Jayamanna M. Wickramasinghe

Mechanistic Investigation of Reversible Hibernation-Driven Immune Suppression in Thirteen-Lined Ground Squirrels

This study investigates immune suppression during torpor in 13-lined ground squirrels using single-cell RNA sequencing and image analysis, identifying metabolic and lineage-specific programs that conserve energy while preserving immune function.

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

ERVmancer is a phylogeny-informed method that resolves read-mapping ambiguity for HERVs, outperforming existing approaches and revealing new biology in breast cancer.

RSAD2/VIPERIN and CMPK2 Coordinate an Immunometabolic Response to Epstein-Barr Virus

This study identifies RSAD2 and CMPK2 as key regulators of EBV reactivation and host interferon responses, revealing their coordinated immunometabolic role in viral latency and immune control.

Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma

This study identifies microbiome-derived protein biomarkers for predicting immunotherapy response and toxicity in melanoma without relying on taxonomic classification.

Chemotherapy Induces an IL1β-dependent Neutrophil Recruitment that Promotes Chemoresistance in Metastatic Ovarian Cancer

This study shows chemotherapy induces IL1β-dependent neutrophil recruitment, promoting chemoresistance in metastatic ovarian cancer through NETs and immune modulation.

LANA-Dependent Transcription-Replication Conflicts and R-Loops at the Terminal Repeats (TR) Correlate with KSHV Episome Maintenance

The paper shows LANA binding at KSHV TRs causes R-loops and histone modifications linked to episome maintenance.

Zinc availability in the tumor microenvironment dictates anti-PD1 response in CDKN2ALow tumors via increased macrophage phagocytosis

This study shows that zinc availability in the tumor microenvironment affects anti-PD1 therapy response in CDKN2A-low tumors through macrophage phagocytosis.

Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops

The paper reconstructs a sparsely interconnected transcriptional hierarchy in leukemia cells stabilized by incoherent feed-forward loops and shows inhibitors disrupt core regulators' programs.

Characterizing the landscape of viral expression in cancer by deep learning

The paper develops viRNAtrap, a deep learning-based pipeline to identify and characterize viral expression in cancer, revealing new viruses and endogenous viruses linked to poor survival.

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

The paper identifies a modular core regulatory circuitry in AML that enforces oncogene expression in KMT2A-rearranged leukemias.