Full publication list (+: co-first authors, ++: co-corresponding authors)

Epigenomics and FFPE

  1. 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. Under review of Science. (2024) https://www.biorxiv.org/content/10.1101/2024.02.28.582647v3.

  2. Henikoff S, Zheng Y, Ahmad K. Mitotic errors do not explain aneuploidy in cancer. Under review of Trends in Genetics. (2024)

  3. [Book] Savonen et al. Choosing Genomics Tools. (2023) Chapter 19 CUT&RUN and CUT&Tag. Full author list: https://hutchdatascience.org/Choosing_Genomics_Tools/about-the-authors.html. Online book chapter: https://hutchdatascience.org/Choosing_Genomics_Tools/index.html.

  4. 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. [Single-cell CUTTag analysis of chromatin modifications in differentiation and tumor progression](https://doi. org/10.1038/s41587-021-00865-z). Nature Biotechnology. 2021.

  5. Zheng Y, Ahmad K, Henikoff K. CUTTag Data Processing and Analysis Tutorial. Protocols.io. (2020) dx.doi.org/10.17504/protocols.io.bjk2kkye. (17,459 views, 4,355 exports, and 239 questions)

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

  7. 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.

Three-dimensional chromatin interaction and long-range gene regulation

  1. Zheng Y+, Shen S+, Keleş S. Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Accepted by Genome Biology. 2022. (*: co-first authors)

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

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

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

  5. 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. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLOS Genetics. 2021.

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

  7. The ENCODE Project Consortium, et al. Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. Nature. 2020 .

  8. The ENCODE Project Consortium, Snyder, M.P., Gingeras, T.R., Moore, J.E., Weng, Z., Gerstein, M.B., Ren, B., Hardison, R.C., Stamatoyannopoulos, J.A., Graveley, B.R., Feingold, E.A. and Pazin, M.J. Perspectives on ENCODE. Nature. 2020.

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

Single-cell Proteomics

  1. 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. BioRxiv. Under review of Nature Communications. (2024) https://www.biorxiv.org/content/10.1101/2022.04.29.489989v2.

Statistical Modeling and Computational Analysis of Immunological and Immunotherapeutic Studies

  1. 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. Conditional accepted at Nature Communications. (2024)

  2. 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. Defining cellular population dynamics at single cell resolution during prostate cancer progression. eLife. 2022.

  3. Hirayama AV, Zheng Y, Dowling MR, Sheih A, Phi TD, 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.

  4. 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, Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models. Neuro-Oncology. 2021.

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

  6. 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. GATA/Heme Multi-omics Reveals a Trace Metal-dependent Cellular Differentiation Mechanism. Developmental Cell. 2018.