eLife

Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos

This important study reports the transcriptomic and proteomic landscapes of the oviducts at four different preimplantation stages during natural fertilization, pseudopregnancy, and superovulation. The ...
Frontiers

Heterogeneity in polyamine metabolism dictates prognosis and immune checkpoint blockade response in hepatocellular carcinoma

Immune checkpoint blockade holds promise in hepatocellular carcinoma (HCC) treatment, but its efficacy remains limited. Dysregulated polyamine metabolism and its interaction with oncogenic pathways ...
GitHub

BingleSeq - A user-friendly R package for Bulk and Single-cell RNA-Seq data analyses.

Manuscript available as a PeerJ publication. A metadata table is also required and its appropriate formating is key for the acquisition of correct results using the Bulk RNA-Seq part of the ...
GitHub

About CellChat and CellChatDB

CellChat is an R package designed for inference, analysis, and visualization of cell-cell communication from single-cell data. CellChat aims to enable users to identify and interpret cell-cell ...
Frontiers

Transcriptome analysis of the adenoma–carcinoma sequences identifies novel biomarkers associated with development of canine colorectal cancer

The concept of adenoma-to-cancer transformation in human colorectal cancer (CRC) is widely accepted. However, the relationship between transcriptome features and adenoma to carcinoma transformation in ...
The Lancet

Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis

gDepartment of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan hDepartment of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan iDepartment of Pathology, Oita Oka ...
eLife

Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development

This fundamental study has successfully identified four key transcription factors (MECOM, PAX8, SOX17, and WT1) that exhibit synergistic effects and are potentially responsible for the transformation ...
C&EN

Identification of Breast Cancer Subtypes by Integrating Genomic Analysis with the Immune Microenvironment

School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei 230012, China Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical ...
The Lancet

Sex and cell-specific gene expression in corticolimbic brain regions associated with psychiatric disorders revealed by bulk and single-nuclei RNA sequencing

aDouglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, H4H 1R3, Canada bLudmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, ...
C&EN

Key Genes Identified in Nonsyndromic Microtia by the Analysis of Transcriptomics and Proteomics

Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China ...