Ioannis S. Vlachos

The paper identifies pre-hematopoietic stem cells and their niche using spatial transcriptomics in the AGM region, revealing spatial signaling patterns and cellular interactions that support HSC development.

This study identifies tumor-myeloid crosstalk as a driver of cisplatin resistance in bladder cancer and proposes PARP14 inhibition as a therapeutic strategy.

The paper integrates coding and noncoding genome annotations to improve transcriptomic analysis, identifying clinically relevant noncoding RNAs in multiple myeloma.

This study identifies miRNA signatures associated with resilience to Alzheimer's disease, revealing potential therapeutic targets for neuroprotection.

The paper creates a miRNA atlas of the human prefrontal cortex across aging, identifying age-related miRNA changes and highlighting miR-34a-5p as a key upregulated miRNA in older individuals.

The paper performs spatial transcriptomics on the human prefrontal cortex across the lifespan to identify aging-related changes in different cortical layers.

The paper characterizes immune microenvironment dysregulation in multiple myeloma using single-cell data and links it to disease progression and patient outcomes.

This study shows that tRNA modification mcm5s2U34 is essential for stress granule formation and melanoma metastasis, suggesting it as a therapeutic target.

This study evaluates how PCR duplication affects RNA-seq data quality across four sequencers, finding that input amount and PCR cycles significantly impact duplication rates, with UMIs effectively reducing duplicates without losing biological information.

This study uses longitudinal multi-omic profiling to identify immune escape mechanisms and predictors of response in multiple myeloma.

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

The paper identifies a dynamic microRNA profile associated with chemotherapy resistance in osteosarcoma and predicts novel therapeutic targets that could reverse resistance.

This study shows that inhibiting Cyp1a protects mice from anthracycline-induced cardiomyopathy by reducing cardiac dysfunction and altering gene expression related to mitophagy and inflammation.

Head-to-head on serial prostate adenocarcinoma sections: Xenium gave higher sensitivity, wider dynamic range and closer agreement with snRNA-seq; CosMx segmented cells better out of the box.

This study introduces a method to generate high-quality single-nucleus transcriptomic data from FFPE samples using recent single-cell genomic technology.

PanomiR identifies miRNAs regulating groups of interacting pathways by analyzing pathway activity and miRNA-mRNA interactions in gene expression data.

The paper identifies glucocorticoid-responsive molecular defects in MS T cells through cell-type-specific transcriptomic profiling and validates potential therapeutic targets.

The paper profiles single-cell RNA sequencing data from diabetic foot ulcers to identify cell types and gene expression patterns associated with wound healing.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

Manatee quantifies small non-coding RNA classes and detects uncharacterized loci from sRNA-Seq data with high accuracy.

The paper reports a detailed genetic and genomic map of multiple sclerosis, identifying susceptibility genes in peripheral immune cells and brain-resident microglia.

The paper introduces mirGFF3, a standardized format for miRNA/isomiR analysis, and mirtop, a tool to convert outputs into this format, enabling data sharing and comparative analysis.