Evidence map›Paper›PMID 27565162›Full record

ArticleGenetics2016

Estimation of Gene Insertion/Deletion Rates with Missing Data.

Utkarsh J Dang, Alison M Devault, Tatum D Mortimer, Caitlin S Pepperell, Hendrik N Poinar, G Brian Golding

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

Article in Genetics, 2016. 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
0.5field-weighted citation impact, top 28% 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, 3 citations in OpenAlex.

  1. SAliBASE: A Database of Simulated Protein Alignments.Evolutionary bioinformatics online · 2019
    Review
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

6 authors at 3 institutions in 2 countries.

Utkarsh J DangDepartments of Biology and Mathematics and Statistics, McMaster University, Hamilton, Ontario L8S-4L8, Canada.
Alison M DevaultMYcroarray, Ann Arbor, Michigan 48105.
Tatum D MortimerDepartments of Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705.
Caitlin S PepperellDepartments of Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705.
Hendrik N PoinarDepartment of Anthropology, McMaster University, Hamilton, Ontario L8S-4K1, Canada.
G Brian GoldingDepartment of Biology, McMaster University, Hamilton, Ontario L8S-4K1, Canada golding@mcmaster.ca.
McMaster University · CAUniversity of Wisconsin–Madison · USMYcroarray (United States) · US

Funding

GRADUATE TRAINING IN MOLECULAR BIOSCIENCEST32GM007215 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI HULL, CHRISTINA M · 1985 to 2018
$22.5M
Drifting to victory: resolving the paradox of M.tuberculosis evolutionR01AI113287 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI Caitlin S Pepperell · 2015 to 2026
$6.5M
NIAID NIH HHS R01 AI113287NIGMS NIH HHS T32 GM007215
6 · The paper itself

Abstract

Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.

Indexed as

Evolution, MolecularMutation RateData Interpretation, StatisticalGardnerella vaginalisGene Transfer, HorizontalGenome, BacterialINDEL MutationMutagenesis, InsertionalMycobacteriumgene insertion/deletionindel ratesmaximum likelihoodunobserved data

Identifiers

PMID27565162
PMCPMC5068843
OpenAlexW2509827291

What OpenQuestion holds

Textmetadata
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.