Subhajyoti De

The circadian gene Dec2 promotes pancreatic cancer dormancy by regulating tumor cell antigen presentation to facilitate immune evasion

This study identifies Dec2 as a circadian gene that promotes pancreatic cancer dormancy by reducing MHC-I antigen presentation, enabling immune evasion.

Distinct clonal dynamics and interactions within the microenvironment near tumor stroma interfaces in rare histologic variants of bladder cancer

The paper analyzes spatial transcriptomics data to reveal distinct clonal dynamics and microenvironment interactions in rare bladder cancer variants compared to urothelial carcinoma.

Revisiting the cancer microbiome using PRISM

PRISM improves microbial analysis in low-biomass sequencing data, identifies tumor-associated microbes in cancer datasets, and reveals potential clinical significance.

Complex HPV-human DNA structures revealed by large-scale DNA analyses in an HPV-cancer derived cell line

The paper uses genomic tools to analyze HPV-human DNA integration structures in a cancer cell line, revealing complex intrachromosomal and extrachromosomal architectures.

Mechanism-aware inference of response to targeted cancer therapies

This paper introduces FORGE, a framework that jointly models drug response and gene essentiality to identify treatment groups and predict efficacy using basal gene expression.

Disruptive changes in tissue microenvironment prime oncogenic processes at different stages of carcinogenesis in lung

The paper profiles lung cancer progression stages to identify microenvironmental changes that support oncogenic processes and cancer hallmarks.

Deconstructing evolutionary histories of complex genomic rearrangements in lung malignancies

The paper analyzes complex genomic rearrangements in lung cancers using optical mapping to uncover their evolutionary patterns and mechanisms.

Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues

SAHMI identifies microbial nucleic acids in mammalian tissues and filters contaminants, enabling co-detection of somatic cells and microorganisms in single-cell and spatial genomic data.

Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation

Census is a hierarchical scRNA-seq cell-type annotation method that outperforms existing tools on benchmark datasets.

Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq

Neighbor-seq reconstructs cell-cell interaction networks from single-cell data without prior knowledge, revealing tissue-specific and tumor microenvironment interactions.

Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens

This study identifies genetic regulators of PARP inhibitor response using CRISPR screens, revealing TIP60 as a key factor that reverses PARPi sensitivity in BRCA2-deficient cells.

FERMI: A novel method for sensitive detection of rare mutations in somatic tissue

FERMI improves detection of rare somatic mutations by reducing sequencing and library preparation errors, enabling tracking of clonal evolution in leukemia.

A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes

The paper introduces SASE-mapper to detect accelerated somatic evolution in cancer genomes and finds recurrent SASE in regulatory regions across multiple cohorts.