Xaralabos Varelas

Age-based shifts in multicellular community organization and abundance in HPV-Negative Head and Neck Cancer

This study identifies age-related changes in cellular composition and organization in HPV-negative head and neck cancer using single-cell data, highlighting MDK as a key factor in stromal remodeling and immunosuppression.

ACKR1-expressing venous endothelial cells establish a pro-fibrotic niche in pulmonary fibrosis

The paper identifies ACKR1-expressing venous endothelial cells as key drivers of fibrosis in IPF and shows ACKR1 inhibition reduces fibrosis in vivo.

A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer

The paper integrates six single-cell datasets to create a high-resolution atlas of HPV-negative HNSCC, revealing new cell populations and associations between transcriptional signatures and clinical outcomes.

Dietary Serine Restriction Impacts H3K27 and H3K4 Methyl Epigenomes to Impede Head and Neck Cancer Cell Plasticity and Tumor Growth

This study shows that dietary serine restriction alters H3K27me3 and H3K4me3 histone modifications, reducing tumor growth and plasticity in head and neck cancer.

LSD1 inhibition corrects dysregulated MHC-I and dendritic cells activation through IFNγ-CXCL9-CXCR3 axis to promote antitumor immunity in HNSCC

This study shows LSD1 inhibition enhances antitumor immunity in HNSCC by upregulating MHC-I and activating the IFNγ-CXCL9-CXCR3 axis through dendritic cells and CD8+ T cells.

Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions

This study identifies hsa-miR-149-5p as a regulator of immune evasion in progressive bronchial premalignant lesions through integrative analysis of RNA and miRNA sequencing data.

Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.

This study uses total RNA sequencing to compare gene expression and microbial profiles between oral premalignant lesions, cancer, and healthy tissues, identifying shared molecular and microbial features associated with progression to cancer.

Virtual screening for small molecule pathway regulators by image profile matching

The paper identifies small molecule regulators of biological pathways by matching compound effects to known pathway phenotypes in public cell image data.

Structure Learning for Hierarchical Regulatory Networks

SHINE improves network structure learning from high-dimensional data with limited samples by leveraging shared structural information across multiple networks.

iEDGE: integration of Epi-DNA and Gene Expression and applications to the discovery of somatic copy number-associated drivers in cancer

iEDGE integrates epi-DNA and gene expression data to identify cis and trans driver genes in cancer, showing enrichment for known oncogenes and tumor suppressors.

CaDrA: A computational framework for performing candidate driver analyses using binary genomic features

CaDrA identifies functionally relevant subsets of binary genomic features associated with specific outcomes, showing sensitivity and specificity in cancer datasets.

Systematic morphological profiling of human gene and allele function reveals Hippo-NF-κB pathway connectivity

The paper uses morphological profiling to identify gene function and connectivity, revealing TRAF2/C-REL's negative regulation of Hippo pathway effectors.