Evidence map›Paper›PMID 35440038›Full record

ArticleGenome biology2022

PEGR: a flexible management platform for reproducible epigenomic and genomic research.

Danying Shao, Gretta D Kellogg, Ali Nematbakhsh, Prashant K Kuntala, Shaun Mahony, B Franklin Pugh, William K M Lai

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Kar4 acts as a Ste12 regulator inbioRxiv : the preprint server for biology · 2025
    Article
  4. Article
  5. Article
  6. Epigenetics-targeted drugs: current paradigms and future challenges.Signal transduction and targeted therapy · 2024
    Review
  7. 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

7 authors.

Danying ShaoInstitute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.ORCID 0000-0002-1920-3081
Gretta D KelloggCornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, USA.ORCID 0000-0002-9171-8696
Ali NematbakhshCornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, USA.
Prashant K KuntalaDepartment of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA.
Shaun MahonyDepartment of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA.ORCID 0000-0002-2641-1807
B Franklin PughDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.ORCID 0000-0001-8341-4476
William K M LaiDepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA. wkl29@cornell.edu.ORCID 0000-0003-4351-7037

Funding

Promoter Regulation in Response to Environmental StressR01ES013768 · NIEHS · PENNSYLVANIA STATE UNIVERSITY, THE · PI PUGH, B FRANKLIN · 2007 to 2019
$4.9M
Genome-wide structural organization of proteins within human gene regulatory complexesR01GM125722 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI MAHONY, SHAUN AENGUS, PUGH, B FRANKLIN · 2018 to 2021
$1.5M
NIEHS NIH HHS R01 ES013768NIGMS NIH HHS R01 GM125722
6 · The paper itself

Abstract

Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform.

Indexed as

EpigenomicsGenomicsComputational BiologyGenomeReproducibility of ResultsSoftwareData management systemGalaxyGenomicsHigh-throughput sequencingReproducibilityScience gateway

Identifiers

PMID35440038
PMCPMC9016988

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.