Mehrtash Babadi
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View article: STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images Open
Spatial transcriptomics (ST) offers insights into gene expression patterns and their spatial context within the tumor microenvironment, but remains limited by the scalability of current sequencing technologies. Existing approaches infer ST…
View article: Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search
Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search Open
Cell type annotation in single-cell RNA sequencing (scRNA-seq) experiments is the fundamental step of assigning cell types to individual cells or clusters of cells based on their gene expression profiles. This process is crucial for develo…
View article: STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images
STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images Open
Spatial transcriptomics (ST) has shown remarkable promise in pathology applications, shedding light on the spatial organization of gene expression and its relationship to the tumor microenvironment. However, its clinical adoption remains c…
View article: A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients Open
View article: Transcriptional profile of the rat cardiovascular system at single-cell resolution
Transcriptional profile of the rat cardiovascular system at single-cell resolution Open
We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed single-nucleus RNA sequencing (snRNA-seq) in 78 samples in 1…
View article: Robust self-supervised denoising of voltage imaging data using CellMincer
Robust self-supervised denoising of voltage imaging data using CellMincer Open
Voltage imaging is a powerful technique for studying neuronal activity, but its effectiveness is often constrained by low signal-to-noise ratios (SNR). Traditional denoising methods, such as matrix factorization, impose rigid assumptions a…
View article: Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning Open
Image-based cell profiling is a powerful tool that compares perturbed cell populations by measuring thousands of single-cell features and summarizing them into profiles. Typically a sample is represented by averaging across cells, but this…
View article: TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning
TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning Open
Spatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment. Despite technological advancements, computa…
View article: Robust self-supervised denoising of voltage imaging data using CellMincer
Robust self-supervised denoising of voltage imaging data using CellMincer Open
Voltage imaging enables high-throughput investigation of neuronal activity, yet its utility is often constrained by a low signal-to-noise ratio (SNR). Conventional denoising algorithms, such as those based on matrix factorization, impose l…
View article: Modeling interpretable correspondence between cell state and perturbation response with CellCap
Modeling interpretable correspondence between cell state and perturbation response with CellCap Open
Single-cell transcriptomics, in conjunction with genetic and compound perturbations, offers a robust approach for exploring cellular behaviors in diverse contexts. Such experiments allow un-covering cell-state-specific responses to perturb…
View article: Learning representations for image-based profiling of perturbations
Learning representations for image-based profiling of perturbations Open
View article: Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data Open
View article: Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses Open
View article: Transcriptional profile of the rat cardiovascular system at single cell resolution
Transcriptional profile of the rat cardiovascular system at single cell resolution Open
Background Despite the critical role of the cardiovascular system, our understanding of its cellular and transcriptional diversity remains limited. We therefore sought to characterize the cellular composition, phenotypes, molecular pathway…
View article: Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning Open
Image-based cell profiling is a powerful tool that compares perturbed cell populations by measuring thousands of single-cell features and summarizing them into profiles. Typically a sample is represented by averaging across cells, but this…
View article: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data Open
View article: High-throughput RNA isoform sequencing using programmed cDNA concatenation
High-throughput RNA isoform sequencing using programmed cDNA concatenation Open
View article: SynapseCLR: Uncovering features of synapses in primary visual cortex through contrastive representation learning
SynapseCLR: Uncovering features of synapses in primary visual cortex through contrastive representation learning Open
View article: High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection Open
View article: A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients Open
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spati…
View article: GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK Biobank
GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK Biobank Open
SUMMARY Copy number variants (CNVs) are major contributors to genetic diversity and disease. To date, exome sequencing (ES) has been generated for millions of individuals in international biobanks, human disease studies, and clinical diagn…
View article: Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism Open
View article: Learning representations for image-based profiling of perturbations
Learning representations for image-based profiling of perturbations Open
Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient and powerful way of studying cell biology, and requires computational methods for transforming images into quantitative data that highlight pheno…
View article: Uncovering features of synapses in primary visual cortex through contrastive representation learning
Uncovering features of synapses in primary visual cortex through contrastive representation learning Open
SUMMARY 3D EM connectomics image volumes are now surpassing sizes of 1 mm 3 , and are therefore beginning to contain multiple meaningful spatial scales of brain circuitry simultaneously. However, the sheer density of information in such da…
View article: Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness Open
Repeated emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR 0 , a hierarchical Baye…
View article: Rare coding variation illuminates the allelic architecture, risk genes, cellular expression patterns, and phenotypic context of autism
Rare coding variation illuminates the allelic architecture, risk genes, cellular expression patterns, and phenotypic context of autism Open
Individuals with autism spectrum disorder (ASD) or related neurodevelopmental disorders (NDDs) often carry disruptive mutations in genes that are depleted of functional variation in the broader population. We build upon this observation an…
View article: High-throughput RNA isoform sequencing using programmable cDNA concatenation
High-throughput RNA isoform sequencing using programmable cDNA concatenation Open
Alternative splicing is a core biological process that enables profound and essential diversification of gene function. Short-read RNA sequencing approaches fail to resolve RNA isoforms and therefore primarily enable gene expression measur…
View article: Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness Open
Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR 0 , a hierarchical Bayesian multinomial logistic regression model th…
View article: COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets Open
View article: A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 Open
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue…