Peng Yu

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors

The paper integrates RNA-Seq datasets to identify key splicing factors in diseases and biological processes using signature comparison analysis.

brt: An R package for integrating biological relevance with p value in omics data

The paper introduces a new statistical method, BRT, to assess biological relevance in omics data by incorporating effect size with p-values, and demonstrates its application on microarray data.

Single cell expression variability in highly homogeneous populations of human cells is widespread, is heritable, and implies cell function

The paper analyzes single-cell expression variability in homogeneous human cell populations, finding it widespread, heritable, and functionally relevant.

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line

The paper presents single-cell RNA sequencing data from two lymphoblastoid cell lines and their mixture, providing insights into population differentiation in gene expression and aiding normalization methods.

A data mining paradigm for identifying key factors in biological processes using gene expression data

This paper introduces a data mining paradigm to identify key factors in biological processes using gene expression data, demonstrating its effectiveness in epidermal development and cold-induced thermogenesis.

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

GEOMetaCuration: A web-based application for accurate manual curation of Gene Expression Omnibus metadata

GEOMetaCuration is a web-based tool for curating Gene Expression Omnibus metadata, streamlining the process and enabling collaborative curation efforts.

CITGeneDB: A comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice

CITGeneDB curates human and mouse genes that enhance or suppress cold-induced thermogenesis through perturbation experiments in mice, providing a searchable database for research on obesity and diabetes.

RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins

RBPMetaDB compiles and organizes 278 mouse RNA-Seq datasets perturbed by 163 RNA-binding proteins, revealing unexplored proteins and enriched DNA-binding activities.

l1kdeconv: an R package for peak calling analysis with LINCS L1000 data

The paper introduces an R package for deconvolution of LINCS L1000 data using outlier detection and aggregate Gaussian mixture modeling, showing improved stability and performance.

SFMetaDB: A Comprehensive Annotation of Mouse RNA Splicing Factor RNA-Seq Datasets

SFMetaDB curates RNA-Seq datasets for mouse splicing factors, revealing a gap in functional studies and highlighting understudied factors.