Brooke E. Howitt

Mouse lymph node colonization models predict human tumor metastasis in melanoma

The paper integrates mouse lymph node tumor data with human melanoma tumors to identify transcriptional programs and ecotypes associated with metastasis.

Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing

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

Clonal lineage tracing of innate immune cells in human cancer

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.

Enriched Methylomes of Low-input and Fragmented DNA Using Fragment Ligation EXclusive Methylation Sequencing (FLEXseq)

The paper introduces FLEXseq, a methylation sequencing method that enriches and sequences DNA fragments flanking the CCGG motif, showing strong correlation with WGBS and potential for diagnostic applications.

scAmp analyzes focal gene amplifications at single-cell resolution

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

Ptpn14 Knockout Mice Reveal Critical Female-Specific Roles for the Hippo Pathway

This study shows that Ptpn14 deficiency in mice causes female-specific Hippo pathway defects, including corneal lesions, uterine defects, and organ abnormalities, with conserved roles in humans.

Deep learning uncovers histological patterns of YAP1/TEAD activity related to disease aggressiveness in cancer patients.

This study uses deep learning to predict YAP1/TEAD activity from histology slides, linking histological patterns to disease aggressiveness in cancer patients.

Same-Slide Spatial Multi-Omics Integration Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment

This paper introduces IN-DEPTH and SGCC for spatial multi-omics analysis, revealing EBV-related immunomodulatory differences in DLBCL.

CRISPRa screening with real world evidence identifies potassium channels as neuronal entry factors and druggable targets for SARS-CoV-2

The paper uses CRISPRa screening and real-world data to identify KCNA6 as a neuronal entry factor for SARS-CoV-2 and shows dalfampridine can suppress viral entry.