DOI Paper

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.

Project DOI

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

Project DOI Paper

Wu S, Furlan S, Mihalas A, Kaya-Okur H, Feroze H, Emerson S, Zheng Y , Carson K, Cimino P, Keene C, Holland E, Sarthy J, Gottardo R, Ahmad K, Henikoff S, Patel A (2021). Single-cell CUTTag analysis of chromatin modifications in differentiation and tumor progression. Nature Biotechnology.

Project DOI Paper

Huang K, Wu Y, Shin J, Zheng Y , Siahpirani A, Lin Y, Ni Z, Chen J, You J, Keleş S, Wang D, Roy S, Lu Q (2021). Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLOS Genetics.

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Vitanza N, Biery M, Myers C, Ferguson E, Zheng Y , Girard E, Przystal J, Park G, Noll A, Pakiam F, Winter C, Morris S, Sarthy J, Cole B, Leary S, Crane C, Lieberman N, Mueller S, Nazarian J, Gottardo R, Brusniak M, Mhyre A, Olson J (2021). Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models. Neuro-Oncology.

Project DOI

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.

Project DOI Paper

The ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ (2020). Perspectives on ENCODE. Nature.

Project DOI Paper

The ENCODE Project Consortium, Admin (2020). Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. Nature.

Project DOI Paper ENCODE Portal

Zheng Y , Keleş S (2020). FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. Nature Methods.

Code Project DOI Paper

Zheng Y , Ahmad K, Henikoff K (2020). CUTTag Data Processing and Analysis Tutorial. Protocols.io.

Project DOI Protocol

Soukup AA, Zheng Y , Mehta C, Liu P, Hofmann I, Zhou Y, Zhang J, Choi K, Johnson KD, Keles S, Bresnick EH (2019). Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer. Journal of Clinical Investigation.

Project DOI Paper

Zheng Y , Ay F, Keleş S (2019). Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. eLife.

Code Project DOI Paper

Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y , Keleş S, Xu J, Coon J, Bresnick E (2018). GATA/Heme Multi-omics Reveals a Trace Metal-dependent Cellular Differentiation Mechanism. Developmental Cell.

Project DOI Paper

Zeng X, Li B, Welch R, Rojo C, Zheng Y , Dewey CN, Keleş S (2015). Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-enhanced Read Mapping. PLOS Computational Biology.

Code Project DOI Paper