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Ramlall V, Gisladottir U, Kefeli J, Tanaka Y, May B, Tatonetti N. Using machine learning probabilities to identify effects of COVID-19. Patterns (N Y) 2023; 4:100889. [PMID: 38106616 PMCID: PMC10724367 DOI: 10.1016/j.patter.2023.100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has had extensive economic, social, and public health impacts in the United States and around the world. To date, there have been more than 600 million reported infections worldwide with more than 6 million reported deaths. Retrospective analysis, which identified comorbidities, risk factors, and treatments, has underpinned the response. As the situation transitions to an endemic, retrospective analyses using electronic health records will be important to identify the long-term effects of COVID-19. However, these analyses can be complicated by incomplete records, which makes it difficult to differentiate visits where the patient had COVID-19. To address this issue, we trained a random Forest classifier to assign a probability of a patient having been diagnosed with COVID-19 during each visit. Using these probabilities, we found that higher COVID-19 probabilities were associated with a future diagnosis of myocardial infarction, urinary tract infection, acute renal failure, and type 2 diabetes.
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Affiliation(s)
- Vijendra Ramlall
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jenna Kefeli
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yutaro Tanaka
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Applied Physics and Applied Mathematics, Fu Foundation School of Engineering and Applied Sciences, Columbia University, New York, NY 10027, USA
| | - Benjamin May
- Herbert Irving Comprehensive Cancer Center, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90069, USA
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4
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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5
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Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv 2020:2020.04.20.048066. [PMID: 32511352 PMCID: PMC7255793 DOI: 10.1101/2020.04.20.048066] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
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Affiliation(s)
- Daniel J. Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
| | - Joel Rosiene
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Alon Shaiber
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A. Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, NY, USA
| | - Craig D. Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
| | | | - Amos J. Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | | | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Stacy M. Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, NC, USA
- Department of Medicine, Duke University Medical Center, NC, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Mirella Salvatore
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Marcin Imielinski
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY, USA
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