Evidence map›Paper›PMID 37480009›Full record

ArticleBMC bioinformatics2023

xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes.

Nuo Liu, Tonatiuh A Gonzalez, Jacob Fischer, Chan Hong, Michelle Johnson, Ross Mawhorter, Fabrizia Mugnatto, Rachael Soh, Shifa Somji, Joseph S Wirth and 2 more

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

Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 37% 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

1 citing paper in PubMed, 2 citations in OpenAlex.

  1. Article
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

12 authors at 4 institutions in 1 country.

Nuo LiuDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Tonatiuh A GonzalezDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Jacob FischerDepartment of Computer Science, Harvey Mudd College, Claremont, CA, USA.
Chan HongDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Michelle JohnsonDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Ross MawhorterDepartment of Computer Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
Fabrizia MugnattoDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Rachael SohDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Shifa SomjiDepartment of Computer Science, Harvey Mudd College, Claremont, CA, USA.
Joseph S WirthDepartment of Biology, Harvey Mudd College, Claremont, CA, USA.
Ran Libeskind-HadasDepartment of Integrated Sciences, Claremont McKenna College, Claremont, CA, USA.
Eliot C BushDepartment of Biology, Harvey Mudd College, Claremont, CA, USA. bush@hmc.edu.ORCID http://orcid.org/0000-0001-5476-8005
Harvey Mudd College · USCenters for Disease Control and Prevention · USClaremont McKenna College · USUniversity of California, Santa Cruz · US

Funding

National Science Foundation IIS-1419739
6 · The paper itself

Abstract

To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are geared toward a complete reconstruction for all families in an entire clade. Here we describe an update to the xenoGI software package which allows users to perform such an analysis using the newly developed DTLOR (duplication-transfer-loss-origin-rearrangement) reconciliation model starting from genome sequences as input.

Indexed as

BacteriaGenome, BacterialSoftwareGene familyGenomic islandHorizontal transferReconciliation

Identifiers

PMID37480009
PMCPMC10362622
OpenAlexW4385064302

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.