Lionel Christiaen

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

The paper shows that starvation-induced cell loss in sea anemones occurs via epithelial cell extrusion, with ERK1/2 signaling regulating extrusion density.

The paper shows that transcriptome maturation during the cell cycle enables multilineage competence in cardiopharyngeal progenitors by coupling fate decisions with cell cycle phases.

The paper introduces pseudovelocity, a method to estimate gene-specific RNA velocity using kNN-G and diffusion-based pseudotime, improving gene-based velocity estimation for downstream analysis.

This paper develops a simple inland culture protocol for Ciona species, showing that body length predicts maturation and improving breeding conditions through size selection.

The paper shows that the RNA switch for acetylcholine receptor clustering is conserved in Ciona robusta, with some structural differences in Nova and regulation by Ebf.

This paper introduces a deep learning framework for gene regulatory network inference and latent transcription factor activity estimation, showing improved performance over existing methods.

This paper shows that the tunicate Ciona can regenerate its heart after complete ablation, revealing evolutionary insights into regenerative cardiogenesis in chordates.

This study identifies GATA4/5/6 as conserved regulators of cardiac versus pharyngeal mesoderm fate by analyzing single-cell gene expression in zebrafish and Ciona.

The paper identifies Rnf149-related as a regulator of pharyngeal muscle fate specification in the cardiopharyngeal lineage, acting independently of the FGF/MAPK pathway.

The paper uses computational modeling and experiments to show that polarized supracellular organization in cardiopharyngeal progenitor cell pairs enhances their migratory persistence and mechanical interactions during morphogenesis.

This study identifies a Tbx1-dependent multilineage primed population in the murine cardiopharyngeal mesoderm using single-cell RNA-sequencing and shows its role in cardiac and skeletal muscle development.

The paper studies zygotic gene expression in Ciona germline by showing cellular remodeling and JAK inhibition initiate transcription in primordial germ cells.

This paper introduces DEWAKSS, a method for denoising single-cell genomics data by optimally tuning kNN- and diffusion-based approaches to preserve biological variance and improve clustering.

This paper develops a proteomics method to quantify protein abundances from as few as 1,000 mammalian cells with high reproducibility and accuracy.

The paper investigates how chromatin accessibility dynamics in cardiopharyngeal progenitors guide fate choices between heart and pharyngeal muscle by analyzing combinatorial regulatory elements in Ciona.

This study uses single-cell genomics in Ciona to map cardiopharyngeal fate decisions, revealing FGF-MAPK signaling's role in maintaining multipotency and the Tbx1/10-Dach pathway's role in suppressing the first heart lineage program.

The paper identifies a conserved regulatory program driving lateral plate mesoderm emergence across chordates using zebrafish and comparative analysis.

The paper identifies an FGF-driven feed-forward circuit that regulates the spatial and temporal differentiation of cardiopharyngeal mesoderm into heart and pharyngeal muscle precursors.

The paper shows that the Discoidin domain receptor (Ddr) has dual roles in coordinating cell-matrix adhesion and BMP-Smad signaling in migratory cardiopharyngeal progenitors.

The paper evaluates and designs efficient CRISPR/Cas9 guide RNAs for mutagenesis in Ciona, identifying sequence correlates of activity and introducing a cloning-free delivery method.

This paper introduces a method for multi-source gene regulatory network inference using fused regression with orthology priors, improving performance across species and platforms.