Sidhartha Goyal

From shielding effect to hierarchical structures: a coarse-grained description of diversity

The paper extends a trade-off-based model to explain microbial diversity by incorporating multiple resources and distinct trade-offs for different taxa, predicting functional clustering and high diversity within low-diversity communities.

Dynamic Regulation of the Immune Repertoire of Bacteria

This study investigates the optimal CRISPR memory size in bacteria by combining immune models with dynamical antigenic traveling wave theory, finding that optimal array length depends on acquisition dynamics and population pressures.

Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity.

This study creates a single-cell atlas of human fetal lung development, revealing epithelial cell plasticity and lineage hierarchies through scRNA-seq and spatial transcriptomics.

Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics

This paper introduces LatentVelo, a method that improves trajectory inference in single-cell RNA-seq by modeling gene dynamics with neural ODEs and a variational autoencoder, enabling lineage-specific dynamics and batch correction.

petiteFinder: An automated computer vision tool to compute Petite colony frequencies in baker's yeast

petiteFinder is a deep learning tool that automates Petite colony frequency calculation in baker's yeast by analyzing images of Petri dishes.

Fluctuations and entropy enable neural crest cell ingression

The paper shows that stochastic fluctuations and entropy, not stiffness gradients, drive neural crest cell ingression in mice.

Inferring metabolic rewiring in embryonic neural development using single cell data

This paper introduces scMetNet, a method to analyze metabolic rewiring in single-cell data, applied to murine embryonic neural development to identify key metabolic pathways and sub-networks involved in stem cell differentiation.

Oscillatory cortical forces promote three dimensional cell intercalations that shape the mandibular arch

The paper shows that oscillatory cortical forces drive 3D cell intercalations in the mouse mandibular arch, shaping embryonic structures through Wnt5a, YAP/TAZ, and PIEZO1.