المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/journal_contribution/Estimated_time_required_to_compute_of_all-vs-all_OptiMap-naive_alignments_/16712114

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.s001

المؤلفون: Eef M. Jonkheer (10642853), Balázs Brankovics (2839439), Ilse M. Houwers (10642856), Jan M. van der Wolf (4709566), Peter J. M. Bonants (10642859), Robert A. M. Vreeburg (10642862), Robert Bollema (10642865), Jorn R. de Haan (10642868), Lidija Berke (2131078), Sandra Smit (11638), Dick de Ridder (17852), Theo A. J. van der Lee (2839442)

مصطلحات موضوعية: Genetics, Pectobacterium, Soft rot Pectobacteriaceae, Plant pathogen, Comparative genomics, Pangenome, Gene repertoire, Phylogeny, Virulence, Pectobacterium brasiliense

Relation: https://figshare.com/articles/journal_contribution/Additional_file_3_of_The_Pectobacterium_pangenome_with_a_focus_on_Pectobacterium_brasiliense_shows_a_robust_core_and_extensive_exchange_of_genes_from_a_shared_gene_pool/14411537

الاتاحة: https://doi.org/10.6084/m9.figshare.14411537.v1

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Homology_modelling_/14263449

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s001

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Fragmentation_patterns_/14263452

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s002

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Predicted_nerolidyl_percentages_/14263458

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s004

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Residue_importance_scores_/14263461

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s005

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Predicted_contacts_from_co-evolutionary_analysis_/14263464

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s006

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Alignment_of_discussed_STSs_/14263467

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s007

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/Classification_framework_/14263473

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s009

المؤلفون: Janani Durairaj (10344975), Elena Melillo (10344978), Harro J. Bouwmeester (10344981), Jules Beekwilder (45525), Dick de Ridder (17852), Aalt D. J. van Dijk (8666520)

مصطلحات موضوعية: Biochemistry, Molecular Biology, Evolutionary Biology, Infectious Diseases, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, reaction pathway selection, Sequence identity-based screening, STS sequence similarity, plant species, STS sequences, enzyme, plant sesquiterpene synthases Sesqu., Integrating structure-based machine, precursor cation formation, precursor cation specificity

Relation: https://figshare.com/articles/journal_contribution/_i_Citrus_bergamia_i_STS_chromatograms_/14263470

الاتاحة: https://doi.org/10.1371/journal.pcbi.1008197.s008

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/The_principle_of_BNG_optical_mapping_/16712117

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g001

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/OptiTools_workflow_/16712120

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g002

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Frame_pairs_as_produced_by_the_BNG_platform_/16712123

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g003

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Frame_stitching_/16712126

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g004

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/The_OptiMap_alignment_procedure_/16712129

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g005

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Molecule_detection_yeast_by_OptiScan_and_BNG_/16712132

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g006

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Comparison_of_3_different_contigs_assembled_by_the_BNG_assembler_using_molecules_extracted_by_OptiScan_and_by_BNG_software_/16712135

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g007

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Distribution_of_alignment_overlap_lengths_for_pairs_aligned_only_by_either_of_the_tools_/16712141

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g009

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Alignment_performance_for_yeast_A_and_eggplant_data_B_C_/16712138

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g008

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Visualization_of_overlapping_parts_of_molecule_pairs_aligned_by_A_OptiMap_and_B_RefAligner_/16712144

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g010