Antonio Scialdone

This study shows that MTRR-1 regulates heterochromatin through mitochondrial homeostasis, not methionine synthesis, in C. elegans.

The paper shows that sampling biases in negative regulatory interactions inflate performance in gene regulatory network inference and proposes a degree-aware sampling approach to address this issue.

This study identifies Aquarius RNA helicase as essential for maintaining genomic resilience and pluripotent stem cell identity by resolving transcription-replication conflicts.

This study shows that yeast cells adapt to changes in mitochondrial DNA copy number through retrograde signaling and protein dosage compensation, allowing robust growth despite mtDNA fluctuations.

The paper benchmarks tools for locus-specific TE analysis in scRNA-seq, finding older TEs are more accurately quantified, while young TEs face challenges due to multi-mapping reads.

The paper introduces IDEAS, a tool for computing intrinsic dimensionality from scRNA-seq data to assess cell potency without clustering, and applies it to reprogramming datasets to study potency changes and trajectories.

This study shows that reprogramming success varies by cell type and is influenced by the expression of genes from the original cell type, with some cells resisting reprogramming and causing developmental issues.

This study uses spatial transcriptomics to map gene expression patterns of gut sensory cells, revealing regional differences in hormone, neurotransmission, immune, and nutrient sensing genes along the gastrointestinal tract.

geneRNIB provides a benchmark for gene regulatory network inference, showing simpler models often outperform complex ones in perturbation-informed metrics.

This study identifies Sema4A as an extrinsic factor that protects myeloid-biased HSCs from inflammatory stress, preserving functional diversity in the hematopoietic stem cell pool.

This study shows that H3K4 methylation acts as an epigenetic memory to support zygotic genome activation and embryonic development in Xenopus laevis.

The paper characterizes the transcriptional dynamics of the mouse Anterior Visceral Enderm (AVE) during migration and identifies Ephrin- and Semaphorin-signalling as critical for its movement.

The paper benchmarks algorithms for inferring gene regulatory networks from single-cell RNA-seq data by evaluating their ability to capture topological properties and identify hubs.

The paper introduces a tool called Community for analyzing differential cell communication in large case-control scRNAseq datasets, showing it outperforms existing methods in speed and robustness.

The paper introduces multiplex-GAM, a ligation-free method for genome-wide chromatin contact mapping, showing it detects different strong contacts compared to Hi-C, particularly involving active genomic regions.

The paper identifies emergent statistical laws in single-cell transcriptomic data that mirror patterns in linguistics, ecology, and genomics, providing a framework to distinguish biological variability from statistical effects.

This study identifies asymmetrically expressed genes in the mouse cardiac crescent during left-right symmetry breaking using single-cell RNA sequencing and validates their expression patterns.

CIARA identifies markers of rare cell types from single-cell RNA-seq data, outperforming existing methods and discovering new cell populations in mouse and human samples.

This study identifies how EBNA2 interacts with EBF1 to drive MYC expression and metabolic processes necessary for cell cycle progression in EBV-infected B cells.

This paper creates a 3D spatial transcriptomics atlas of the mouse olfactory mucosa, revealing spatial gene distribution patterns and supporting the chromatographic theory of olfaction.

This paper presents a spatially resolved single-cell transcriptome atlas of human gastrulation, identifying novel cell types and revealing key differences from mouse gastrulation.

The paper identifies mitochondrial defects in eliminated cells during early mouse development and shows that cell competition removes cells with mitochondrial DNA mutations and sequence changes.

The paper examines gene expression changes across multiple organs during short-term fasting in mice, identifying a brain-liver-fats network with significant immune system regulation.

COMUNET is a tool for analyzing and visualizing cell-cell communication from single-cell data, applied to mouse embryos and leukemia datasets.

This paper introduces methods to identify globally and locally relevant genes in nonlinear low-dimensional embeddings of single-cell RNA-seq data, demonstrating their versatility across datasets and embedding techniques.

The paper compares olfactory preferences across flies, mice, and humans, finding positive correlation between flies and mice, negative correlation between flies and humans, and no evidence of shared preferences between humans and mice.