المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/journal_contribution/Evaluation_of_sensitivity_of_Read2Pheno_modeling_to_different_window_sizes_of_convolutional_layers_/16662762

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s011

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/journal_contribution/Gevers_data_set_testing_performance_on_different_read_length_/16662777

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s016

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/journal_contribution/Secondary_structure_and_attention_weights_of_a_i_Pseudomonas_aeruginosa_i_sequence_/16662786

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s019

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/dataset/One-hot_coding_map_/16662732

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s001

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Sample-level_predictor_Majority_vote_method_/16662735

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s002

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Sample-level_predictor_Pseudo_OTU_/16662741

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s004

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Sample-level_predictor_Sample-level_embedding_/16662738

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s003

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/dataset/American_Gut_Project_AGP_metadata_/16662744

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s005

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Overall_training_and_testing_experiment_/16662747

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s006

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/dataset/Hyperparameter_search_space_table_/16662753

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s008

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Read2Pheno_training_process_/16662750

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s007

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Training_and_validation_loss_as_a_function_of_epochs_for_the_Read2Pheno_model_on_American_Gut_Project_data_/16662756

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s009

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/2-D_projection_of_embedded_i_Prevotella_i_read_vectors_/16662765

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s012

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Training_data_size_effect_of_Read2Pheno_classifier_/16662759

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s010

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Visualization_of_the_attention_weights_without_smoothing_/16662768

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s013

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Oligotypes_for_i_Prevotella_i_reads_/16662771

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s014

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Oligotypes_and_body_site_association_41_of_i_Prevotella_i_reads_/16662774

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s015

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/2-D_projection_of_embedded_read_vectors_from_i_Ruminococcus_i_Left_and_i_Blautia_i_Right_/16662780

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s017

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Attention_weights_visualization_of_a_body_site_classification_model_trained_by_reads_from_400_AGP_samples_/16662795

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s022

المؤلفون: Zhengqiao Zhao (6400832), Stephen Woloszynek (771172), Felix Agbavor (11467482), Joshua Chang Mell (7490840), Bahrad A. Sokhansanj (9389502), Gail L. Rosen (8115077)

مصطلحات موضوعية: Microbiology, Genetics, Molecular Biology, Biotechnology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, recurrent neural networks, provide biological insight, manual interpretation required, 16s ribosomal rna, predict taxonomic classifications, level phenotypic prediction, natural language processing, microbial community sample, div >< p, short dna reads, microbiome sequence classification, sequence level, taxonomic classification, capture short, level information, widely used, python package, particularly informative, network model, meaningful representations, marker genes, least comparable, intermediate layer

Relation: https://figshare.com/articles/figure/Attention_weights_visualization_of_a_Crohn_s_disease_classification_model_trained_by_reads_from_160_Gevers_samples_/16662801

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009345.s024