Guoliang Li

cfMethDB compiles 4828 cfDNA methylation datasets, identifies 1,048,770 DMCs as potential cancer biomarkers, and provides tools for biomarker discovery and analysis.

The paper introduces a new DNA methylation data format and associated tools to reduce storage and improve analysis efficiency.

AraENCODE provides a comprehensive epigenomic database for Arabidopsis thaliana with 4,511 datasets and integrated resources for studying epigenetic regulation.

MCIBox is a toolkit for analyzing single-molecule chromatin interactions and identifying micro-domains through visualization and clustering algorithms.

The paper maps chromatin interactions in lung cancer to identify regulatory networks and dysregulation of cancer-related genes using ChIA-PET data.

CoolBox is a flexible open-source toolkit for visualizing genomics data, compatible with Python, offering customization and integration with Jupyter and web browsers.

RiceLncPedia compiles and characterizes 6978 rice lncRNAs using 2313 RNA-seq libraries and multi-omics data, providing features like expression profiles, genome browser, SNPs, and miRNA interactions.

The paper shows that stimulation rate, along with concentration, determines MAPK signaling and cell survival in budding yeast through a rate threshold mechanism.

The paper uses live single-cell imaging and computational modeling to show that diverse kinetic stimulations improve prediction of signaling dynamics by better constraining model parameters.

This study identifies copper-induced myelin defects in zebrafish via disruption of Wnt/Notch-hoxb5b signaling and DNA methylation of fam168b/pou3f1 genes.

The paper introduces DLO Hi-C Tool for analyzing DLO Hi-C data, providing a pipeline from raw reads to contact maps with quality controls and efficient processing.

The paper shows that KDM7A and UTX demethylate repressive histone marks to enable NF-κB-dependent inflammatory gene activation in endothelial cells.

The paper updates the ChIA-PET Tool (V3) for analyzing ChIA-PET data, showing improved performance in detecting chromatin interactions compared to existing tools.

The paper introduces CellDissect, a method for automated cell and nuclear segmentation in suspension cells using widefield images, and evaluates its accuracy against manual segmentation.

The paper develops experimental methodologies to control temporal changes in extracellular stimuli for studying dynamic cellular processes in single cells.

The paper describes a smFISH protocol to quantify mRNA levels and localization in single yeast cells under osmotic stress and provides raw data and processed counts for further analysis.

CoolBox provides an interactive genomic data exploration tool for Jupyter Notebook with a ggplot2-like API and GUI support for multi-omics data.

The paper develops a computational approach to model gene regulation by addressing distributional challenges in single-cell mRNA data, leading to predictive insights into transcription mechanisms.