المؤلفون: Linda K Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris

المصدر: PLoS Computational Biology, Vol 17, Iss 1, p e1008400 (2021)

مصطلحات موضوعية: Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

URL الوصول: https://doaj.org/article/2e2c7a038087427aaf69ce77002b06e4

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Example_of_a_clone_tree_with_three_subclones_and_the_germline_/13609614

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s001

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_dataset_without_CNAs_containing_A_5_B_20_and_C_50_subclones_/13609632

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s007

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Overview_of_SubMARine_in_extended_mode_/13609626

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s005

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Partial_clone_tree_where_one_completing_clone_tree_is_not_a_solution_to_the_basic_clone_tree_reconstruction_problem_i_t_i_/13609617

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s002

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Overview_of_SubMARine_in_basic_mode_/13609623

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s004

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_dataset_with_CNAs_containing_20_subclones_and_different_numbers_of_CNA_events_and_segments_/13609635

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s008

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Valid_partial_clone_tree_without_a_valid_completion_/13609620

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s003

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_A_dataset_without_CNAs_and_B_dataset_with_CNAs_/13609629

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s006

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_dataset_with_noise_and_different_effective_read_depths_/13609650

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s013

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Runtimes_of_the_depth-first_search_DFS_to_enumerate_all_valid_and_equivalent_clone_trees_completing_a_subMAR_sorted_by_the_number_of_undefined_ancestral_relationships_in_the_subMARs_/13609641

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s010

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/_A_D_E_Recall_and_B_D_F_false_positive_error_of_differently_defining_a_relationship_in_the_subMAR_for_A_B_5_C_D_20_and_E_F_50_subclones_/13609665

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s018

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Maximum_values_in_the_noise_buffer_sets_for_different_effective_read_depths_/13609647

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s012

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Recall_of_defined_ancestral_relationships_for_datasets_without_and_with_CNAs_and_20_subclones_/13609638

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s009

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Distribution_among_the_different_noise_buffer_statutes_/13609644

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s011

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/False_positive_errors_of_A_falsely_defining_a_relationship_in_the_subMAR_that_is_undefined_in_the_noise-free_MAR_and_B_differently_defining_a_relationship_in_the_subMAR_/13609662

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s017

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_dataset_with_noise_5_subclones_and_different_effective_read_depths_/13609653

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s014

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Proportion_of_subclones_with_uncertain_parentage_for_dataset_with_noise_20_subclones_and_different_effective_read_depths_/13609656

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s015

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/Partial_clone_trees_built_by_SubMARine_based_on_raw_and_or_adapted_CCFs_of_Gundem_et_al_/13609686

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s023

المؤلفون: Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067)

مصطلحات موضوعية: Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree

Relation: https://figshare.com/articles/journal_contribution/SubMARs_for_five_patients_from_the_TRACERx_cohort_/13609671

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008400.s019