المؤلفون: Meredith J. Zeller (11984377), Ashok Nuthanakanti (1921492), Kelin Li (1545454), Jeffrey Aubé (1314141), Alexander Serganov (2533270), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Molecular Biology, Pharmacology, Immunology, Chemical Sciences not elsewhere classified, unfavorable structural rearrangement, subsite ligand recognition, soluble structural analogue, methylene diphosphonic acid, identifying small molecules, 1 mm affinities, show high levels, potent linked rna, mdp moderately improves, notable high affinity, thiamine pyrophosphate riboswitch, high affinity, tpp riboswitch, work inform, still yields, rna specifically, proximal subsites, principles derived, modest affinity, like fragments, global folding, divalent ions, crystal structures

Relation: https://figshare.com/articles/journal_contribution/Subsite_Ligand_Recognition_and_Cooperativity_in_the_TPP_Riboswitch_Implications_for_Fragment-Linking_in_RNA_Ligand_Discovery/18858235

الاتاحة: https://doi.org/10.1021/acschembio.1c00880.s001

المؤلفون: Thomas W. Christy (10967271), Catherine A. Giannetti (10967274), Gillian Houlihan (8034050), Matthew J. Smola (2225818), Greggory M. Rice (1727200), Jian Wang (5901), Nikolay V. Dokholyan (84409), Alain Laederach (243452), Philipp Holliger (441594), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Molecular Biology, Virology, Computational Biology, Biological Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Higher-Order RNA Interactions, RNA cross-link site, SHAPE-JuMP measures RNA, DNA, cross-linked nucleotides, SHAPE-JuMP Higher-order structure, RNA molecules

Relation: https://figshare.com/articles/journal_contribution/Direct_Mapping_of_Higher-Order_RNA_Interactions_by_SHAPE-JuMP/14778816

الاتاحة: https://doi.org/10.1021/acs.biochem.1c00270.s001

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Effects_of_removing_ambiguous_deletions_and_enforcing_exact_edge_matching_/17199902

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s001

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Improvement_in_TBIA-specific_deletion_rate_measurement_upon_background_subtraction_/17199908

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s002

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Insertion_length_effects_on_deletion_site_assignment_accuracy_and_experimental_deletion_frequency_/17199911

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s003

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Effect_of_5_and_3_shifts_in_site_assignment_on_through-space_distances_/17199917

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s004

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Progress_of_ShapeJumper_optimization_steps_for_through-space_interaction_identification_/17199920

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s005

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/SHAPE-JuMP_experimental_overview_/17199932

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g001

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/dataset/Text_files_containing_complete_lists_of_raw_and_processed_deletions_obtained_for_each_of_the_RNAs_reported_in_this_work_/17199926

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.s006

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/ShapeJumper_overview_/17199938

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g002

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Alignment_optimization_/17199950

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g004

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Accuracy_analysis_for_candidate_aligners_/17199944

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g003

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/Effect_of_shifting_deletion_site_assignment_on_through-space_distance_/17199953

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g005

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/ShapeJumper_detects_deletions_from_known_crosslink_site_/17199959

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g006

المؤلفون: Thomas W. Christy (11836547), Catherine A. Giannetti (10967274), Alain Laederach (243452), Kevin M. Weeks (367405)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Evolutionary Biology, Infectious Diseases, Virology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, +shape%22">xlink "> shape, nucleotide resolution using, jump sequencing data, complex jump datasets, shapejumper , engineered reverse transcriptase, process shape, introduce shapejumper, engineered crosslink, determined using, traversing reverse, templated reverse, unique non, transcription profile, space interactions, rna molecules, rna interactions, ribose moieties, replace adapter, reactive reagent, inspired strategies

Relation: https://figshare.com/articles/figure/ShapeJumper_measures_deletions_obtained_from_diverse_crosslinkers_/17199965

الاتاحة: https://doi.org/10.1371/journal.pcbi.1009632.g007