COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Toni Delorey, Carly G.K. Ziegler, Graham Heimberg, +105

Nature

Covid-19 Tissue AtlasesCovid-19 PandemicPathologyVirologyCovid-19 Epidemiology +2

Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions

Michael R. Filbin, Arnav Mehta, Alexis M. Schneider, +40

Cell Reports Medicine

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

Christoph Muus, Malte D. Luecken, Gökcen Eraslan, +98

Inflammatory Lung DiseaseLung InflammationImmunologyViral PathogenesisPathology +14

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

Graham Heimberg, Rajat Bhatnagar, Hana El‐Samad, +1

Cell Systems

A cell atlas foundation model for scalable search of similar human cells

Graham Heimberg, Tony Kuo, Daryle J. DePianto, +11

Nature

BiologyBioinformaticsHuman CellEngineeringCell Division +11

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

Cameron Sokolik, Yanxia Liu, David Bauer, +6

Cell Systems

Authentic SignalsCell LineageEmbryonic Stem CellDevelopmental BiologyMedicine +7

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

Weiyue Ji, Derrick Lee, Eric B. Wong, +15

ACS Synthetic Biology

Systems BiologyEngineeringEngineered Crispr InterferenceCrispri SystemMolecular Biology +12

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients

Michael R. Filbin, Arnav Mehta, Alexis M. Schneider, +40

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Toni Delorey, Carly G.K. Ziegler, Graham Heimberg, +98

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

Graham Heimberg, Tony Kuo, Daryle J. DePianto, +11

EngineeringPathologyTranscriptomics TechnologyAbstract Single-cell Rna-seqMetric Learning Framework +28