Ansuman T. Satpathy

This study shows that systemic iron sequestration via hepcidin reduces CD8+ T cells in pancreas cancer, linking iron dysregulation to tumoral immunity.

This study introduces match-seq, a method to trace cell-cell interactions in vivo using CRISPR screens, revealing genetic regulators of tumor-immune interactions.

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

The paper compares bulk and single-cell RNA-seq/ATAC-seq data and models to assess their impact on predicting causal genes from GWAS variants in TNFα-treated endothelial cells.

Genome-scale CRISPRi perturb-seq in 22 million primary human CD4+ T cells maps stimulation-specific regulators and links perturbation signatures to T cell states and autoimmune genetics.

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

The paper uses mtDNA mutations to trace clonal relationships of innate immune cells in cancer, showing myeloid clones are linked to monocytes and have distinct epigenetic profiles.

The paper identifies off-target effects in CRISPRi Perturb-seq experiments by analyzing transcriptional similarity between on-target and off-target guide effects.

The paper uses Molecular Pixelation to analyze surface proteomic signatures of CAR T cells under acute and chronic stimulation, identifying spatial patterns linked to exhaustion.

Combining TCE therapy with IL-2 enhances TCE efficacy in aggressive small-cell lung cancer and melanoma models with low target antigen density through T cell clonal replacement and CD8+ effector T cell differentiation.

This paper shows that FAK inhibition remodels the metastatic ECM, enhancing CD8+ T cell infiltration and immunosurveillance in breast cancer.

CRISPR-All enables genome-scale, combinatorial genetic perturbations in human cells, revealing additive functional improvements through multiplexed modifications.

The paper identifies cis-regulatory elements and transcription factors controlling FOXP3 expression in human Tregs and Tconvs, revealing mechanisms that restrict FOXP3 to Tregs in mice.

The paper develops and applies a scalable method to map transcription factor binding in human T cells, revealing novel regulatory dynamics and gene targets.

This paper introduces EPI-clone, a method using DNA methylation to trace clonal lineages in hematopoiesis without genetic engineering, showing clonal complexity declines with age in mice and expands in humans.

This study identifies induced B-cell receptor diversity as a predictor of PD-1 blockade immunotherapy response across multiple cancer types.

This paper introduces non-viral intron targeting to improve genetic editing flexibility and simplify cell selection by integrating synthetic exons into endogenous introns.

This study shows that exhausted T cells can form functional memory T cells after antigen clearance, and checkpoint blockade expands these memory clones.

This study engineers a minimal EDV for genome editing by removing viral components, showing improved efficiency and reduced size.

This paper designs novel transcription factors using evolutionary principles to generate T cell states with enhanced functionality.

This paper introduces PERFF-seq, a method to profile rare cell states via scRNA-seq by enriching for specific RNA transcripts, demonstrating its application in immune and brain tissues.

The paper identifies a synonymous mtDNA variant that affects codon-anticodon affinity and shows its impact on cellular fitness in immune cells.

The paper uses single-cell multi-omics to study how pathogenic mtDNA mutations are subject to purifying selection in immune cells from Pearson syndrome patients.

SMRT-Tag enables low-input, single-molecule sequencing for simultaneous detection of genetic and epigenetic variations in human samples.

The paper develops a method to detect mitochondrial mutations from single-cell RNA-seq to identify clonal expansions in human hematopoiesis.

This paper introduces ENTER-seq, a method using engineered lentiviral particles to systematically discover receptor-ligand interactions and map TCR specificity in single cells.

TCR-BERT uses self-supervised transfer learning on unlabeled T-cell receptor sequences to learn representations that improve antigen-binding prediction, specificity clustering, and computational TCR sequence design.

The paper examines dynamic chromatin changes in human CAR T cells during exhaustion, identifying regulatory networks and enhancer roles in exhaustion-associated genes.

This study shows XIST is required in adult human B cells to silence X-linked immune genes and identifies TRIM28 as a B cell-specific XIST cofactor involved in X-inactivation and atypical B cell formation.