Izaskun Mallona

Co-option of CENP-A for activity-induced neuronal plasticity

This study shows that CENP-A, a centromere-specific histone variant, is dynamically regulated by synaptic activity in neurons and is required for activity-dependent gene expression and hippocampus-dependent learning and memory.

fastder: fast, annotation-agnostic detection of expressed regions from RNA-seq coverage and splicing data

fastder detects expressed regions from RNA-seq data without relying on annotations, achieving high accuracy and speed for large-scale analysis.

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

The paper evaluates five single-cell RNA sequencing pipelines using Omnibenchmark, highlighting differences in parameter implementation across tools.

rhapsodist: a reproducible Snakemake workflow for BD~Rhapsody single-cell RNA-seq data

rhapsodist processes BD Rhapsody scRNA-seq data using a Snakemake workflow, enabling cross-aligner comparison and generating count tables in SingleCellExperiment format.

BiCLUM: Bilateral Contrastive Learning for Unpaired Single-Cell Multi-Omics Integration

BiCLUM integrates unpaired single-cell multi-omics data by aligning cell and feature spaces through bilateral contrastive learning, outperforming existing methods in visualization and quantitative metrics.

RoCK and ROI: Single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

RoCK and ROI improves single-cell transcriptomics by targeting specific transcripts and regions, enhancing detection of critical biological features.

A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia

The paper develops a xenotransplantation model to study human microglia's processing of dying neurons, identifying a lipid-rich compartment called the gastrosome involved in neurodegeneration.

Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment

The paper identifies transcription factors and chromatin regulators critical for haemato-endothelial mesoderm formation using CRISPR-Cas9 screens in mouse embryonic stem cells.

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

This paper meta-analyzes single-cell method benchmarks to identify challenges in extensibility, interoperability, and reproducibility.

Flanking sequence preference modulates de novo DNA methylation in the mouse genome

The paper identifies sequence preferences for de novo DNA methylation by DNMT3A and DNMT3B in mouse stem cells, showing structural basis for context-specific methylation.

DNA co-methylation networks outline the structure and remodeling dynamics of colorectal cancer epigenome

The paper analyzes DNA methylation co-variation in colon cancer cohorts to reveal epigenome remodeling dynamics and novel genomic compartments.