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High-resolution, genome-wide mapping of positive supercoiling in chromosomes

eLife(2021)10.7554/elife.67236Source: DataRank Database

High-resolution, genome-wide mapping of positive supercoiling in chromosomes is a research paper published in eLife (2021). On theSindex it has a DataRank of 2.5. It has been cited 88 times, with 82 citing works in its 1-hop citation network.

N/A

2.5DataRank · unranked

Scored on demand from live citation data

Deposits data Open Access88 citations · 82 citing works in its network

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Linked data & code

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Data availability

Repositories this paper deposited data in (declared in PubMed).

GEOGSE152882 GSM2690550 GSM3668254 GSM3069971 GSM1705337 GSM3141352

DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?

›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (18 grants)OA: goldTopics (47)IDs (PubMed, PMC)Annotations (1)

FAIR Checklist

Context only (not used in score)

Findable (1/2)

Has DOI

Accessible (1/2)

Open Access

Interoperable (0/2)

Reusable (0/3)

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DataRank Breakdown

Base Score 27%Citation Network 73%

Base Score Contribution

0.673

From this paper's citation signal

Citation Network Contribution

1.8

From 70 citing papers with measurable signal

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Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 82 citers.

Enricherator: A Bayesian Method for Inferring Regularized Genome-wide Enrichments from Sequencing Count Data
Journal of Molecular Biology20243 citations11 referencesContributes 0.126
Condensin-driven loop extrusion on supercoiled DNA
Nature Structural & Molecular Biology202273 citations43 referencesContributes 0.100
TOP1 CAD-seq: A protocol to map catalytically engaged topoisomerase 1 in human cells
STAR Protocols202212 citations35 referencesContributes 0.073
La transcription, clé de voûte de l’architecture du chromosome bactérien
médecine/sciences20241 citations10 referencesContributes 0.069
Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils
Molecular Cell202446 citations59 referencesContributes 0.065

Authors (5)

Ryo Kawamura,Megan L. Littlehale ORCID,John F. Marko ORCID,Michael T. Laub ORCID,Monica S. Guo ORCID

Live enrichment

PubMed:34279217 PMC:PMC8360656

NIGMS NIH HHS

Grant: R01 GM082899

NIGMS NIH HHS

Grant: R00 GM134153

NHGRI NIH HHS

Grant: UM1 HG011536

NIH HHS

Grant: S10 OD026741

National Institutes of Health

Grant: U54DK107980

Howard Hughes Medical Institute

Grant: Investigator

NIGMS NIH HHS

Grant: K99 GM134153

NIGMS NIH HHS

Grant: R01 GM105847

National Institutes of Health

Grant: U54CA193419

National Institutes of Health

Grant: UM1-HG011536

National Institutes of Health

Grant: 1K99GM134153-01

Control of topoisomerase activity during DNA replication by bacterial chromosome structuring proteins

National Institutes of Health

Grant: 5R01GM082899-13

Cell cycle regulation and chromosome organization in Caulobacter crescentus

National Institutes of Health

Grant: 1S10OD026741-01

Azure Sapphire Bioimager

National Institutes of Health

Grant: 2R01GM105847-05A1

Activities of nucleoprotein complexes visualized in single-molecule experiments

National Institutes of Health

Grant: 5UM1HG011536-03

Center for 3D Structure and Physics of the Genome

National Institutes of Health

Grant: 3U54CA193419-05S1

Spatio-Temporal Organization of Chromatin and Information Transfer in Cancer

National Institutes of Health

Grant: 3U54DK107980-04S1

Center for 3D Structure and Physics of the Genome

Howard Hughes Medical Institute

goldLicense: cc-by

publisherhttps://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNjcyMzYvZWxpZmUtNjcyMzYtdjIucGRmP2Nhbm9uaWNhbFVyaT1odHRwczovL2VsaWZlc2NpZW5jZXMub3JnL2FydGljbGVzLzY3MjM2/elife-67236-v2.pdf?_hash=xDpYr%2BnW0d1twj2V3gmGP8FLWmA1oCYBJli9Vg5JqTo%3D

repositoryhttps://doaj.org/article/b2cec7f1e03c4f74a4e36b60201f5103

repositoryhttps://www.ncbi.nlm.nih.gov/pmc/articles/8360656

Unpaywallhttps://doi.org/10.7554/elife.67236

Europe_PMChttps://europepmc.org/articles/PMC8360656

Fields of Study

0301 basic medicine03 medical and health sciences0303 health sciences

MeSH Terms

ChromosomesChromosomes, BacterialChromosome StructuresEscherichia coliSaccharomyces cerevisiaeBacterial ProteinsCell Cycle ProteinsChromosomal Proteins, Non-HistoneDNADNA, BacterialChromatin ImmunoprecipitationDNA ReplicationTranscription, GeneticBinding SitesProtein BindingCohesins

Keywords

S. cerevisiaeE. colichromosomesGene ExpressionChromosome StructureSupercoilingDNA ReplicationDNA, BacterialChromatin ImmunoprecipitationTranscription, GeneticQH301-705.5Chromosomal Proteins, Non-HistoneScienceCell Cycle ProteinsSaccharomyces cerevisiaeBacterial ProteinsEscherichia coliBiology (General)CohesinsBinding SitesQRDNAChromosomes, BacterialChromosomes and Gene ExpressionChromosome StructuresMedicineProtein Binding