Evidence map›Paper›PMID 28521008›Full record

ArticleNucleic acids research2017

GeMSTONE: orchestrated prioritization of human germline mutations in the cloud.

Siwei Chen, Juan F Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu

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

Article in Nucleic acids research, 2017. 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
–field-weighted citation impact, top 78% 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, 18 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

8 authors at 4 institutions in 2 countries.

Siwei ChenDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Juan F BeltránDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Clara Esteban-JuradoGastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain.
Sebastià Franch-ExpósitoGastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain.
Sergi Castellví-BelGastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, 08036 Barcelona, Catalonia, Spain.
Steven LipkinDepartment of Medicine, Weill Cornell College of Medicine, NY 10021, USA.
Xiaomu WeiWeill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
Haiyuan YuDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Cornell University · USCentro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas · ESConsorci Institut D'Investigacions Biomediques August Pi I Sunyer · ESUniversitat de Barcelona · ES

Funding

Clinical and Translational Science CenterUL1TR000457 · NCATS · WEILL MEDICAL COLL OF CORNELL UNIV · PI IMPERATO-MCGINLEY, JULIANNE L · 2012 to 2016
$46.0M
Identification and Functional Validation of Human Infertility AllelesR01HD082568 · NICHD · CORNELL UNIVERSITY · PI SCHIMENTI, JOHN C · 2015 to 2024
$6.0M
High-throughput functional characterization of human enhancersUM1HG009393 · NHGRI · CORNELL UNIVERSITY · PI LIS, JOHN T, YU, HAIYUAN · 2017 to 2021
$4.1M
Whole Genome Sequencing to Discover Familial Myeloma Risk GenesR01CA167824 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI LIPKIN, STEVEN M, OFFIT, KENNETH · 2012 to 2016
$1.9M
Towards a comprehensive protein interactome network in Schizosaccharomyces pombeR01GM097358 · NIGMS · CORNELL UNIVERSITY · PI YU, HAIYUAN · 2012 to 2016
$1.7M
Using Protein Interactome Networks to Understand the Functional Role of Coding DNR01GM104424 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI LIPKIN, STEVEN M, YU, HAIYUAN · 2013 to 2016
$1.7M
Computational Methods for Unraveling Combinatorial Gene RegulationR01GM108716 · NIGMS · UNIVERSITY OF IOWA · PI TAN, KAI · 2014 to 2017
$1.2M
NCATS NIH HHS UL1 TR000457NCI NIH HHS R01 CA167824NHGRI NIH HHS UM1 HG009393NICHD NIH HHS R01 HD082568NIGMS NIH HHS R01 GM097358NIGMS NIH HHS R01 GM104424NIGMS NIH HHS R01 GM108716
6 · The paper itself

Abstract

Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone.yulab.org/). GeMSTONE generates and readily accepts a shareable 'recipe' file for each run to either replicate previous results or analyze new data with identical parameters and provides a centralized workflow for prioritizing germline mutations in human disease within a streamlined workflow rather than a pool of program executions.

Indexed as

Germ-Line MutationSoftwareCloud ComputingColorectal NeoplasmsDiseaseHigh-Throughput Nucleotide SequencingHumansInternet

Identifiers

PMID28521008
PMCPMC5556704
OpenAlexW2949484021

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.