Jarny Choi

Frataxin deficiency drives cardiac dysfunction and transcriptional dysregulation in Friedreich ataxia iPSC model

Jarmon G. Lees, Haoxiang Zhang, Anne M. Kong, Ren Jie Phang et autres

Friedreich ataxia (FRDA) is a progressive neuromuscular degenerative disorder caused by GAA repeat expansions in the FXN gene, leading to frataxin deficiency and multisystem pathology. Cardiomyopathy is the leading cause of mortality in individuals with FRDA. To investigate the cellular and molecular …

au, us, sg (code pays fourni par la source)

Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies

Jiadong Mao, Jarny Choi, Kim‐Anh Lê Cao

We introduce Φ-Space ST, a platform-agnostic method to identify continuous cell states in spatial transcriptomics (ST) data using multiple scRNA-seq references. For ST with supercellular resolution, Φ-Space ST achieves interpretable cell-type deconvolution with significantly faster computation. For subcellular resolution, Φ-Space ST annotates …

au (code pays fourni par la source)

Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies

Jiadong Mao, Jarny Choi, KIM-ANH LE CAO

Frataxin deficiency drives cardiac dysfunction and transcriptional dysregulation in Friedreich ataxia iPSC model

Jarmon G. Lees, Haoxiang Zhang, Lebei Jiao, Anne M. Kong et autres

Abstract Friedreich ataxia (FRDA) is a progressive neuromuscular degenerative disorder caused by GAA repeat expansions in the FXN gene, leading to frataxin deficiency and multisystem pathology. Cardiomyopathy is the leading cause of mortality in individuals with FRDA. To investigate the cellular and …

PhiSpace ST: a platform-agnostic method to identify cell states in spatial transcriptomics studies

Jiadong Mao, Jarny Choi, Kim-Anh Lê Cao

We introduce PhiSpace ST, a platform-agnostic method to identify continuous cell states in spatial transcriptomics (ST) data using multiple scRNA-seq references. For ST with supercellular resolution, PhiSpace ST achieves interpretable cell type deconvolution with significantly faster computation. For subcellular resolution, PhiSpace ST …

au (code pays fourni par la source)

PhiSpace ST: a platform-agnostic method to identify cell states in spatial transcriptomics studies

Jiadong Mao, Jarny Choi, Kim-Anh Lê Cao

We introduce PhiSpace ST, a platform-agnostic method to identify continuous cell states in spatial transcriptomics (ST) data using multiple scRNA-seq references. For ST with supercellular resolution, PhiSpace ST achieves interpretable cell type deconvolution with significantly faster computation. For subcellular resolution, PhiSpace ST …

au (code pays fourni par la source)

Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet

Yidi Deng, Jiadong Mao, Jarny Choi, KIM-ANH LE CAO

Gene networks provide a fundamental framework for understanding the molecular mechanisms that govern gene expression. Advances in single-cell RNA sequencing (scRNA-seq) have enabled network inference at cellular resolution; however, most existing approaches rely on predefined clusters or cell states, implicitly assuming static …

au (code pays fourni par la source)

NeighbourNet: Scalable cell-specific co-expression networks for granular regulatory pattern discovery

Yidi Deng, Jiadong Mao, Jarny Choi, Kim‐Anh Lê Cao

Abstract Gene regulatory networks (GRNs) provide a fundamental framework for understanding the molecular mechanisms that govern gene expression. Advances in single-cell RNA sequencing (scRNA-seq) have enabled GRN inference at cellular resolution; however, most existing approaches rely on predefined clusters or cell states, …

au (code pays fourni par la source)

StableMate: a statistical method to select stable predictors in omics data

Yidi Deng, Jiadong Mao, Jarny Choi, Kim‐Anh Lê Cao

Identifying statistical associations between biological variables is crucial to understanding molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, making …

au (code pays fourni par la source)

Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells

Jarny Choi, Suzanne Butcher, Paul W. Angel, Jack Bransfield et autres

Stemformatics.org has been serving the stem cell research community for over a decade, by making it easy for users to find and view transcriptional profiles of pluripotent and adult stem cells and their progeny, comparing data derived from multiple tissues and derivation …

au (code pays fourni par la source)

IsoVis – a webserver for visualization and annotation of alternative RNA isoforms

Ching Yin Wan, J. Davis, Manveer Chauhan, Josie Gleeson et autres

Genes commonly express multiple RNA products (RNA isoforms), which differ in exonic content and can have different functions. Making sense of the plethora of known and novel RNA isoforms being identified by transcriptomic approaches requires a user-friendly way to visualize gene isoforms …

au (code pays fourni par la source)

StableMate: a statistical method to select stable predictors in omics data

Yidi Deng, Jiadong Mao, Jarny Choi, Kim‐Anh Lê Cao

Abstract Identifying statistical associations between biological variables is crucial to understand molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, …

au (code pays fourni par la source)