Pedro L. Baldoni

Gene-specific exponent-corrected normalization for library size in bulk RNA-seq

The paper introduces gecco, a gene-specific normalization method for bulk RNA-seq that reduces library size bias while preserving biological signal, improving differential expression and pathway analysis.

Pre-existing levels of pro-survival proteins and induction of BCL-XL dictate cell fate after p53 activation

The paper shows that pre-existing levels of pro-survival proteins and BCL-XL induction determine cell fate after p53 activation, with implications for cancer therapy.

Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR

The paper introduces limma and edgeR pipelines for differential transcript usage analysis that account for read-to-transcript ambiguity, improving power and FDR control in small and large datasets.

MORC2 phosphorylation fine tunes its DNA compaction activity

This study characterizes MORC2 phosphorylation's role in DNA compaction and chromatin remodelling, showing it regulates ATP hydrolysis and DNA binding.

Towards accurate, reference-free differential expression: A comprehensive evaluation of long-read de novo transcriptome assembly

This study evaluates long-read de novo transcriptome assembly tools for differential expression analysis without a reference genome, finding RNA-Bloom2 with Corset as the most accurate and efficient.

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets

edgeR v4 adds a continuous negative binomial for fractional counts, bias-corrected quasi-likelihood for small counts, C-based fitting, and new transcript, exon, methylation and fold-change-threshold analyses.

Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4

The paper introduces an improved differential transcript expression analysis pipeline using edgeR v4 and Salmon's Gibbs sampling, showing it is faster and more accurate than previous methods.

Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR

This paper shows that dividing out quantification uncertainty from transcript counts improves differential expression analysis using edgeR.

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

Efficient Detection and Classification of Epigenomic Changes Under Multiple Conditions

The paper introduces a method to detect and classify differential epigenomic activity across multiple conditions, showing improved performance and speed compared to existing tools.