Daniel Diniz De Carvalho

Benchmarking CUT&RUN analysis using motif enrichment

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

Enrichment of methylated cell-free placental DNA

The paper uses cfMeDIP-seq to analyze cell-free placental DNA methylation in maternal plasma, identifying enriched regions associated with preterm birth and IUGR.

Targeting an RNA Editor to Impede H3K27M+ Pediatric Gliomas

This study identifies ADAR as a key mediator of immune evasion in H3K27M+ pediatric gliomas and shows that ATRA can induce ADAR degradation, enhancing antiviral responses and tumor immunogenicity.

Repeats Mimic Pathogen-Associated Patterns Across a Vast Evolutionary Landscape

The paper quantifies viral mimicry in genomes across species and shows how repetitive elements maintain pathogen-like features under selection.

Plasma cell-free DNA methylome as early detection and prognostic marker for pancreatic cancer

This study identifies cell-free DNA methylation markers for early detection and prognosis of pancreatic cancer with high accuracy and survival stratification.

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

This paper introduces synthetic spike-in controls for cfMeDIP-seq to enable accurate and reproducible quantification of DNA methylation, reducing batch effects and technical biases.

A Chemical Biology Toolbox for the Study of Protein Methyltransferases and Epigenetic Signaling

The paper presents a chemical probe collection for studying protein methyltransferases, showing their utility in modulating epigenetic marks and affecting T cell differentiation.