SpatialDWLS: accurate deconvolution of spatial transcriptomic data

by Rui Dong, Guo-Cheng Yuan
Published 2021-05-01

GiniClust3: a fast and memory-efficient tool for rare cell type identification

by Rui Dong, Guo-Cheng Yuan
Published 2020-04-01

Genomic sequence is highly predictive of local nucleosome depletion.

by Guo-Cheng Yuan, Jun S Liu
Published 2008-01-01

GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection

by Daphne Tsoucas, Guo-Cheng Yuan
Published 2018-05-01

Chromatin states accurately classify cell differentiation stages.

by Jessica L Larson, Guo-Cheng Yuan
Published 2012-01-01

RESCUE: imputing dropout events in single-cell RNA-sequencing data

by Sam Tracy, Guo-Cheng Yuan, Ruben Dries
Published 2019-07-01

Passing messages between biological networks to refine predicted interactions.

by Kimberly Glass, Curtis Huttenhower, John Quackenbush, Guo-Cheng Yuan
Published 2013-01-01

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

by Qian Zhu, Nan Liu, Stuart H. Orkin, Guo-Cheng Yuan
Published 2019-09-01

Modeling the dynamics of bivalent histone modifications.

by Wai Lim Ku, Michelle Girvan, Guo-Cheng Yuan, Francesco Sorrentino, Edward Ott
Published 2013-01-01

Accurate estimation of cell-type composition from gene expression data

by Daphne Tsoucas, Rui Dong, Haide Chen, Qian Zhu, Guoji Guo, Guo-Cheng Yuan
Published 2019-07-01

Estimating Sample-Specific Regulatory Networks

by Marieke Lydia Kuijjer, Matthew George Tung, GuoCheng Yuan, John Quackenbush, Kimberly Glass
Published 2019-04-01

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas

by Shengbao Suo, Qian Zhu, Assieh Saadatpour, Lijiang Fei, Guoji Guo, Guo-Cheng Yuan
Published 2018-11-01

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

by Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Published 2017-04-01

Chromatin signature of widespread monoallelic expression

by Anwesha Nag, Virginia Savova, Ho-Lim Fung, Alexander Miron, Guo-Cheng Yuan, Kun Zhang, Alexander A Gimelbrant
Published 2013-12-01

Dissecting super-enhancer hierarchy based on chromatin interactions

by Jialiang Huang, Kailong Li, Wenqing Cai, Xin Liu, Yuannyu Zhang, Stuart H. Orkin, Jian Xu, Guo-Cheng Yuan
Published 2018-03-01

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

by Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo-Cheng Yuan, Guoji Guo
Published 2018-04-01

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis

by Guoji Guo, Luca Pinello, Xiaoping Han, Shujing Lai, Li Shen, Ta-Wei Lin, Keyong Zou, Guo-Cheng Yuan, Stuart H. Orkin
Published 2016-02-01

Mapping the evolving landscape of super-enhancers during cell differentiation

by Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, Hye Ji Cha, Stuart H. Orkin, Wenqing Cai, Jialiang Huang, Guo-Cheng Yuan
Published 2021-09-01

Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5+ Intestinal Stem Cells

by Tae-Hee Kim, Assieh Saadatpour, Guoji Guo, Madhurima Saxena, Alessia Cavazza, Niyati Desai, Unmesh Jadhav, Lan Jiang, Miguel N. Rivera, Stuart H. Orkin, Guo-Cheng Yuan, Ramesh A. Shivdasani
Published 2016-08-01

Challenges and emerging directions in single-cell analysis

by Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani, Itay Tirosh
Published 2017-05-01