Marcos Jesus Araúzo-Bravo

NEURO-IMMUNE CRYPT-ASSOCIATED CELLS AND REST-MEDIATED REPROGRAMMING: PATHOGEN-DRIVEN STROMAL ACTIVATION, HERVS INDUCTION, AND ABORTIVE ANTIVIRAL SIGNALING IN COLORECTAL CARCINOMA

This paper identifies NICA cells as a pathogen portal in CRC and shows how EBV and HERVs contribute to tumor progression through epigenetic and antiviral mechanisms.

TET3 regulates cellular terminal differentiation at the metabolic level

This study shows TET3 regulates terminal differentiation by affecting mitochondrial metabolic maturation and oxidative phosphorylation in intestinal epithelial cells.

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

The paper develops a method to profile extrachromosomal circular DNA (eccDNA) in plasma and finds higher eccDNA levels in lung adenocarcinoma patients compared to healthy donors.

Lack of evidence for increased transcriptional noise in aged tissues

The paper develops tools to quantify transcriptional noise in aging tissues and finds no universal increase in noise, but detects age-related changes in cell type composition.

Triku: a feature selection method based on nearest neighbors for single-cell data

Triku selects genes defining main cell populations in single-cell data by prioritizing genes expressed in closely grouped cells.

FOntCell: Fusion of Ontologies of Cells

FOntCell merges cell ontologies by integrating name matching and structure mapping using graph convolution, enabling unified knowledge representation for cell classification.

BigMPI4py: Python module for parallelization of Big Data objects

BigMPI4py enables efficient parallelization of large data objects in Python, validated on DNA methylation data to identify differentially methylated CpGs across germ layers.

Newly developed single-cell computational approach elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo

The paper develops a new clustering algorithm, HOkM, to identify developmental sub-stages in mouse embryos and finds Oct4 expression stabilization is linked to chromatin remodeling and pluripotency.