Jiannis Ragoussis

The paper identifies LINC00536 as a lncRNA that regulates TRPS1, a transcriptional repressor, in breast cancer, linking their overexpression to poor patient prognosis.

This study identifies 59 gene expression programs in RCC that reveal subtype identity and metastatic trajectories, including a metastatic signature linked to poor clinical outcomes.

The paper investigates five BRIP1/FANCJ variants for their clinical relevance in breast and ovarian cancer, finding three likely damaging variants associated with cellular sensitivity to chemotherapy drugs.

The paper uses long-read RNA-seq to analyze temporal transcriptional dynamics in single medfly embryos, identifying novel genes and developmental transitions.

This study maps the metabolic complex genetic interaction network of chromosome 4p loss in basal breast cancer to identify targetable vulnerabilities.

The paper presents the genome sequence of the hemlock woolly adelgid, including chromosome assembly, gene annotation, and mitogenome data.

The paper presents chromosome-level genome assemblies for five Tephritid species using long-read sequencing, short-read polishing, and Hi-C scaffolding.

The paper identifies a cold fibrotic network in LUSC TME driven by CAFs and shows its conservation in other CIACs, suggesting therapeutic targets.

The paper benchmarks SARS-CoV-2 whole genome sequencing methods and introduces an improved ARTIC-Amp protocol for better coverage in low RNA samples.

The paper identifies a fibroblast state called STIF that drives YAP-dependent regenerative programs and (pre)malignancy through mechanotransduction in response to tissue injury.

This study investigates ependymal cilia dysfunction in multiple sclerosis, finding dysregulated ciliary genes and impaired ciliary function in MS patients and animal models.

The paper analyzes germline DNA repair gene variants in BRCA1 and BRCA2 families to assess the prevalence of damaging variants in DNA repair genes beyond established breast cancer predisposing genes.

This paper benchmarks sequencing technologies and variant callers for detecting SNPs, indels, and SVs, finding that SRS is optimal for small variants while LRS excels in SV detection and complex regions.

This study performs a genome-wide association study for Long COVID, identifying a significant association with the FOXP4 locus and highlighting the role of pulmonary dysfunction and COVID-19 severity.

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

This study shows psilocybin induces cell-type specific transcriptional changes in mouse medial prefrontal cortex, with sustained neuroplastic effects mediated by 5-HT2C signaling in L5/6 NP neurons.

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.

WEGS combines low-depth whole genome and high-depth whole exome sequencing to reduce costs while maintaining variant detection accuracy in genetic studies.

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.

This study shows that SARS-CoV-2 evolves in the absence of immune pressure, leading to antibody resistance, interferon suppression, and lineage-specific phenotypic changes.

The paper introduces a new Nanopore cDNA library preparation protocol that improves PCR efficiency and gene body coverage for full-length transcript sequencing.

This paper identifies FANCI c.1813C>T as a candidate familial ovarian cancer risk allele in a French Canadian population with founder effects.

The paper identifies two distinct epithelial cell lineages in the oviduct, spatially separated along the distal-proximal axis, with distinct developmental origins.

This study provides a chromosome-scale genome assembly for Greenland Halibut and identifies a nascent XY sex determination system with a putative Y-autosomal fusion.

The paper investigates the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19 and finds no significant association.

This study uses Oxford Nanopore long-read RNA-Seq to characterize the transcriptome of the olive fruit fly embryo during early development, revealing novel genes and transcriptional dynamics.

This study uses single-cell RNA sequencing to analyze spinal cord microglia responses to nerve injury, identifying sex- and time-specific changes and a role for ApoE in neuropathic pain.

The paper introduces a probabilistic model to estimate and correct sample index hopping in single-cell RNA-seq data, reducing phantom molecules by up to 85%.

The paper identifies a conserved gene responsible for the white pupae phenotype in multiple fruit fly species and demonstrates its utility for creating sexing strains in pest control.

The paper uses single-nucleus RNA sequencing to identify gene expression changes in specific cell types associated with major depressive disorder.