Shikhar Uttam

Overcoming segmentation bottlenecks in brain tissue for spatial proteomic inference at population scale

The paper introduces SPInfer, a workflow for spatial proteomic inference that improves cell segmentation in human brain tissue, enabling better biological discovery at population scale.

SpaReg: sparsity-based 3D reconstruction of tissue microenvironments at native resolution across morphological and spatial molecular modalities

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

Microplastics inhibit macrophage bioenergetics impairing homeostatic function and immune responsiveness

This study shows that microplastics impair macrophage bioenergetics and immune function, reducing antigen presentation and increasing disease susceptibility.

MitoChontrol: Adaptive mitochondrial filtering for robust single-cell RNA sequencing quality control

MitoChontrol improves single-cell RNA sequencing quality control by using a probabilistic framework to filter out compromised cells while preserving biologically relevant mitochondrial content.

Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV

This study develops a quantitative model to show that antigenic stimulation and clonal heterogeneity shape the persistence of the HIV-1 latent reservoir.

Local Mean Suppression Filter for Effective Background Identification in Fluorescence Images

The paper introduces a nonlinear filter for background identification in fluorescence images and shows it performs well compared to existing methods.

UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples

UNSEG provides an unsupervised method for segmenting cells and their nuclei in complex tissue samples without training data, outperforming deep learning methods in generalization and consistency.