Erica A. K. DePasquale

HLiCA: An integrated cell atlas of the healthy human liver

The paper integrates multiple datasets to create a comprehensive human liver cell atlas, identifying new cell types and associations with demographic factors.

MisTIC: Missegmented Transcript Inference Correction for Improved Spatial Transcriptomics Analysis

MisTIC corrects transcript misassignment in spatial transcriptomics data, improving cell type identification, differential expression analysis, and RNA localization.

Co-Stimulatory Blockade Prevents Intragraft Accrual of Class-Switched, Activated B Cells Despite Failing to Prevent T-Cell Mediated Rejection

The paper investigates the effects of co-stimulatory blockade on B cell accrual and T cell subsets during T-cell-mediated renal allograft rejection using single-cell RNA sequencing.

Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution

This study defines the transcriptional landscape of CD8+ T cells in pediatric liver transplant rejection using single-cell sequencing and identifies persistent CD8+ clones associated with graft failure.

Oncogenic Role of Aberrant EZH2 in Hepatoblastoma

This study identifies EZH2 as an oncogenic driver in hepatoblastoma, showing its role in promoting tumor progression through epigenetic silencing and noncanonical signaling, and highlights its potential as a therapeutic target.

Translation Initiation Represents an Acute Myeloid Leukemia Cell Vulnerability That Can Be Co-Targeted With BCL-2 Inhibition

The paper identifies EIF4A1 as a vulnerability in AML cells and shows that combining Zotatifin with Venetoclax enhances apoptosis and survival in AML models.

Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations

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

KRSA: Network-based Prediction of Differential Kinase Activity from Kinome Array Data

KRSA predicts differential kinase activity from kinome array data by analyzing phosphorylation differences and comparing results to gene expression databases.

Identification and Removal of Doublets with DoubletDecon

DoubletDecon identifies and removes doublets from scRNA-seq data using deconvolution and gene expression analysis.

Transcriptional profile of pyramidal neurons in chronic schizophrenia reveals lamina-specific dysfunction of neuronal immunity

The paper identifies lamina-specific gene expression changes in pyramidal neurons from schizophrenia patients compared to controls, highlighting immune and synaptic pathway disruptions.

DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets

DoubletDecon identifies and removes doublets in scRNA-Seq data using deconvolution and cell-state gene expression analysis, improving cell state delineation.

cellHarmony: Cell-level matching and holistic comparison of single-cell transcriptomes

cellHarmony matches and compares single-cell transcriptomes to identify disease-specific gene regulatory programs and cell-state changes.

Connectivity analyses of bioenergetic changes in schizophrenia: Identification of novel treatments

The paper identifies PPAR agonists as potential treatments for schizophrenia by analyzing bioenergetic changes in the DLPFC using bioinformatics and experimental validation.