Pavak Kirit Shah

Variation in the embryonic cell lineages of Caenorhabditis elegans natural populations

The paper quantifies developmental variation in C. elegans natural populations using embGAN, finding genotype-specific differences in cell-cycle timing that exceed within-strain variation.

Mitochondria transported by Kinesin 3 prevent localized calcium spiking to inhibit caspase-dependent specialized cell death

The paper investigates the role of mitochondrial transport by kinesin motors in preventing localized calcium spiking and caspase-dependent cell death during specialized elimination in C. elegans neurons.

Computational method for mapping mass signatures along developmental gradients reveals a novel role for a monosaccharide tetrose in maize salt-stress response.

The paper develops DIMPLE, a computational method to analyze metabolite patterns along developmental gradients in maize roots, revealing D-erythrose's role in salt-stress response.

Long-term ex ovo culture of Caenorhabditis elegans embryos

This paper develops a method to culture C. elegans embryos ex ovo, enabling long-term exposure to small molecules for studying developmental processes.

Notch-dependent left-right asymmetry in β-catenin-TCF activity instructs anteroposterior positioning of motor neurons in the C. elegans ventral nerve cord

Automated Cell Lineage Reconstruction using Label-Free 4D Microscopy

This paper introduces embGAN, a deep learning pipeline for automated cell detection and tracking in label-free 3D time-lapse imaging without manual annotation.

IPPK-1 and IP6 contribute to ventral nerve cord assembly in C. elegans

This study shows that IPPK-1 and IP6 are critical for ventral nerve cord assembly in C. elegans, with IP6 rescue of mutant defects.

Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development

This paper introduces a new metric called branch distance to analyze developmental phenotypes in C. elegans embryos, revealing previously unnoticed heterogeneity and links between cell fate and cell cycle pathways.