Alexis Vandenbon

DeepSpaceDB 2.0 expands its database to include 1,539 public Xenium datasets, offering improved tools for interactive exploration and analysis of spatial transcriptomics data.

oCELLoc improves cell-type prediction in scRNA-seq and spatial transcriptomics data by filtering relevant reference cell types, leading to more accurate downstream analyses.

DeepSpaceDB provides an interactive spatial transcriptomics database with advanced analysis tools for comparing gene expression across tissue regions and samples.

The paper identifies 11,000 housekeeping CREs (HK-CREs) and shows their reduced activity in cancer, correlating with lower gene expression and poorer patient survival.

The paper updates singleCellHaystack to predict differentially active features across single-cell, spatial, and bulk genomics data with improved performance and scalability.

This study shows that blocking ACTIVIN/NODAL and FGF signals in human pESCs leads to GATA3-expressing syncytia resembling trophoblasts, revealing a cell-autonomous differentiation pathway.

The paper evaluates data processing steps for accurate gene co-expression prediction from RNA-seq data, finding that sample size, normalization, batch correction, and correlation measure significantly impact results.

singleCellHaystack identifies differentially expressed genes in single-cell data without requiring clustering, using Kullback-Leibler Divergence to detect non-random gene expression patterns in 2D plots.

The paper shows that codon bias affects mRNA stability in humans through ILF2, with GC3 codons stabilizing and AT3 codons destabilizing mRNA.

The paper examines the temporal dynamics of histone modifications in mouse dendritic cells after LPS stimulation, revealing distinct patterns and links to transcription factor activity.