ArticleNature biotechnology2022
Multiscale PHATE identifies multimodal signatures of COVID-19.
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Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38citing papers in PubMed
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38 citing papers in PubMed.
- Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.Experimental & molecular medicine · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- CellPhenoX: An Explainable Machine Learning Method for Identifying Cell Phenotypes To Predict Clinical Outcomes from Single-Cell Multi-Omics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Connecting chemical structure to single cell signaling profiles.Communications biology · 2025Article
- Conserved noncoding cis elements associated with hibernation modulate metabolic and behavioral adaptations in mice.Science (New York, N.Y.) · 2025Article
- Joint representation and visualization of derailed cell states with Decipher.Genome biology · 2025Article
- Applying multimodal AI to physiological waveforms improves genetic prediction of cardiovascular traits.American journal of human genetics · 2025Article
- Biases in machine-learning models of human single-cell data.Nature cell biology · 2025Review
- Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.Nature biotechnology · 2025Article
- Diffusive topology preserving manifold distances for single-cell data analysis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Detecting global and local hierarchical structures in cell-cell communication using CrossChat.Nature communications · 2024Article
- Mapping the gene space at single-cell resolution with gene signal pattern analysis.Nature computational science · 2024Article
- QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics.Briefings in bioinformatics · 2024Article
- Single-cell spatial transcriptomics in cardiovascular development, disease, and medicine.Genes & diseases · 2024Review
- Multi-omic analysis of Huntington's disease reveals a compensatory astrocyte state.Nature communications · 2024Article
- Building and analyzing metacells in single-cell genomics data.Molecular systems biology · 2024Review
- Geometric Scattering on Measure Spaces.Applied and computational harmonic analysis · 2024Article
- Archetype analysis and the PHATE algorithm as methods to describe and visualize pregnant women's levels of physical activity knowledge.BMC public health · 2024Article
- Utilizing multimodal AI to improve genetic analyses of cardiovascular traits.medRxiv : the preprint server for health sciences · 2024Article
- Toward the novel AI tasks in infection biology.mSphere · 2024Review
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Authors and funding
31 authors.
Manik Kuchroo *Department of Neuroscience, Yale University, New Haven, CT, USA.
Jessie Huang *Department of Computer Science, Yale University, New Haven, CT, USA.
Patrick Wong *Department of Immunobiology, Yale University, New Haven, CT, USA.
Jean-Christophe GrenierMontreal Heart Institute, Montreal, Quebec, Canada.
Dennis ShungDepartment of Medicine, Yale University, New Haven, CT, USA.
Alexander TongDepartment of Computer Science, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-2031-4096
Carolina LucasDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-4590-2756
Jon KleinDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-3552-7684
Daniel B BurkhardtDepartment of Genetics, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7744-1363
Scott GiganteComputational Biology, Bioinformatics Program, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-4544-2764
Abhinav GodavarthiDepartment of Applied Mathematics, Yale University, New Haven, CT, USA.
Bastian RieckDepartment of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.ORCID http://orcid.org/0000-0003-4335-0302
Benjamin IsraelowDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-1308-8246
Michael SimonovDepartment of Medicine, Yale University, New Haven, CT, USA.
Tianyang MaoDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-9251-8592
Ji Eun OhDepartment of Immunobiology, Yale University, New Haven, CT, USA.
Julio SilvaDepartment of Immunobiology, Yale University, New Haven, CT, USA.
Takehiro TakahashiDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-1061-356X
Camila D OdioDepartment of Medicine, Yale University, New Haven, CT, USA.
Arnau Casanovas-MassanaDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
John FournierSection of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
Yale IMPACT Team
Shelli FarhadianSection of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7230-1409
Charles S Dela CruzSection of Pulmonary and Critical Care Medicine, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
Albert I KoSection of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-9023-2339
Matthew J HirnDepartment of Mathematics, Michigan State University, East Lansing, MI, USA.ORCID http://orcid.org/0000-0003-0290-4292
F Perry WilsonClinical and Translational Research Accelerator, Department of Medicine, Yale University, New Haven, CT, USA.
Julie G HussinMontreal Heart Institute, Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0003-4295-3339
Guy WolfMila - Quebec AI institute, Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0002-6740-059X
Akiko IwasakiDepartment of Immunobiology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-7824-9856
Smita KrishnaswamyDepartment of Computer Science, Yale University, New Haven, CT, USA. smita.krishnaswamy@yale.edu.ORCID http://orcid.org/0000-0001-5823-1985
Funding
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MSystems investigation of vaccine responses in B cell depleted autoimmune patientsU19AI089992 · NIAID · YALE UNIVERSITY · PI Steven H. Kleinstein · 2010 to 2026
$50.4MRenal Physiology and Phenotyping CoreP30DK079310 · NIDDK · YALE UNIVERSITY · PI ARONSON, PETER S. · 2008 to 2022
$16.8MTRAINING IN THE PATHOGENESIS OF INFECTIOUS DISEASEST32AI007517 · NIAID · YALE UNIVERSITY · PI Jaimie Meyer, Albert C Shaw · 1997 to 2026
$6.1MViral and immune-mediated CNS pathology during SARS-CoV-2 infectionR01AI157488 · NIAID · YALE UNIVERSITY · PI FARHADIAN, SHELLI, IWASAKI, AKIKO · 2020 to 2024
$4.7MOptimizing Electronic Alerts for Acute Kidney InjuryR01DK113191 · NIDDK · YALE UNIVERSITY · PI WILSON, FRANCIS PERRY · 2018 to 2022
$3.1MDeciphering the regulatory code that specifies different cell fates in development using single cell genomicsR01HD100035 · NICHD · YALE UNIVERSITY · PI GIRALDEZ, ANTONIO J, KRISHNASWAMY, SMITA · 2020 to 2024
$2.8MDeciphering Genetic and Epigenetic Regulatory Logic of Germ Layer Differentiation with Manifold LearningR01GM130847 · NIGMS · YALE UNIVERSITY · PI KRISHNASWAMY, SMITA · 2019 to 2023
$2.0MPersonalized Recommendations for Acute Kidney Injury (AKI) Care Using a Kidney Action Team: A Randomized TrialR01HS027626 · AHRQ · YALE UNIVERSITY · PI WILSON, FRANCIS PERRY · 2021 to 2025
$1.9MFinding emergent structure in multi-sample biological data with the dual geometry of cells and features R01GM135929 · NIGMS · MICHIGAN STATE UNIVERSITY · PI BROWN, EDWARD · 2019 to 2022
$1.4MDeep Learning Approaches to Risk Stratification in Acute Gastrointestinal BleedingK23DK125718 · NIDDK · YALE UNIVERSITY · PI SHUNG, DENNIS · 2021 to 2025
$969kUnderstanding the cellular basis for persistent immune activation in the central nervous system during virologically suppressed HIVK23MH118999 · NIMH · YALE UNIVERSITY · PI FARHADIAN, SHELLI · 2018 to 2021
$770kAHRQ HHS R01 HS027626Howard Hughes Medical InstituteNCATS NIH HHS UL1 TR001863NIAID NIH HHS F30 AI157270NIAID NIH HHS R01 AI157488NIAID NIH HHS T32 AI007517NIAID NIH HHS U19 AI089992NICHD NIH HHS R01 HD100035NIDDK NIH HHS K23 DK125718NIDDK NIH HHS P30 DK079310NIDDK NIH HHS R01 DK113191NIGMS NIH HHS R01 GM130847NIGMS NIH HHS R01 GM135929NIMH NIH HHS K23 MH118999
Abstract
As the biomedical community produces datasets that are increasingly complex and high dimensional, there is a need for more sophisticated computational tools to extract biological insights. We present Multiscale PHATE, a method that sweeps through all levels of data granularity to learn abstracted biological features directly predictive of disease outcome. Built on a coarse-graining process called diffusion condensation, Multiscale PHATE learns a data topology that can be analyzed at coarse resolutions for high-level summarizations of data and at fine resolutions for detailed representations of subsets. We apply Multiscale PHATE to a coronavirus disease 2019 (COVID-19) dataset with 54 million cells from 168 hospitalized patients and find that patients who die show CD16
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COVID-19Single-Cell AnalysisChromatinExome SequencingHumansTransposasesChromatinTransposases
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