J. Patrick Pett

This paper develops a continual learning framework to map colorectal cancer cell states to causal mechanisms through integration of single-cell data and perturbation experiments.

This study creates a single-cell multiomics atlas of B cell development in prenatal and adult bone marrow and in vitro models, identifying novel cell subsets and molecular signatures.

The paper creates a regulon atlas mapping TF activity across human cell types and uses it to link disease signatures to cell types and TFs, improving disease risk locus analysis.

This study constructs a multiomic atlas of human early skeletal development using single-nuclei transcriptomics, epigenomics, and spatial transcriptomics to uncover regulatory mechanisms and cell states involved in bone and joint formation.

This study develops a multi-omic reference of human cardiac development and identifies disruptions in Trisomy 21 hearts.

RNA sequencing in bronchial biopsies from wheezing infants and children < 2 years shows evidence for an airway epithelial hillock-to-squamous differentiation pathway that marks the development of asthma.

This paper uses spatial transcriptomics and single-cell data to identify cellular niches in the human heart, revealing new insights into cardiac function and potential drug targets.

SODAR is a software package that manages multi-omics study data and metadata using a web interface and APIs, supporting the ISA-Tab format and iRODS storage.

The paper constructs a human fetal lung cell atlas from 5-22 post conception weeks, identifying new cell states and regulators of epithelial fates.

The paper examines circRNA expression in circadian rhythms, finding that Cdr1as shows dynamic expression in the SCN and is linked to light-induced phase shifts.

The paper shows that weak coupling between feedback loops in circadian clocks leads to dissociated gene expression dynamics at the single-cell level.

The paper identifies tissue-specific circadian feedback loops by fitting mathematical models to gene expression data from different mammalian tissues.