| Expanded encyclopaedias of DNA elements in the human and mouse genomes JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ... Nature 583 (7818), 699-710, 2020 | 1159 | 2020 |
| Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression SJ Wu, SN Furlan, AB Mihalas, H Kaya-Okur, AH Feroze, SN Emerson, ... Nature Biotechnology https://doi.org/10.1038/s41587-021-00865, 2021 | 134 | 2021 |
| Perspectives on ENCODE MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, ... Nature 583 (7818), 693-698, 2020 | 92 | 2020 |
| Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer AA Soukup, Y Zheng, C Mehta, J Wu, P Liu, M Cao, I Hofmann, Y Zhou, ... The Journal of clinical investigation 129 (3), 1180-1192, 2019 | 53 | 2019 |
| Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models NA Vitanza, MC Biery, C Myers, E Ferguson, Y Zheng, EJ Girard, ... Neuro-oncology 23 (3), 376-386, 2021 | 52 | 2021 |
| GATA/heme multi-omics reveals a trace metal-dependent cellular differentiation mechanism N Tanimura, R Liao, GM Wilson, MR Dent, M Cao, JN Burstyn, P Hematti, ... Developmental cell 46 (5), 581-594. e4, 2018 | 36 | 2018 |
| Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies Y Zheng, F Ay, S Keles Elife 8, e38070, 2019 | 28 | 2019 |
| FreeHi-C simulates high fidelity Hi-C data for benchmarking and data augmentation Y Zheng, S Keles Nature Methods doi:10.1038/s41592-019-0624-3, 2019 | 26 | 2019 |
| Discovering how heme controls genome function through heme-omics R Liao, Y Zheng, X Liu, Y Zhang, G Seim, N Tanimura, GM Wilson, ... Cell reports 31 (13), 2020 | 25 | 2020 |
| Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D Y Zheng, S Shen, S Keleş Genome Biology, 2022 | 22* | 2022 |
| Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder K Huang, Y Wu, J Shin, Y Zheng, AF Siahpirani, Y Lin, Z Ni, J Chen, J You, ... PLoS genetics 17 (2), e1009309, 2021 | 15 | 2021 |
| Perm-seq: mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping X Zeng, B Li, R Welch, C Rojo, Y Zheng, CN Dewey, S Keleş PLOS Computational Biology 11 (10), e1004491, 2015 | 15 | 2015 |
| Defining cellular population dynamics at single-cell resolution during prostate cancer progression AA Germanos, S Arora, Y Zheng, ET Goddard, IM Coleman, AT Ku, ... Elife 11, e79076, 2022 | 10 | 2022 |
| CUT&Tag Data Processing and Analysis Tutorial. Y Zheng, K Ahmad, S Henikoff Protocols.io. dx.doi.org/10.17504/protocols.io.bjk2kkye, 2020 | 7 | 2020 |
| Robust normalization and integration of single-cell protein expression across CITE-seq datasets Y Zheng, SH Jun, Y Tian, M Florian, R Gottardo bioRxiv, 2022.04. 29.489989, 2022 | 5 | 2022 |
| Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary, CTCF-mediated chromatin looping and a long-range intergenic enhancer J Cheng, JS Clayton, RD Acemel, Y Zheng, RL Taylor, S Keleş, M Franke, ... Frontiers in Immunology, 2675, 2022 | 5 | 2022 |
| Approximate Bayesian Computation Algorithms for Estimating Network Model Parameters Y Zheng, S Aris-Brosou bioRxiv, 2017 | 3 | 2017 |
| scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data S Shen, Y Zheng, S Keleş Bioinformatics 38 (14), 3642-3644, 2022 | 2 | 2022 |
| FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection Y Zheng, P Zhou, S Keleş Methods 189, 3-11, 2021 | 2 | 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 AV Hirayama, Y Zheng, MR Dowling, A Sheih, TD Phi, DR Kirchmeier, ... Blood 138, 1749, 2021 | 1 | 2021 |
Sunduz KelesProfessor of Statistics and Biostatistics, University of WisconsinVerified email at stat.wisc.edu
