The paper introduces a region-based causal mediation analysis method for DNA methylation data, showing improved power for detecting mediated effects compared to single CpG site analysis.

Epigenetics · Mar 23, 2021Peer-reviewedGenomics

Sample demultiplexing, multiplet detection, experiment planning and novel cell type verification in single cell sequencing

Hongyi Xin, Qiuyu Lian, Yale Jiang, Jiadi Luo, Xinjun Wang, Carla Erb, Zhongli Xu, Xiaoyi Zhang, Elisa Heidrich-O’Hare, Qi Yan, Richard H. Duerr, Kong Chen, Wei Chen

This paper introduces GMM-Demux, a method to identify and remove multiplets in scRNA-seq data, showing improved accuracy and error reduction.

Genome biology · Jul 30, 2020Peer-reviewedBioinformatics

Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma

Soyeon Kim, Erick Forno, Rong Zhang, Hyun Jung Park, Zhongli Xu, Qi Yan, Nadia Boutaoui, Edna Acosta‐Pérez, GLORISA J. CANINO, Wei Chen, Juan Carlos Celedon

The paper identifies methylation-gene expression associations in nasal epithelium from Puerto Rican children with and without asthma, revealing epigenetic regulation of gene expression in atopic asthma.

CHEST Journal · Jun 20, 2020Peer-reviewedGenomics