Graham Heimberg
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View article: Inferring cellular communication through mapping cells in space using Tangram 2
Inferring cellular communication through mapping cells in space using Tangram 2 Open
Cell-to-cell communication (CCC) shapes development, immunity, and disease, yet current spatial transcriptomics (SRT) platforms rarely achieve both single-cell resolution and high-quality transcriptome-wide coverage to accurately character…
View article: Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases
Foundation Model Attributions Reveal Shared Inflammatory Program Across Diseases Open
Determining a gene’s functional significance within a specific cellular context has long been a challenge. We introduce a framework for quantifying gene importance by leveraging attributions learned by foundation models (FMs) trained on la…
View article: A cell atlas foundation model for scalable search of similar human cells
A cell atlas foundation model for scalable search of similar human cells Open
View article: Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states Open
Single-cell RNA-seq (scRNA-seq) has become a prominent tool for studying human biology and disease. The availability of massive scRNA-seq datasets and advanced machine learning techniques has recently driven the development of single-cell …
View article: SCimilarity Tutorial Data
SCimilarity Tutorial Data Open
SCimilarity is a unifying representation of single-cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. This enables a novel cell search capabil…
View article: Identification of markers for the isolation of neuron-specific extracellular vesicles
Identification of markers for the isolation of neuron-specific extracellular vesicles Open
Extracellular vesicles (EVs) are released by all cells and contain RNA and protein from their cell of origin. EVs in biofluids could be used as diagnostic biomarkers to non-invasively report the state of inaccessible cells, such as neurons…
View article: SCimilarity Models
SCimilarity Models Open
SCimilarity is a unifying representation of single-cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. This enables a novel cell search capabil…
View article: SCimilarity Models
SCimilarity Models Open
SCimilarity is a unifying representation of single-cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. This enables a novel cell search capabil…
View article: SCimilarity Models
SCimilarity Models Open
SCimilarity is a unifying representation of single-cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. This enables a novel cell search capabil…
View article: SCimilarity Tutorial Data
SCimilarity Tutorial Data Open
SCimilarity is a unifying representation of single-cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. This enables a novel cell search capabil…
View article: Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages
Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages Open
Single-cell RNA-seq (scRNA-seq) studies have profiled over 100 million human cells across diseases, developmental stages, and perturbations to date. A singular view of this vast and growing expression landscape could help reveal novel asso…
View article: Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions
Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions Open
View article: Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions
Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions Open
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: Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics Open
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact a…
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…
View article: Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients
Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients Open
Summary COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls …
View article: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Open
The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2…
View article: Statistical inference of a single cell gene expression model for heterogeneous tissues
Statistical inference of a single cell gene expression model for heterogeneous tissues Open
Biological tissues are made up of many individual cells that perform different tasks in concert to carry out sophisticated and essential processes. Knowing the behavior of each cellular subpopulation in a tissue can therefore provide funda…
View article: Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing
Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing Open
View article: Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise
Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise Open