Yuchen Yang

发表

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

Yin Shen, Yun Li, Yuchao Jiang, 2019, Nucleic acids research.

Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data

Y. Duan, Di Wu, Yuchen Yang, 2021, bioRxiv.

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Yun Li, A. Sancar, Yuchen Yang, 2020, The Journal of Biological Chemistry.

FIREcaller: Detecting frequently interacting regions from Hi-C data

B. Ren, Yun Li, Ming Hu, 2020, Computational and structural biotechnology journal.

HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets

Yin Shen, Yun Li, Ming Hu, 2020, bioRxiv.

Schizophrenia and a high-resolution map of the three-dimensional chromatin interactome of adult and fetal cortex

Yun Li, Yan Li, Danielle Posthuma, 2018, bioRxiv.

Section SAFE-clustering : Single-cell Aggregated ( From Ensemble ) Clustering for Single-cell RNA-seq Data

Houston W. Culpepper, Yun Li, Ruth Huh, 2018 .

Common variants contribute to intrinsic human brain functional networks

Weili Lin, Hongtu Zhu, Yun Li, 2020, bioRxiv.

Nucleotide excision repair hotspots and coldspots of UV-induced DNA damage in the human genome

Yun Li, Yuchao Jiang, A. Sancar, 2020, bioRxiv.

Coal elemental (compositional) data analysis with hierarchical clustering algorithms

M. Engle, R. Finkelman, Yuchen Yang, 2021, International Journal of Coal Geology.

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data

Taylor M. Lagler, B. Ren, Yun Li, 2021, Nature Methods.

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

Yuan Lin, Michael I. Love, Yun Li, 2017, bioRxiv.

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Bing Ren, Miao Yu, Yuchen Yang, 2018, bioRxiv.

Direct cell reprogramming: approaches, mechanisms and progress

Yuchen Yang, L. Qian, Jiandong Liu, 2021, Nature Reviews Molecular Cell Biology.

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

Gang Li, Li Qian, Yuchen Yang, 2020, bioRxiv.

Dropout imputation and batch effect correction for single-cell RNA sequencing data

Yun Li, Yuchen Yang, Gang Li, 2019, Journal of Bio-X Research.

SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection

Yuchen Yang, Yin Shen, Gang Li, 2019, bioRxiv.

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

Yin Shen, Yuchen Yang, Ruth Huh, 2019, bioRxiv.

Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types

Taylor M. Lagler, A. Reiner, Yun Li, 2021, bioRxiv.

eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data

A. Reiner, Yun Li, J. Broome, 2020, bioRxiv.

Development of next-generation tumor-homing induced neural stem cells to enhance treatment of metastatic cancers

C. Anders, Wulin Jiang, Yuchen Yang, 2021, Science Advances.

Common variants contribute to intrinsic human brain functional networks

Weili Lin, Yun Li, J. Stein, 2022, Nature Genetics.

A comprehensive comparison on cell type composition inference for spatial transcriptomics data

Yun Li, G. Gupta, Jia Wen, 2022, bioRxiv.

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

Yuan Lin, Yuchen Yang, Michael I. Love, 2017, bioRxiv.

ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells

Yun Li, Robert Zelt, Yuchen Yang, 2021, International journal of molecular sciences.

Mucosal-associated invariant T cell responses differ by sex in COVID-19

C. Woods, E. Tsalik, T. Burke, 2021, Med.

Functional coordination of non‐myocytes plays a key role in adult zebrafish heart regeneration

Joshua D. Welch, Yun Li, Yuchen Yang, 2021, EMBO reports.

FIREcaller: Detecting frequently interacting regions from Hi-C data

Di Wu, Yuchen Yang, Yun Li, 2019, bioRxiv.

MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples

Yun Li, Ming Hu, Yuchen Yang, 2021, HGG advances.

MUNIn—multiple-sample-unifying long-range chromatin Interaction detector: a statistical framework for identifying long-range chromatin interactions from multiple samples

Yun Li, Ming Hu, Yuchen Yang, 2021 .

MUNIn (Multiple cell-type UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple cell types

Yuchen Yang, Armen Abnousi, Ming Hu, 2020, bioRxiv.

D. Kiel, J. Murabito, A. Baccarelli, 2019, Epigenetics.

Unravelling the molecular mechanisms of abscisic acid-mediated drought-stress alleviation in pomegranate (Punica granatum L.).

Yan Yan, Yuchen Yang, Qian Zhou, 2020, Plant physiology and biochemistry : PPB.

HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test

Taylor M. Lagler, Yuchen Yang, Armen Abnousi, 2020, bioRxiv.

Down-regulation of Beclin1 promotes direct cardiac reprogramming

C. Yin, Yuchen Yang, L. Qian, 2020, Science Translational Medicine.

Delineating chromatin accessibility re-patterning at single cell level during early stage of direct cardiac reprogramming.

Yuchen Yang, L. Qian, Jiandong Liu, 2021, Journal of molecular and cellular cardiology.

Single cell dual-omics reveals the transcriptomic and epigenomic diversity of cardiac non-myocytes.

Yun Li, Yuchen Yang, L. Qian, 2021, Cardiovascular research.

Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome

Yun Li, Yuchao Jiang, A. Sancar, 2021, The Journal of biological chemistry.

Molecular dissection of cadmium-responsive transcriptome profile in a low-cadmium-accumulating cultivar of Brassica parachinensis.

Yuchen Yang, Zhongyi Yang, Qian Zhou, 2019, Ecotoxicology and environmental safety.

A SNP panel and online tool for checking genotype concordance through comparing QR codes

Eric Yi Liu, John McGee, Matthias Geihs, 2017, PloS one.

MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples

Yun Li, Ming Hu, Yuchen Yang, 2021, HGG advances.