المؤلفون: Lennert Verboven, Steven Callens, John Black, Gary Maartens, Kelly E Dooley, Samantha Potgieter, Ruben Cartuyvels, SMARTT team, Kris Laukens, Robin M Warren, Annelies Van Rie

المصدر: PLoS ONE, Vol 19, Iss 9, p e0306101 (2024)

مصطلحات موضوعية: Medicine, Science

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1932-6203

URL الوصول: https://doaj.org/article/1179cd02ccde4d34ba148e7d1cd3bf69

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

المصدر: PLoS Computational Biology, Vol 19, Iss 11 (2023)

مصطلحات موضوعية: Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10686480/?tool=EBI; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

URL الوصول: https://doaj.org/article/341f31dad2b949e1b88155817cd8879f

المؤلفون: Annelies Van Rie, Elise De Vos, Emilyn Costa, Lennert Verboven, Felex Ndebele, Tim H. Heupink, Steven Abrams, SMARTT team, Boitumelo Fanampe, Anneke Van der Spoel Van Dyk, Salome Charalambous, Gavin Churchyard, Rob Warren

المصدر: Trials, Vol 23, Iss 1, Pp 1-15 (2022)

مصطلحات موضوعية: Drug resistance, Tuberculosis, Whole-genome sequencing, Clinical trial, Pragmatic, Strategy trial, Medicine (General), R5-920

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1745-6215

URL الوصول: https://doaj.org/article/f5ceb4d6254c47bb83c29ade3dc9634e

المؤلفون: Lennert Verboven, Toon Calders, Steven Callens, John Black, Gary Maartens, Kelly E. Dooley, Samantha Potgieter, Robin M. Warren, Kris Laukens, Annelies Van Rie

المصدر: BMC Medical Informatics and Decision Making, Vol 22, Iss 1, Pp 1-11 (2022)

مصطلحات موضوعية: Clinical decision support system, Treatment individualisation, Machine learning, Computer applications to medicine. Medical informatics, R858-859.7

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1472-6947

URL الوصول: https://doaj.org/article/e9c5a705a93944bba7b196480038f145

المؤلفون: Lennert Verboven, Jody Phelan, Tim H Heupink, Annelies Van Rie

المصدر: PLoS ONE, Vol 17, Iss 12, p e0279644 (2022)

مصطلحات موضوعية: Medicine, Science

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1932-6203

URL الوصول: https://doaj.org/article/2e88094d0394492b84f7aac587bed381

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/journal_contribution/Contains_supplementary_text_with_figures_A-K_/24661265

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.s001
https://figshare.com/articles/journal_contribution/Contains_supplementary_text_with_figures_A-K_/24661265

المؤلفون: Lennert Verboven (14311426), Jody Phelan (3543014), Tim H. Heupink (14311429), Annelies Van Rie (36715)

مصطلحات موضوعية: Medicine, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Ecology, Cancer, Hematology, Infectious Diseases, Virology, Space Science, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, successfully converted 98, next generation sequencing, mycobacterium tuberculosis <, huge global effort, div >< p, critical step towards, standardized hgvs format, 56 clinical isolates, 339 clinical isolates, tbprofiler classified 13, tbprofiler classified 105, 8 %) classified, genomic variants translates, )- endorsed catalogue, 15 %) variants, clinical practice

Relation: https://figshare.com/articles/journal_contribution/Conversion_of_variants_in_the_WHO_catalogue_format_used_in_the_WHO_catalogue_to_the_standard_HGVS_format_Generic_regular_expressions_by_variant_type_and_examples_/21794833

الاتاحة: https://doi.org/10.1371/journal.pone.0279644.s001

المؤلفون: Lennert Verboven, Steven Callens, John Black, Gary Maartens, Kelly E. Dooley, Samantha Potgieter, Ruben Cartuyvels, SMARTT team, Kris Laukens, Robin M. Warren, Annelies Van Rie

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::61fb0d3ac18cebd40754c2653494e7cf
https://doi.org/10.21203/rs.3.rs-2525765/v1

المؤلفون: Vincent Rennie, Annelies Van Rie, Tim Heupinck, Lennert Verboven, Abhinav Sharma, Rob Warren

Relation: https://doi.org/10.5281/zenodo.8233517; https://doi.org/10.5281/zenodo.8233518; oai:zenodo.org:8233518

الاتاحة: https://doi.org/10.5281/zenodo.8233518

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/Drug_resistance_variants_for_TM280_identified_by_MAGMA_/24661271

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.s003
https://figshare.com/articles/dataset/Drug_resistance_variants_for_TM280_identified_by_MAGMA_/24661271

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/MAGMA_mapping_statistics_and_quality_thresholds_for_the_79_SMARTT_samples_/24661268

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.s002
https://figshare.com/articles/dataset/MAGMA_mapping_statistics_and_quality_thresholds_for_the_79_SMARTT_samples_/24661268

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/figure/Fig_1_-/24661280

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.g001
https://figshare.com/articles/figure/Fig_1_-/24661280

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/figure/Density_distribution_of_the_variant_quality_score_log-odds_VQSLOD_for_the_identified_SNP_variants_/24661286

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.g002
https://figshare.com/articles/figure/Density_distribution_of_the_variant_quality_score_log-odds_VQSLOD_for_the_identified_SNP_variants_/24661286

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/figure/iTOL_visualizations_of_the_MAGMA_ExComplex_phylogeny_annotated_with_drug_resistance_and_lineage_for_71_primary_liquid_culture_samples_that_passed_MAGMA_quality_control_/24661289

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.g003
https://figshare.com/articles/figure/iTOL_visualizations_of_the_MAGMA_ExComplex_phylogeny_annotated_with_drug_resistance_and_lineage_for_71_primary_liquid_culture_samples_that_passed_MAGMA_quality_control_/24661289

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/figure/Diagram_representing_the_different_analyses_which_occur_in_the_pipeline_/24661298

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.g005
https://figshare.com/articles/figure/Diagram_representing_the_different_analyses_which_occur_in_the_pipeline_/24661298

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/figure/FigTree_visualization_of_the_phylogeny_annotated_with_5SNP_cluster_information_each_color_represents_a_different_cluster_and_indicating_the_newly_added_samples_to_the_phylogenetic_tree_/24661295

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.g004
https://figshare.com/articles/figure/FigTree_visualization_of_the_phylogeny_annotated_with_5SNP_cluster_information_each_color_represents_a_different_cluster_and_indicating_the_newly_added_samples_to_the_phylogenetic_tree_/24661295

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/Selection_Criteria_to_filter_samples_for_the_cohort_workflow_/24661313

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.t004
https://figshare.com/articles/dataset/Selection_Criteria_to_filter_samples_for_the_cohort_workflow_/24661313

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/Comparison_of_resistance_reported_by_MAGMA_and_MTBSeq_pipelines_/24661307

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.t002
https://figshare.com/articles/dataset/Comparison_of_resistance_reported_by_MAGMA_and_MTBSeq_pipelines_/24661307

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/Drug_resistance_information_as_reported_by_MAGMA_and_MTBseq_including_the_variant_and_resistance_annotation_in_the_WHO_catalogue_of_mutations_in_i_Mycobacterium_tuberculosis_i_/24661304

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.t001
https://figshare.com/articles/dataset/Drug_resistance_information_as_reported_by_MAGMA_and_MTBseq_including_the_variant_and_resistance_annotation_in_the_WHO_catalogue_of_mutations_in_i_Mycobacterium_tuberculosis_i_/24661304

المؤلفون: Tim H. Heupink, Lennert Verboven, Abhinav Sharma, Vincent Rennie, Miguel de Diego Fuertes, Robin M. Warren, Annelies Van Rie

مصطلحات موضوعية: Microbiology, Genetics, Pharmacology, Biotechnology, Evolutionary Biology, Cancer, Infectious Diseases, Virology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, maximum accessible genome, joint variant calling, holds great potential, resistance classification based, whole genome sequencing, comprehensive genomic analyses, drug resistance information, drug resistance annotations, low mycobacterial burden, low (< 20x, magma automatically generates, candidate resistance genes, mycobacterium tuberculosis <, mtbseq pipeline reported, drug resistance, sequencing data, comprehensive output, magma pipeline, bioinformatics pipeline, rrs <

Relation: https://figshare.com/articles/dataset/MAGMA_approach_to_overcome_open_issues_in_whole_genome_sequencing_of_i_Mycobacterium_tuberculosis_i_1_/24661310

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011648.t003
https://figshare.com/articles/dataset/MAGMA_approach_to_overcome_open_issues_in_whole_genome_sequencing_of_i_Mycobacterium_tuberculosis_i_1_/24661310