scGPT: toward building a foundation model for single-cell multi-omics using generative AI

Haotian Cui, Hassaan Maan, Kuan Pang, +3

Nature Methods

Artificial IntelligenceEngineeringMachine LearningSingle-cell Multi-omicsMedicine +12

scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI

Haotian Cui, Hassaan Maan, Kuan Pang, +2

Artificial IntelligenceLlm Fine-tuningEngineeringMachine LearningGenetics +26

A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

Jalees A. Nasir, Robert Kozak, Patryk Aftanas, +14

Viruses

Viral DiagnosticsGenomicsHigh Throughput SequencingCovid-19Viral Evolution +14

Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses

Arinjay Banerjee, Nader El-Sayes, Patrick Budylowski, +25

iScience

Colony stimulating factor-1 producing endothelial cells and mesenchymal stromal cells maintain monocytes within a perivascular bone marrow niche

Takuo Emoto, Jessie Lu, Tharini Sivasubramaniyam, +22

Immunity

InflammationRegenerative MedicineEndothelial CellsMedicineStem Cell Mobilization +9

DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics

Haotian Cui, Hassaan Maan, Maria Vladoiu, +3

Genome biology

Characterizing the impacts of dataset imbalance on single-cell data integration

Hassaan Maan, Lin Zhang, Chengxin Yu, +3

Nature Biotechnology

Dataset ImbalanceData ModelingEngineeringBiomedical Data IntegrationData Science +11

DeepVelo: Deep Learning extends RNA velocity to multi-lineage systems with cell-specific kinetics

Haotian Cui, Hassaan Maan, Michael D. Taylor, +1

EngineeringTranscriptomics TechnologyGene Regulatory NetworkCell DifferentiationTrajectory Analysis +22

Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease

Michael G. Sugiyama, Haotian Cui, Dar’ya S. Redka, +20

Scientific Reports

Drug TargetEngineeringImmunologyMolecular BiologyHost Cell Proteins +22

Diagnostic performance of 2015 American Thyroid Association guidelines and inter-observer variability in assigning risk category

Zhiyu Pang, M Margolis, Ravi Menezes, +2

European Journal of Radiology Open