Tara Chari

Characterization of spatial homogeneous regions in tissues with concordex

This paper introduces concordex, a method to identify spatially homogeneous regions in tissues by decomposing gene expression patterns into cell-type and spatial variation, demonstrating its effectiveness across datasets.

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

The paper detects viral sequences in single-cell data to identify novel viruses affecting host gene expression in rhesus macaques.

Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data

The paper introduces meK-Means, a method for clustering cells from multimodal sequencing data by integrating biophysical models of transcription to identify shared cellular states.

Stochastic Modeling of Biophysical Responses to Perturbation

This paper uses stochastic biophysical modeling to analyze perturbation data and uncover transcriptional dynamics and kinetic responses in cells.

3D genome organization around nuclear speckles drives mRNA splicing efficiency

The paper shows that gene proximity to nuclear speckles increases spliceosome binding and co-transcriptional splicing efficiency, highlighting the role of 3D genome organization in mRNA splicing.

Spectral neural approximations for models of transcriptional dynamics

This paper introduces neural network approximations for solving steady-state distributions in multi-species transcriptional models, enabling efficient inference of biophysical parameters from transcriptomic data.

The Specious Art of Single-Cell Genomics

The paper critiques the use of extreme dimension reduction in single-cell genomics and proposes alternative approaches for more effective biological analysis.

Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data

The paper introduces Monod, a Python package that integrates single-cell RNA sequencing data using biophysical models of transcription to distinguish biological and technical variation and reveal regulatory processes.

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types

The paper presents a whole-animal transcriptomic cell atlas of Clytia hemisphaerica using multiplexed scRNA-seq to study cell type plasticity under starvation.