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matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Bioinformatics(2022)10.1093/bioinformatics/btac401Source: DataRank Database

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 is a research paper published in Bioinformatics (2022). On theSindex it has a DataRank of 1.4. It has been cited 40 times, with 30 citing works in its 1-hop citation network.

N/A

1.4DataRank · unranked

Scored on demand from live citation data

Deposits data Open Access40 citations · 30 citing works in its network

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Linked data & code

gen refseq doi

Data availability

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

figshare10.6084/m9.figshare.19799374

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›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (12 grants)OA: bronzeTopics (47)IDs (PubMed, PMC)Annotations (3)SDGs (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 39%Citation Network 61%

Base Score Contribution

0.557

From this paper's citation signal

Citation Network Contribution

0.867

From 26 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 30 citers.

Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa
GigaScience202419 citations25 referencesContributes 0.120
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets
GigaScience20228 citations21 referencesContributes 0.105
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Journal of Mathematical Biology202310 citations31 referencesContributes 0.077
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
Science202370 citations70 referencesContributes 0.061
F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny
Virus Evolution20241 citations13 referencesContributes 0.053

Authors (9)

Bryan Thornlow ORCID,Angie S. Hinrichs ORCID,Alexander Krämer ORCID,Cade Mirchandani ORCID,Devika Torvi

Live enrichment

PubMed:35731204 PMC:PMC9344837

Centers for Disease Control and Prevention BAA

Grant: 200-2021-11554

National Institutes of Health

Grant: T32HG008345

National Institutes of Health

Grant: F31HG010584

Australian Research Council Discovery

Grant: DP200103151

Discovery Projects - Grant ID: DP200103151

National Institutes of Health

Grant: R35GM128932

National Institutes of Health

Grant: 1R35GM128932-01

Genetic variation, admixture and genome structure evolution through the lense of Drosophila genomics

National Institutes of Health

Grant: 1T32HG008345-01

UC Santa Cruz Training Program In Genomic Sciences

National Institutes of Health

Grant: 1F31HG010584-01

Evolutionary dynamics of tRNA genes

National Institutes of Health

Grant: 2R37AA000200-19

CHRONIC ALCOHOL CONSUMPTION: NEUROBIOLOGICAL CORRELATES

Chan-Zuckerberg Initiative Grant for Essential Open Source Software for Science

Eric and Wendy Schmidt Foundation

Australian National University Futures

bronzeLicense: CC BY NC

publisherhttps://academic.oup.com/bioinformatics/article-pdf/38/15/3734/45213212/btac401.pdf

publisherhttps://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac401/44318848/btac401.pdf

publisherhttps://academic.oup.com/bioinformatics/article-pdf/38/15/3734/49884099/btac401.pdf

repositoryhttps://escholarship.org/uc/item/239165nd

repositoryhttps://www.ncbi.nlm.nih.gov/pmc/articles/9344837

Fields of Study

0206 medical engineering02 engineering and technology

MeSH Terms

HumansPhylogenySoftwarePandemicsCOVID-19SARS-CoV-2

Keywords

570Online phylogeneticsCoronavirusesBioinformatics3102 Bioinformatics and Computational Biology (for-2020)Bioinformatics and Computational BiologySARS-CoV-2 (mesh)08 Information and Computing Sciences (for)Phylogeny (mesh)Mathematical SciencesEmerging Infectious Diseases (rcdc)Information and Computing Sciences31 Biological sciences (for-2020)HumansSoftware (mesh)46 Information and computing sciences (for-2020)PandemicsPhylogenySARS-CoV-2 phylogeneticsHumans (mesh)3 Good Health and Well Being (sdg)COVID-19 (mesh)SARS-CoV-2Pandemics (mesh)Coronaviruses (rcdc)COVID-19Biological Sciences49 Mathematical sciences (for-2020)Original PapersTree optimization00406 Biological Sciences (for)Emerging Infectious DiseasesInfectious DiseasesGood Health and Well BeingBioinformatics (science-metrix)Infectious Diseases (rcdc)01 Mathematical Sciences (for)Software

Sustainable Development Goals

SDG 3: 3. Good health