Caleb A. Lareau

This study identifies host factors and cellular contexts governing anellovirus persistence through genomic, transcriptomic, and functional analyses.

This study shows that HBV BCP mutations enhance viral replication and alter hepatocyte transcription, linking to specific HCC subtypes.

AlphaGenome Atlas predicts regulatory effects of non-coding variants across the human genome, improving their prioritization and interpretation.

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

VIPerturb-seq enables genome-wide CRISPR perturbation screens using probe-based detection, improving throughput and efficiency for single-cell analysis.

GIFT enables high-accuracy genotyping in single cells, revealing mutation-dependent hematopoietic responses in MPN patients.

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 HSV-1 reactivation in healthy brain tissue using petabase-scale sequencing data and links it to neuronal loss in dementia.

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

This study evaluates AI-designed protein binders for CAR T cell therapy, identifying challenges and developing strategies to improve their efficacy and safety.

The paper introduces Cryo-mtscATAC-seq to genotype mitochondrial DNA and trace clones in frozen human tissues, revealing clonal patterns in various diseases.

This study identifies FASLG expression patterns and shows that FAS-L/FAS auto-regulation governs CAR-T and CAR-NK cell persistence, enhancing antitumor efficacy when FAS is inhibited.

The paper uses population-scale whole genome sequencing to identify EBV DNA as a biomarker for respiratory, autoimmune, and cardiovascular diseases and identifies genetic determinants of EBV persistence.

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 paper develops a method to engineer specific mtDNA deletions in human cells using end-joining machinery and targeted endonucleases, revealing a 75% heteroplasmy threshold for mitochondrial dysfunction.

This study identifies a pathogenic subpopulation of glioma-associated macrophages (mGAMs) linked to glioma progression through GRN analysis and functional validation.

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

The paper identifies artifacts in single-cell mtDNA variant calling that mislead phylogenetic inference and warns against using low-evidence variant workflows.

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.

This paper develops FigR, a framework to integrate scATAC-seq and scRNA-seq data to infer gene regulatory networks and identify TF regulators in immune responses.

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

Signac extends Seurat with a ChromatinAssay for single-cell chromatin and multimodal analysis, adds modified TF-IDF weighting, peak-gene linkage and mitochondrial-variant clonotyping, and scales to 733,526 cells.

The paper uses single-cell transcriptomics and epigenomics to analyze immune cell subsets in human tonsils, revealing that autoimmune risk variants have strong regulatory potential in germinal center cells.

The paper introduces SHARE-seq, a method to profile RNA and chromatin in single cells, and identifies DORCs that predict lineage commitment by chromatin accessibility changes.

The paper introduces PHAGE-ATAC, a method for simultaneous single-cell measurement of surface proteins, chromatin accessibility, and mtDNA-based clonal tracing, and demonstrates its application in human immune cells.

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.