José Dávila-Velderrain

This study shows that Nematostella vectensis larvae use a developing sensory-motor system to control movement and achieve efficient dispersal.

The paper investigates dispersal behavior in cold-water coral larvae, showing how physiological changes drive shifts from passive to active swimming behaviors.

NeuRoDev provides a computational resource to analyze human cortical gene expression across development, revealing temporal and cellular variation in neuronal and glial cells.

The paper visualizes axoneme assembly in situ using cryo-electron tomography and identifies conserved microtubule luminal proteins and assembly intermediates.

This study identifies WWOX as a critical regulator of oligodendrocyte differentiation and myelin repair, showing its interaction with SOX10 and its role in myelin regeneration.

The paper studies voltage-gated ion channel diversity across 623 organisms to understand its role in neuronal excitability and nervous system evolution, finding that diversity, not quantity, correlates with complexity.

The paper quantifies gene expression specificity across tissues, cell types, and species using 2D landscapes and finds that brain cell subtype specificity conservation mirrors evolutionary divergence times.

This study identifies WWOX mutations' impact on neurogenesis and neuronal function in human organoids, showing gene therapy can restore function.

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

The paper uses MPRA to identify functional regulatory variants associated with schizophrenia and shows they differ from eQTLs in genomic location and regulatory impact.

The paper introduces a method to analyze the role of specific genes in reachability properties of GRNs using the Arabidopsis thaliana flower development GRN, finding 79 inducible attractor transitions with external control inputs.

The paper identifies that DNA double strand breaks in neurons activate immune pathways, leading to microglia activation in neurodegeneration.

The paper uses single-cell transcriptomics to analyze the hippocampus and entorhinal cortex in Alzheimer's disease, identifying stage-specific molecular changes across cell types.

The paper compares in vivo and in vitro gene essentiality estimates to assess functional constraints and identifies genes with contrasting mutational tolerance.

NEBULA improves differential expression and co-expression analysis in large-scale multi-subject single-cell data by efficiently handling overdispersion with a negative binomial mixed model.

The paper deconvolves 3,387 post-mortem brain samples using SPLITR to identify cell-type-specific eQTLs and genetic effects in mental disorders.

ACTIONet is a multiresolution framework that uses archetypal analysis and network theory to characterize single-cell state landscapes across tissues and organisms.

The paper introduces SCINET, a framework to reconstruct cell-type-specific interactomes from single-cell data, revealing disease-specific gene networks and cell-type convergence in brain disorders.

The paper introduces a machine learning method to identify active enhancers using cell type-specific epigenomic signatures, showing improved performance and generalizability across human and mouse tissues.

The paper analyzes tissue-specific transcription factor networks to reveal structural plasticity and robustness across development.

The paper introduces DECODE, an algorithm that identifies gene presence/absence patterns in single-cell RNA-seq data and distinguishes biological from technical zeros, improving functional inference and imputation.

This paper introduces a Bayesian method to identify causal genes in Alzheimer’s disease by distinguishing mediation from pleiotropy using summary statistics, finding 206 causal genes.

The paper introduces a probabilistic framework to identify cell-type-specific regulatory elements and risk variants associated with complex traits using epigenomic data.