Evidence map›Paper›PMID 22247275›Full record

ArticleBioinformatics (Oxford, England)2012

Roundup 2.0: enabling comparative genomics for over 1800 genomes.

Todd F DeLuca, Jike Cui, Jae-Yoon Jung, Kristian Che St Gabriel, Dennis P Wall

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
3.2field-weighted citation impact, top 7% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

25 citing papers in PubMed, 48 citations in OpenAlex.

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  10. Towards Consensus Gene Ages.Genome biology and evolution · 2016
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 1 country.

Todd F DeLucaThe Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston MA 02115, USA. todd_deluca@hms.harvard.edu
Jike Cui
Jae-Yoon Jung
Kristian Che St Gabriel
Dennis P Wall
Beth Israel Deaconess Medical Center · USHarvard University · US

Funding

Building a framework for exploration of orthologs and evolutionary distances.R03LM009261 · NLM · HARVARD MEDICAL SCHOOL · PI WALL, DENNIS PAUL · 2007 to 2009
$211k
NLM NIH HHS LM009261NLM NIH HHS R03 LM009261
6 · The paper itself

Abstract

unlabelledRoundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available. AVAILABILITY: http://roundup.hms.harvard.edu.

Indexed as

AlgorithmsPhylogenyAnimalsArchaeaBacteriaCluster AnalysisEvolution, MolecularGenomeGenomicsHumansViruses

Identifiers

PMID22247275
PMCPMC3289913
OpenAlexW2120987877

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.