Pengyi Yang

This study benchmarks 12 scRNA-seq simulation methods using 35 experimental datasets, identifying performance differences and limitations in capturing biological signals and heterogeneity.

The paper introduces hRUV, a hierarchical method to remove unwanted variation in large-scale metabolomics data, showing improved preservation of biological signals.

This paper describes a protocol to generate cortical brain organoids and optic nerve-like structures from retinal confluent cultures of pluripotent stem cells, showing transcriptional similarity to fetal cortex and functional network activity.

The paper analyzes clonal evolution in liver cancer at single-cell and single-variant resolution, revealing genetic and phenotypic heterogeneity and their evolutionary relationships.

The paper shows LSD1 associates with RNA polymerase II pausing at gene promoters in mouse ESCs and influences gene expression patterns.

The paper introduces a method to infer temporal ordering of omics events from time series data with higher resolution than the experiment, using event maps and sparklines for visualization.

scClassify improves cell type classification in scRNA-seq data by using ensemble learning, achieving more accurate and fine-grained results than original publications.

CiteFuse is a tool for analyzing CITE-seq data, integrating RNA and protein data, and offering clustering, differential expression, and visualization features.

PhosR provides tools for processing and analyzing phosphoproteomic data, enabling data imputation, normalization, and functional analysis of kinase activity and signaling pathways.

The paper introduces an autoencoder-based cluster ensemble framework for scRNA-seq data to improve cell type-specific clustering.

This study evaluates stably expressed genes (SEGs) in single cells using a computational framework and finds they are more stable than traditional housekeeping genes across species.

This study shows NF-Y maintains nucleosome-depleted regions at promoters to ensure accurate transcription initiation, preventing aberrant gene expression.

The paper maps multi-omic changes during mouse pluripotency transition, showing phosphoproteome dynamics precede epigenome and transcriptome changes.

scMerge integrates multiple scRNA-Seq datasets by removing unwanted variation through stably expressed genes and pseudo-replicates, enhancing biological discovery.