Arnau Sebé-Pedrós

Diversity and evolution of chromatin regulatory states across eukaryotes

The paper profiles histone post-translational modifications across eukaryotic lineages to assess conservation of chromatin states, finding conserved euchromatin states but diverse repressive heterochromatin configurations.

Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery

The paper generates a single-cell transcriptomic atlas of coral during heat stress and recovery, revealing cell type-specific transcriptional responses and symbiont dynamics.

Zygotic genome activation is timed by the egg DNA-to-cytoplasm ratio across animals

The paper investigates ZGA timing across 61 animal species and finds that genome size to cytoplasm volume ratio predicts ZGA onset.

Convergent evolution of cluster-wide Hox gene regulation in Bilateria

The paper identifies a conserved global control region for Hox gene regulation in annelids and shows convergent evolution of cluster-wide regulatory mechanisms in vertebrates and spiralians.

Functional characterization of specialized immune cells in a cnidarian reveals an ancestral antiviral program

The paper identifies a novel antiviral immune cell type in cnidarians by analyzing gene expression and function in Nematostella vectensis embryos.

Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals

This study shows that freshwater sponges acquired the microbial gene rquA via lateral gene transfer, enabling rhodoquinone biosynthesis and adaptation to hypoxia.

GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis

GeneExt improves gene annotation using scRNA-seq data, enhancing gene expression quantification and cross-species cell type comparisons.

Life-stage-specific specialities in the cell atlases of the Clytia hemisphaerica planula and medusa

The paper compares cell atlases of Clytia hemisphaerica planula and medusa stages using single-cell transcriptomics to identify stage-specific cell types and their transcriptional profiles.

Decoding cnidarian cell type gene regulation

The paper identifies regulatory elements and reconstructs gene regulatory networks in cnidarian cell types using chromatin accessibility data.

Adenine DNA methylation associated to transcription is widespread across eukaryotes

The paper profiles 6mA methylation in 18 eukaryotes and finds it is linked to transcription and associated with H3K4me3-enriched nucleosomes, but is lost in major multicellular lineages.

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

The paper introduces ACME, a cell fixation-dissociation method for single-cell transcriptomics that preserves RNA integrity and enables cryopreservation and sorting, validated with SPLiT-seq in planarians.

MetaCell: analysis of single cell RNA-seq data using k-NN graph partitions

MetaCell partitions scRNA-seq data into homogeneous metacells to address sparsity, enabling clustering and gene expression analysis without enforcing global structure.

Signaling via GABAB receptors regulates early development and neurogenesis in the basal metazoan Nematostella vectensis

This study identifies GABAB receptor homologs in Nematostella vectensis and shows that activating GABABR signaling inhibits neurogenesis and disrupts nervous system development.

Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

The paper uses whole-organism single-cell RNA-seq to analyze cell type diversity in Nematostella vectensis, identifying 35% of genes and 51% of TFs as cell type-specific.