المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/journal_contribution/Technical_description_of_the_platform_capabilities_and_their_implementation_/14983297

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.s002

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Overview_of_the_COVIDomic_platform_/14983300

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g001

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Schematic_representation_of_the_workflow_of_the_platform_with_its_four_components_/14983294

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.s001

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Metatranscriptome_analysis_for_COVID-19_patients_/14983303

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g002

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Overview_of_selected_functionalities_offered_by_the_platform_and_their_associated_displays_/14983306

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g003

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/LR_coefficients_obtained_from_the_biochemistry_data_/14983315

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g005

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Scores_obtained_with_the_two_best_models_LGBM_and_LR_/14983321

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g007

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Feature_importance_analysis_using_SHAP_method_/14983324

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g008

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Feature_importance_analysis_using_PFI_method_/14983327

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g009

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Results_from_the_DT_model_trained_on_the_biochemistry_data_/14983318

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g006

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Analysis_of_the_predicted_features_common_to_the_PFI_and_SHAP_methods_/14983330

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g010

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Description_of_approaches_for_building_models_on_different_data_types_/14983333

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g011

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/Results_for_the_training_of_models_on_various_types_of_data_/14983339

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g012

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/dataset/Top_12_overlapping_Genomic_features_and_amino-acid_changes_obtained_with_the_PFI_and_SHAP_methods_/14983345

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.t001

المؤلفون: Vladimir Naumov (8582277), Evgeny Putin (2575033), Stefan Pushkov (11133892), Ekaterina Kozlova (9529157), Konstantin Romantsov (11133895), Alexander Kalashnikov (11133898), Fedor Galkin (11133901), Nina Tihonova (11133904), Anastasia Shneyderman (11133907), Egor Galkin (11133910), Arsenii Zinkevich (11133913), Stephanie M. Cope (11133916), Ramanathan Sethuraman (11133919), Tudor I. Oprea (153954), Alexander T. Pearson (4781601), Savas Tay (11133922), Nishant Agrawal (79775), Alexey Dubovenko (11133925), Quentin Vanhaelen (5044136), Ivan Ozerov (11133928), Alex Aliper (5044139), Evgeny Izumchenko (2808274), Alex Zhavoronkov (347712)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, COVID -19 patients, disease severity, bioinformatic tools, multi-modal cloud-based platform, COVID -19, SARS-CoV -2, December 2019, health data, SARS-CoV -2 strains, patient stratification, risk factors, antibiotic resistance, COVIDomic platform, pathogens community analysis, COVID -19 severity Coronavirus dise., multi-modal metatranscriptomic data., COVID -19 pandemic, coronavirus strain, SARS-CoV -2 genomes

Relation: https://figshare.com/articles/figure/PFI_and_SHAP_values_for_the_feature_importance_analysis_/14983342

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009183.g013