Tara Chari
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View article: Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes Open
The increasing use of high-throughput sequencing methods in research, agriculture and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus-disease correlation. However, existi…
View article: Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data Open
Here we present biVI, which combines the variational autoencoder framework of scVI with biophysical models describing the transcription and splicing kinetics of RNA molecules. We demonstrate on simulated and experimental single-cell RNA se…
View article: Stochastic Modeling of Biophysical Responses to Perturbation
Stochastic Modeling of Biophysical Responses to Perturbation Open
Recent advances in high-throughput, multi-condition experiments allow for genome-wide investigation of how perturbations affect transcription and translation in the cell across multiple biological entities or modalities, from chromatin and…
View article: biVI supporting data
biVI supporting data Open
Simulated and experimental single cell RNA sequencing datasets analyzed to benchmark biVI and illustrate biVI's ability to infer biophysical parameters are included in data.zip. All data files are described in README_data.md. Parameter inf…
View article: biVI supporting data
biVI supporting data Open
Simulated and experimental single cell RNA sequencing datasets analyzed to benchmark biVI and illustrate biVI's ability to infer biophysical parameters are included in data.zip. All data files are described in README_data.md. Parameter inf…
View article: Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression
Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression Open
There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain and often remain undetected. Efficient and accurate detection of viral infe…
View article: Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data
Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data Open
Multimodal, single-cell genomics technologies enable simultaneous capture of multiple facets of DNA and RNA processing in the cell. This creates opportunities for transcriptome-wide, mechanistic studies of cellular processing in heterogene…
View article: The specious art of single-cell genomics
The specious art of single-cell genomics Open
Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with reduction to 2 or 3 dimensions to produce “all-…
View article: Characterization of spatial homogeneous regions in tissues with concordex
Characterization of spatial homogeneous regions in tissues with concordex Open
The rapid advancement of spatially resolved transcriptomics (SRT) technologies has facilitated exploration of how gene expression varies across tissues. However, identifying spatially variable genes remains challenging due to confounding v…
View article: Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data Open
We motivate and present biVI , which combines the variational autoencoder framework of scVI with biophysically motivated, bivariate models for nascent and mature RNA distributions. While previous approaches to integrate bimodal data via th…
View article: RNA velocity unraveled
RNA velocity unraveled Open
We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying…
View article: Spectral neural approximations for models of transcriptional dynamics
Spectral neural approximations for models of transcriptional dynamics Open
The advent of high-throughput transcriptomics provides an opportunity to advance mechanistic understanding of transcriptional processes and their connections to cellular function at an un-precedented, genome-wide scale. These transcription…
View article: RNA velocity unraveled
RNA velocity unraveled Open
We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying…
View article: Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across <i>Clytia</i> medusa cell types
Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across <i>Clytia</i> medusa cell types Open
Whole-organism perturbations reveal single-cell responses across the Clytia medusa.
View article: The Specious Art of Single-Cell Genomics
The Specious Art of Single-Cell Genomics Open
Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with reduction to two or three dimensions to produce…
View article: The Split Senate
The Split Senate Open
The theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylogenetic trees, are widely used in evolut…
View article: The Split Senate
The Split Senate Open
The theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylogenetic trees, are widely used in evolut…
View article: Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of<i>Clytia</i>Medusa Cell Types
Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of<i>Clytia</i>Medusa Cell Types Open
We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica , and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were index…
View article: The Split Senate
The Split Senate Open
The theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylogenetic trees, are widely used in evolut…
View article: The Split Senate
The Split Senate Open
The theory of split systems provides a mathematical formalism for understanding and visualizing collections of partitions of sets into two parts. In particular, split networks, which generalize phylogenetic trees, are widely used in evolut…