Full publication list

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. 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.

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

  4. 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.

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

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

  7. 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.

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

Integrative Modeling of Single-cell and Bulk-cell Transcriptomics, Epigenomics, Proteomics, and 3D genomics

  1. Zheng Y, Seong-Hwan J, Tian Y, Florian M, Gottardo R. Robust Normalization and Integration of Single-cell Protein Expression across CITE-seq Datasets. BioRxiv. 2022.

  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. 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.

  4. Zheng Y, Ahmad K, Henikoff K. CUTTag Data Processing and Analysis Tutorial. Protocols.io. 2020. (15,266 views, 4,355 exports, and 194 questions)

  5. 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.

Statistical Modeling and Computational Analysis of Immunological and Immunotherapeutic Studies

  1. Fiorenza S+, Zheng Y+, Sarthy J, Sheih AS, Wu Q, Hirayama AV, Kimble EL, Kirchmeier D, Gottardo R, Henikoff S, Turtle CJ. 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. (+ Co-first author)

  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. BioRxiv. 2022. Under review for eLife.

  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. 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. (+co-first authors, ++co-corresponding authors)

  6. 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.

  7. 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.