Evidence map›Paper›PMID 28541456›Full record

ArticleBioinformatics (Oxford, England)2017

CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.

Hyun-Hwan Jeong, Seon Young Kim, Maxime W C Rousseaux, Huda Y Zoghbi, Zhandong Liu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Review
  6. Article
  7. Review
  8. Article
  9. Article
  10. Functional Genomics via CRISPR-Cas.Journal of molecular biology · 2019
    Review
  11. A Druggable Genome Screen Identifies Modifiers of α-Synuclein Levels via a Tiered Cross-Species Validation Approach.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2018
    Article
  12. Article
  13. Article
  14. 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

5 authors.

Hyun-Hwan JeongDepartment of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.
Seon Young KimDepartment of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.
Maxime W C RousseauxDepartment of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.
Huda Y ZoghbiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.
Zhandong LiuJan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.

Funding

Imaging Mass Spectrometry for metabolome mappingR01GM120033 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI LIU, ZHANDONG, MALETIC-SAVATIC, MIRJANA · 2017 to 2021
$2.5M
NIGMS NIH HHS R01 GM120033
6 · The paper itself

Abstract

summaryWe present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, CRISPRcloud, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, CRISPRcloud serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data. AVAILABILITY AND IMPLEMENTATION: http://crispr.nrihub.org. CONTACT: zhandong.liu@bcm.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

SoftwareClustered Regularly Interspaced Short Palindromic RepeatsComputational BiologyHigh-Throughput Nucleotide SequencingSequence Analysis, DNA

Identifiers

PMID28541456
PMCPMC5870715

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.