Fabiana M. Duarte

The paper introduces ExIGS, a method linking nuclear abnormalities to chromatin repression hotspots in progeria fibroblasts.

The paper shows that the epigenetic state of the cell of origin influences susceptibility to Tet2 mutation, with Sox4 promoting dedifferentiation and increased clonal output in hematopoietic stem cells.

The paper introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

The paper identifies Twist2 as a key regulatory node in adipogenesis using kinetic networks derived from ATAC-seq and PRO-seq data.

This paper develops FigR, a framework to integrate scATAC-seq and scRNA-seq data to infer gene regulatory networks and identify TF regulators in immune responses.

AtacWorks denoises and identifies accessible chromatin regions from low-quality ATAC-seq data, achieving high-resolution results with minimal input.

This study shows GAF, a Drosophila pioneer factor, works with chromatin remodelers PBAP and NURF to activate transcription by opening chromatin and facilitating Pol II recruitment and elongation.

The paper identifies and quantifies barcode multiplets in 10x Chromium scATAC-seq data, showing their potential to confound single-cell analyses.

The paper introduces an R package to infer primary transcript annotations from run-on data, improving sensitivity in detecting differentially expressed transcripts and RNA polymerase pause indices.

The paper improves the auxin-inducible degron system to enable rapid, specific protein depletion while preserving native protein levels and patterns.

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

The paper identifies systemic genomic instability in yeast, showing non-independent accumulation of loss-of-heterozygosity events across multiple chromosomes.