Mario Looso

This study maps tRNA expression dynamics across human hematopoiesis using sc-STM-seq and identifies tRNAs linked to stemness, differentiation, and cell lineages.

SC-Framework provides a unified, containerized environment for single-cell data analysis to improve reproducibility and scalability.

The paper investigates how ischemic injury affects microglial response to Aβ pathology, finding a protective microglial phenotype that promotes benign Aβ plaque formation.

This study identifies REG3β as a factor that removes aged neutrophils after myocardial infarction, promoting inflammation resolution and cardiac repair.

FRED generates FAIR-compliant metadata for omics experiments, enabling structured data management and interoperability.

This study shows ischemic stroke causes long-term changes in brain stromal progenitor cells, leading to vascular dysfunction and potential recurrent stroke.

This study shows that loss of KDM6A in hematopoietic cells impairs cardiac recovery after heart failure by causing epigenetic changes in myeloid cells that increase inflammation and worsen cardiac outcomes.

This study identifies TNFSF14 as a driver of alveolar macrophage depletion after influenza, increasing susceptibility to pneumococcal pneumonia, and shows targeting this pathway can reduce disease severity.

PEAKQC evaluates single-cell ATAC-seq quality using wavelet-based convolution of fragment length distribution patterns, improving downstream analysis by filtering low-quality cells.

This study identifies Gpnmb as a critical regulator of immune and fibrotic responses during zebrafish heart regeneration, showing its role in macrophage function and ECM regulation.

This study shows that inactivating flt1 in zebrafish enhances cardiac regeneration by improving vascularization and reducing fibrosis.

This study shows that DNMT3A mutations in CHIP lead to metabolic changes in macrophages that drive inflammation, and targeting these changes can improve heart failure outcomes.

This study shows that endocardial HDAC3 is essential for myocardial trabeculation by regulating TGFβ3 expression through miR-129-5p repression in mice.

This paper introduces DENIS, a framework for de novo motif discovery from ATAC-seq footprints to identify uncharacterized transcription factor binding.

This study identifies DUXBL as a key factor promoting the silencing of the 2C transcriptional program during exit from totipotency.

Scanpro is a tool for differential proportion analysis in single-cell data, supporting both replicated and unreplicated datasets.

The paper identifies HIF1α-AS1 as a DNA:DNA:RNA triplex-forming lncRNA that interacts with the HUSH complex to repress gene expression and modulates angiogenesis in pulmonary hypertension.

TF-COMB identifies co-occurring transcription factors and their binding grammar using ChIP-seq data and ATAC-seq footprinting.

i2dash creates customizable, interactive web dashboards for visualizing omics data, integrating with R-based analysis pipelines and supporting single-cell RNA-seq workflows.

multicrispr is a gRNA design tool that enables efficient and specific gRNA creation for CRISPR-based applications like Prime Editing and large-scale screening.

TOBIAS enables genome-wide analysis of TF binding dynamics using ATAC-seq data, revealing complex TF interactions during zygotic genome activation in humans and mice.

The paper uses single-cell RNA-seq and ATAC-seq to study cardiac progenitor cell fate transitions, identifying roles for Isl1 and Nkx2-5 in lineage commitment and gene regulatory networks.

This study identifies Myh10 as critical for alveolar development and ECM remodeling, linking its deficiency to pulmonary disease and emphysema.

This study identifies KCNJ13 as critical for tracheal tubulogenesis by maintaining ion homeostasis and actin polymerization in smooth muscle cells.

The paper introduces a web-based GUI for the UROPA tool to simplify genomic region annotation for biologists and clinicians.