Publication_olds

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
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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 …
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
Project
TreeHiC: Hierarchical Testing for Differential Chromatin Interactions.
Hi-C sequencing technology provides key insights into the 3D structures of the human genome. Although peak detection from Hi-C …
Duy Nguyen, Ye Zheng(co-first author), Sündüz Keleş
Sep 2, 2018
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TreeHiC: Hierarchical Testing for Differential Chromatin Interactions.
Perm-seq: mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping.
Segmental duplications and other highly repetitive regions of genomes contribute significantly to cells’ regulatory programs. …
Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keleş
Oct 20, 2015
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Perm-seq: mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping.
Approximate Bayesian Computation algorithms for estimating network model parameters.
Studies on Approximate Bayesian Computation (ABC) replacing the intractable likelihood function in evaluation of the posterior …
Ye Zheng, Stephane Aris-Brosou
Sep 12, 2013
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Approximate Bayesian Computation algorithms for estimating network model parameters.
An example conference paper
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Ye Zheng, Ph.D., Robert Ford
Jul 1, 2013
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An example conference paper