Peter A. Sims

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

The paper uses single-nuclei RNA sequencing to analyze intracranial thrombi, identifying distinct cell populations and transcriptional changes, and inferring ligand-receptor interactions relevant to stroke.

This study identifies 36 genetic loci associated with recurrent UTIs and highlights PSCA as a key gene involved in urinary epithelial defense against bacteria.

The paper identifies programmed clonal expansion during V(D)J recombination as an ATM-dependent vulnerability causing preferential lymphocyte depletion and myeloid bias after DNA damage.

This study identifies the MAPK/ERK pathway as a key regulator of glioma susceptibility to immune checkpoint blockade, showing it modulates interferon responses, T cell recruitment, and tumor-microglia interactions.

This study shows that IDH1-mutant glioma cells are more sensitive to cysteine-methionine deprivation and ferroptosis inducers, and that IDH inhibitors enhance this sensitivity.

This study identifies TMPO as a driver of CTC heterogeneity and metastasis in prostate cancer by enhancing survival under metabolic stress.

This study identifies tissue-specific transcriptional and protein profiles of human macrophages in various organs during homeostasis and activation, showing homology to mouse macrophages and responsiveness to cytokine stimuli.

This paper evaluates convection-enhanced delivery of dexamethasone in glioma models, showing reduced systemic toxicity and suppressed myeloid inflammation.

The paper analyzes T-cell responses and glial pathology in Parkinson's disease substantia nigra using single nucleus RNA sequencing and spatial transcriptomics, revealing CD8+ T-cell characteristics and altered cellular interactions.

The paper identifies microglia subsets in ALS brain and spinal cord, finding an undifferentiated phenotype and enrichment of interferon response microglia in aggressive cases.

ADTnorm normalizes and integrates CITE-seq datasets to remove batch effects and improve cell-type separation across 13 public datasets.

The paper uses single-cell data to identify factors regulating an Alzheimer's disease-related microglial signature and proposes a new analytic framework for microglial classification.

The paper develops ConnectionMiner to integrate scRNAseq and connectome data, revealing gene expression patterns linked to synaptic connectivity in Drosophila leg motor circuits.

This study investigates how mTOR inhibition reverses glioma-induced changes in excitatory neurons, showing effects on mRNA, dendritic spines, and neuronal activity.

This paper introduces DEFND-seq, a method for jointly profiling DNA and RNA from individual nuclei, enabling analysis of gene expression with copy number and SNV associations.

This study compares transcriptional profiles of memory T cells in infants and adults to identify age-specific regulatory mechanisms.

This paper introduces MMoCHi, a multimodal classifier for CITE-seq data that improves immune cell subset annotation by integrating transcriptomic and proteomic data.

This study identifies STAT3 as a key driver of resistance to spindle inhibitors in glioblastoma, showing that therapy-induced senescence contributes to drug resistance by promoting quiescence and secreting factors that induce quiescence in proliferating cells.

The paper uses HDAC inhibitors to mimic human DAM in vitro and identifies shared marker genes.

The paper identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer's disease by characterizing their effects on human microglial subtypes in vitro and in a zebrafish model.

The paper introduces consensus scHPF, a method to identify robust gene signatures from scRNA-seq data, and applies it to discover cell type-specific drug responses in glioma.

The paper identifies treatment-resistant Cancer Stem-Like Cells in breast cancer using single-cell RNA sequencing and validates a drug combination to target them effectively.

The paper shows IFN-γ induces MHC-I expression in ventral midbrain neurons and glia, but with lower amplitude in neurons, and MHC-II is restricted to microglia.

The paper validates an RNA-based platform for predicting drug sensitivity in treatment-resistant cancers using patient-derived xenograft models and multi-protein therapies.

This study identifies disease-enriched microglial subsets and validates compounds that modulate their states using single-cell RNA sequencing and in vitro experiments.

This study introduces riboPLATE-seq, a method for generating paired libraries of ribosome-associated and total mRNA, and demonstrates its use in detecting translational changes caused by kinase inhibitors.

The paper uses subcellular proteomics to show Parkinson's disease-linked genes are enriched in axons of dopaminergic neurons in the mouse brain.

The paper investigates mRNA localization and translation in midbrain dopaminergic neurons, finding no axonal localization but dendritic ribosomes and mRNAs related to dopamine synthesis and release.

SCOPE-seq2 integrates single-cell imaging and RNA-seq with improved throughput and accuracy for analyzing human glioblastoma cells.