Evidence map›Paper›PMID 37552705›Full record

ArticleG3 (Bethesda, Md.)2023

Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus).

Elizabeth Dong Nguyen, Vahid Nikoonejad Fard, Bernard Y Kim, Sarah Collins, Miranda Galey, Branden R Nelson, Paul Wakenight, Simone M Gable, Aaron McKenna, Theo K Bammler and 9 more

Abstract read
In one paragraph

Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors.

Elizabeth Dong NguyenDepartment of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Vahid Nikoonejad FardSchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA.
Bernard Y KimDepartment of Biology, Stanford University, Stanford, CA 94305, USA.
Sarah CollinsCenter for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA.
Miranda GaleyDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Branden R NelsonCenter for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
Paul WakenightCenter for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
Simone M GableSchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA.
Aaron McKennaDepartment of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03755, USA.
Theo K BammlerDepartment of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
Jim MacDonaldDepartment of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
Daryl M OkamuraDepartment of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Jay ShendureBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.
David R BeierDepartment of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Jan Marino RamirezCenter for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
Mark W MajeskyDepartment of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Kathleen J MillenDepartment of Pediatrics, University of Washington, Seattle, WA 98195, USA.
Marc TollisSchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA.
Danny E MillerBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.

Funding

Mechanisms of Brain Dysmorphology in MN1 C-Terminal Truncation Syndrome, a Novel Intellectual Developmental Disability Disorder P50HD103524 · NICHD · UNIVERSITY OF WASHINGTON · PI DANIEL DOHERTY · 2020 to 2026
$9.9M
The Role of the Microbiome in Cancer Suppression and Susceptibility Across SpeciesU54CA217376 · NCI · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI MALEY, CARLO, SHIBATA, DARRYL K · 2018 to 2022
$8.6M
Long-read DNA and RNA sequencing to identify disease-causing genetic variation and streamline testingDP5OD033357 · OD · UNIVERSITY OF WASHINGTON · PI MILLER, DANNY ERWIN · 2022 to 2025
$1.9M
Acomys cahrinus: a new paradigm for kidney wound repairR01DK114149 · NIDDK · SEATTLE CHILDREN'S HOSPITAL · PI MAJESKY, MARK W. · 2018 to 2020
$847k
Building transgenic tools in Acomys cahirinus, an emerging model for mammalian regenerative biology and healthy agingR21OD030107 · OD · SEATTLE CHILDREN'S HOSPITAL · PI MILLEN, KATHLEEN JOYCE · 2021 to 2022
$518k
New transgenic tools for mammalian fibrosis and regenerative repair researchR21OD023838 · OD · SEATTLE CHILDREN'S HOSPITAL · PI MILLEN, KATHLEEN JOYCE, NELSON, BRANDEN R · 2017 to 2018
$504k
Mechanisms of Retinal Ganglion Cell PatterningF32EY015631 · NEI · UNIVERSITY OF WASHINGTON · PI NELSON, BRANDEN R · 2004 to 2007
$142k
Howard Hughes Medical InstituteNCI NIH HHS U54 CA217376NEI NIH HHS F32 EY015631NEI NIH HHS L40 EY016882NICHD NIH HHS P50 HD103524NIDDK NIH HHS R01 DK114149NIH HHS DP5 OD033357NIH HHS R21 OD023838NIH HHS R21 OD030107
6 · The paper itself

Abstract

There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from 4 different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.

Indexed as

MurinaeSkinAnimalsMuscle, SkeletalSequence Analysis, RNAAcomys cahirinusgenome assemblyNanopore sequencingregenerative wound healingspiny mouse

Identifiers

PMID37552705
PMCPMC10542272

What OpenQuestion holds

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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.