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scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data
Quantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) …
Shen S, Zheng Y++, Keleş S++
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scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data
Long-Term Follow-up and Single-Cell Multiomics Characteristics of Infusion Products in Patients with Chronic Lymphocytic Leukemia Treated with CD19 CAR-T Cells
Lymphodepletion chemotherapy followed by infusion of autologous T cells engineered to express a CD19-targeted chimeric antigen receptor …
Hirayama AV, Zheng Y, Dowling MR, Sheih A, Phi TD, Kirchmeier DR, Chucka AW, Gauthier J, Maloney DG, Gottardo R, Turtle CJ
PDF DOI
Long-Term Follow-up and Single-Cell Multiomics Characteristics of Infusion Products in Patients with Chronic Lymphocytic Leukemia Treated with CD19 CAR-T Cells
FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection
High-throughput genome-wide chromatin conformation capture assay (Hi-C) is routinely used to profile long-range genomic interactions …
Zheng Y++, Zhou P, Keleş S++
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FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection
Discovering How Heme Controls Genome Function Through Heme-omics. Cell Reports
Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A …
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++
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Discovering How Heme Controls Genome Function Through Heme-omics. Cell Reports
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation
The ability to simulate high-throughput chromatin conformation (Hi-C) data is foundational for benchmarking Hi-C data analysis methods. …
Zheng Y, Keleş S
PDF Code DOI
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation
The ability to simulate high-throughput chromatin conformation (Hi-C) data is foundational for benchmarking Hi-C data analysis methods. …
Ye Zheng, Sündüz Keleş
Nov 11, 2019
PDF Code DOI
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation
Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies
Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological …
Zheng Y, Ay F, Keleş S
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Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies
Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies.
Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological …
Ye Zheng, Ferhat Ay, Sündüz Keleş
Jan 31, 2019
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Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies.
GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism.
By functioning as an enzyme cofactor, hemoglobin component, and gene regulator, heme is vital for life. One mode of heme-regulated …
Nobuyuki Tanimura, Ruiqi Liao, Gary M. Wilson, Matthew R. Dent, Miao Cao, Judith N. Burstyn, Peiman Hematti, Xin Liu, Yuannyu Zhang, Ye Zheng, Sündüz Keleş, Jian Xu, Joshua J. Coon, Emery H. Bresnick
Sep 10, 2018
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GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism.
Single-Nucleotide Human Disease Mutation Inactivates a Blood-Regenerative Enhancer.
Soukup AA, Zheng Y, Mehta C, Liu P, Hofmann I, Zhou Y, Zhang J, Choi K, Johnson KD, Keleş S, Bresnick EH
Sep 10, 2018
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