Lucas A. Salas

Epithelial-Mesenchymal Transition is Associated with Altered Immune Composition and Cytotoxic Function in Triple-Negative Breast Cancer

This study shows that EMT progression in breast cancer correlates with reduced immune cell infiltration and function, including decreased cytotoxic T cells and altered B cell composition.

Endothelial cell-specific DNA methylation alterations identified in breast cancer with epigenetic deconvolution

This study identifies DNA methylation alterations in tumor endothelial cells using bulk specimens and deconvolution methods, revealing potential therapeutic targets in breast cancer.

Differential Transcript Usage Reveals Isoform-Level Remodeling of Tumor Biology in Clear Cell Renal Cell Carcinoma

The paper identifies isoform-level changes in ccRCC using DTU analysis, revealing subgroups with distinct survival outcomes and potential biomarkers.

Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma

This study identifies RE methylation subtypes in ccRCC linked to immune phenotypes and survival, validated across multiple cohorts.

Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition

This study shows HGSC transcriptomic subtypes are driven by tumor cellular composition rather than intrinsic biology, with high predictive accuracy using deconvolution methods.

Single-cell RNA sequencing of peripheral blood cells identifies transcriptomic signatures in Parkinson's disease

This study uses single-cell RNA sequencing to identify immune cell-specific gene expression signatures and sex differences in Parkinson's disease patients compared to healthy controls.

Integrative epigenetics and transcriptomics identify aging genes in human blood

This study identifies aging genes in human blood by integrating epigenetic and transcriptomic data, finding genes enriched for immune functions that better replicate across populations and link to aging outcomes.

Oncometabolite-driven enhancer hypermethylation promotes a hyporesponsive microglial state in IDH-mutant gliomas

This study shows that oncometabolite D-2HG drives enhancer hypermethylation in IDH-mutant gliomas, leading to hyporesponsive microglia and reduced immune reactivity.

Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling

The paper enhances cell deconvolution of peripheral blood using DNA methylation to provide high-resolution immune profiling by including 12 leukocyte subtypes and validated libraries.

MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Network, Inspired by Capsule Networks

The paper introduces MethylCapsNet and MethylSPWNet, deep learning models that organize DNA methylation data into biologically relevant capsules to improve interpretability in classifying CNS tumors.

MethylNet: An Automated and Modular Deep Learning Approach for DNA Methylation Analysis

MethylNet is a deep learning framework for DNA methylation analysis that constructs embeddings, makes predictions, and uncovers heterogeneity with minimal user input.

Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer

The paper identifies DNA methylation changes in breast milk associated with future breast cancer risk using epigenome-wide association studies.

Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

The paper evaluates and validates reference and library selection methods for deconvolving cord blood DNA methylation data, finding that the IDOL library outperforms automatic selection methods.