Shalin H. Naik

This study identifies γδ T cell infiltration in SCLC and shows their anti-tumor activity, suggesting they could be therapeutic targets.

This study uses genetic barcoding to analyze clonal composition in solid and liquid biopsies of breast cancer models, revealing differences in clonal diversity and DNA shedding patterns.

The paper identifies clonal fate modules in human HSPCs using machine learning, revealing molecular predictors of lineage commitment and improving dendritic cell purity for immunotherapy.

MiniMarS identifies the minimal number of protein markers for cell type annotation across multiple datasets and improves rare population identification.

TIRE-seq streamlines RNA-seq workflows by integrating mRNA purification into library preparation, improving efficiency and data quality in perturbation studies.

The paper compares functional properties of fetal and adult hematopoietic stem/progenitor cells through transplantation, revealing differences in lineage bias and clonal multi-lineage differentiation.

This study uses cellular barcoding and agent-based modeling to reveal clonal fate patterns in hematopoiesis, showing that stem and progenitor cells are often less multipotent than previously thought.

This study evaluates sample multiplexing reagents and protocols for scRNA-Seq, finding that workflow improvements and reagent choice impact data quality and cost-effectiveness.

The paper develops LoxCode barcoding to trace clonal fate of epiblast cells in vivo, finding lineage biases and tissue-specific contributions across fetal development.

The paper benchmarks scRNA-seq analysis methods using synthetic datasets generated from mixed cancer cell lines, identifying methods that perform well across tasks like normalization, clustering, and integration.

SIS-seq links gene expression with cell fate by analyzing clonal progeny, identifying early gene signatures of dendritic cell subset development.

scPipe provides a flexible R/Bioconductor pipeline for preprocessing scRNA-seq data, handling multiple barcoding strategies and generating quality reports for downstream analysis.

The paper uses cellular barcoding and DiSNE visualization to study hematopoietic fate in primates, identifying novel progenitor clusters with early T cell and later granulocyte production.

The paper assesses clonal kinetics in dendritic cell development and identifies multiple distinct trajectories with intrinsic programming.