المؤلفون: Lalita Shahu (14283563), S. Roy Chowdhury (4907137), H. Peter Lu (380336)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Cell Biology, Genetics, Molecular Biology, Developmental Biology, Cancer, Mental Health, Computational Biology, Environmental Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, basic repeating unit, dna gets accessed, biological force fluctuation, dna binding molecules, protein molecules, biological entities, pulling force, compressive force, dna around, dna accessible, unfolding pathways, turn makes, thermally available, structural rupture, squeezing rather, spontaneous ruptures, room temperature

Relation: https://figshare.com/articles/journal_contribution/Single-Molecule_Human_Nucleosome_Spontaneously_Ruptures_under_the_Stress_of_Compressive_Force_A_New_Perspective_on_Gene_Stability_and_Epigenetic_Pathways/21757214

الاتاحة: https://doi.org/10.1021/acs.jpcb.2c04449.s001

المؤلفون: Sehui Bae (11141646), Jun Soo Kim (1737499)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Cell Biology, Molecular Biology, Pharmacology, Cancer, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, ∼ 10 nm, extensive research interest, 25 , two dna sequences, scale dna structures, dna around proteins, ac )< sub, np wrapped around, less flexible dna, dependent dna flexibility, dna wrapping around, )< sub, flexible dna, dependent binding, stranded dna, dna wrapping, dna nanotechnologies, dna molecule, dna bending

Relation: https://figshare.com/articles/journal_contribution/Potential_of_Mean_Force_for_DNA_Wrapping_Around_a_Cationic_Nanoparticle/17041224

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00797.s001

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/The_WT_fPC_scores_i_i_coloured_with_respect_to_the_Pearson_clustering_using_all_genes_/25056978

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s002
https://figshare.com/articles/figure/The_WT_fPC_scores_i_i_coloured_with_respect_to_the_Pearson_clustering_using_all_genes_/25056978

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/First_10_fPCs_for_WT_A_all_genes_/25056981

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s003
https://figshare.com/articles/figure/First_10_fPCs_for_WT_A_all_genes_/25056981

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Cluster_significance_test_for_all_genes_in_WT_replicate_A_/25056975

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s001
https://figshare.com/articles/figure/Cluster_significance_test_for_all_genes_in_WT_replicate_A_/25056975

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/The_small-gene_fPC_effect_in_i_chd1_i_i_rsc8_i_strains_/25057002

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s008
https://figshare.com/articles/figure/The_small-gene_fPC_effect_in_i_chd1_i_i_rsc8_i_strains_/25057002

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/The_large-gene_fPC_effect_in_WT_/25056987

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s005
https://figshare.com/articles/figure/The_large-gene_fPC_effect_in_WT_/25056987

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Heatmaps_for_small-gene_nucleosome_profiles_reveal_antagonistic_roles_for_Rsc8_and_Chd1_to_establish_phasing_boundaries_/25056984

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s004
https://figshare.com/articles/figure/Heatmaps_for_small-gene_nucleosome_profiles_reveal_antagonistic_roles_for_Rsc8_and_Chd1_to_establish_phasing_boundaries_/25056984

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Pearson_clusters_of_small_genes_lose_separability_with_respect_to_their_fPC_scores_/25056993

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s007
https://figshare.com/articles/figure/Pearson_clusters_of_small_genes_lose_separability_with_respect_to_their_fPC_scores_/25056993

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/The_Pearson_coefficient_clusters_for_exclusively_small_genes_correspond_to_the_gene_size_/25056990

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s006
https://figshare.com/articles/figure/The_Pearson_coefficient_clusters_for_exclusively_small_genes_correspond_to_the_gene_size_/25056990

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Cluster_significance_test_for_large_genes_/25057008

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s009
https://figshare.com/articles/figure/Cluster_significance_test_for_large_genes_/25057008

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Pearson_clusters_of_large_genes_are_linearly_separable_with_respect_to_their_fPC_scores_replicate_A_/25057014

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s010
https://figshare.com/articles/figure/Pearson_clusters_of_large_genes_are_linearly_separable_with_respect_to_their_fPC_scores_replicate_A_/25057014

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Example_of_an_arbitrary_mutant_that_only_influences_the_MNase-seq_average_but_not_the_collective_behaviour_of_the_nucleosome_array_/25057023

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s012
https://figshare.com/articles/figure/Example_of_an_arbitrary_mutant_that_only_influences_the_MNase-seq_average_but_not_the_collective_behaviour_of_the_nucleosome_array_/25057023

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Pearson_clusters_and_fPCA_considering_all_protein-coding_genes_/25057038

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.g001
https://figshare.com/articles/figure/Pearson_clusters_and_fPCA_considering_all_protein-coding_genes_/25057038

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Nucleosome_phasing_is_strictly_limited_to_the_gene_body_which_is_maintained_by_Rsc8_but_antagonised_by_Chd1_/25057041

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.g002
https://figshare.com/articles/figure/Nucleosome_phasing_is_strictly_limited_to_the_gene_body_which_is_maintained_by_Rsc8_but_antagonised_by_Chd1_/25057041

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Clustering_using_WARD_and_an_Euclidean_distance_metric_indicates_also_a_separation_along_the_first_two_fPCs_/25057029

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s014
https://figshare.com/articles/figure/Clustering_using_WARD_and_an_Euclidean_distance_metric_indicates_also_a_separation_along_the_first_two_fPCs_/25057029

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Clustering_distribution_using_PCA_and_their_principal_components_/25057032

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s015
https://figshare.com/articles/figure/Clustering_distribution_using_PCA_and_their_principal_components_/25057032

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/AT-ratio_distribution_with_respect_to_the_fPC_scores_/25057035

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s016
https://figshare.com/articles/figure/AT-ratio_distribution_with_respect_to_the_fPC_scores_/25057035

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Remodeler_deletions_have_varying_effects_on_the_interdependence_with_other_genomic_properties_/25057053

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.g006
https://figshare.com/articles/figure/Remodeler_deletions_have_varying_effects_on_the_interdependence_with_other_genomic_properties_/25057053

المؤلفون: Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Genetics, Molecular Biology, Infectious Diseases, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, spatially constraining nucleus, ndr maintenance —, main descriptive functions, despite strong efforts, compared wild type, >- depleted conditions, δ strains displayed, wide comprehensive analysis, whilst chd1 plays, saccharomyces cerevisiae <, dna around nucleosomes, global nucleosome organisation, div >< p, collective arrangement along, classify nucleosome distributions, yeast , chd1 <, nucleosome arrangement, rsc8 <, dna repair, deficient strains

Relation: https://figshare.com/articles/figure/Interdependence_of_Pearson_clusters_of_MNase-seq_profiles_and_other_nuclear_factors_/25057026

الاتاحة: https://doi.org/10.1371/journal.pcbi.1011799.s013
https://figshare.com/articles/figure/Interdependence_of_Pearson_clusters_of_MNase-seq_profiles_and_other_nuclear_factors_/25057026