Simon C. Watkins

SpaReg reconstructs 3D tissue microenvironments from histology, spatial proteomics, and spatial transcriptomics data, preserving morphology and enabling accurate classification and disease modeling.

This study identifies CD205 as a B cell receptor that facilitates HIV-1 binding and transfer to CD4+ T cells through CD40L/IL-4 stimulation.

This study shows that loss of TFAM in alveolar type 2 cells leads to mitochondrial dysfunction and fibrosis by promoting senescence and a profibrotic secretory program.

This study shows ATR kinase inhibitors cause mitochondrial fission and impair immune memory in CD8+ T cells during viral infection.

This study identifies cited4a as a regulator that suppresses cardiomyocyte dedifferentiation and proliferation during zebrafish heart regeneration.

This study shows that deleting the Envelope gene in SARS-CoV-2 increases cell surface Spike protein and cell-to-cell transmission, reducing neutralizing antibody inhibition.

This study shows that sequential binding of CypA and CPSF6 to HIV-1 capsid is necessary for nuclear entry and integration, and that lenacapavir targets this process.

The paper identifies long-range chromosomal loops spanning over 100 Mb and shows they form via multivalent binding, independent of known nuclear structures, suggesting a distributed mechanism for chromosome organization.

The paper identifies Ribosome-Associated Vesicles (RAVs) as dynamic platforms that facilitate activity-dependent local translation in neurons by transporting ribosomes to distal processes.

Maternal administration of mitochondrial-targeted JP4-039 mitigates fetal brain injury and preserves mitochondrial function after mid-gestation radiation exposure.

The paper introduces iDiscoid, a human stem cell model of post-implantation development that recapitulates key morphogenetic features and offers a platform for studying early human development.

The paper investigates the role of sap130a in zebrafish heart development, showing it regulates SHF cell accretion and maturation, leading to ventricular hypoplasia.

This study identifies a reduction in ER chaperones in PWS β-cells, leading to impaired insulin secretion and ER stress.

The paper uses proximity labeling and mass spectrometry to identify proteins associated with internalized EGFR, revealing TFG's role in endosomal sorting.

The paper develops a live-cell imaging platform to study phenotypic transitions, revealing dynamics missed by snapshot data.

This study evaluates the toxicity of CAG repeat-derived RAN polypeptides in C. elegans, finding that polyLeu is toxic independently of polyQ.

The paper uses evolutionary rate covariation analysis to identify genes coevolving with Drosophila E-cadherin, revealing novel regulators of cell adhesion and actin dynamics.

The paper investigates the role of BDNF transcript variants in altered inhibitory circuitry in depression by analyzing gene expression and behavioral changes in humans and mice.

The paper shows myosin 1d is essential for establishing left-right asymmetry in zebrafish through actin-myosin driven chirality.

The paper develops genetically-encoded reagents for cell-type specific synapse labeling and connectivity analysis in mouse brain tissue, revealing PV inputs as the dominant inhibitory source onto L2 pyramidal neurons.

The paper shows that TGF-β signaling duration is interpreted through pathway crosstalk that controls SNAIL1 expression.

This study shows that targeting the temporal dynamics of microenvironmental factors can halt tumor migration and overcome tumor heterogeneity.