iSAFE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool iSAFE
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Tool usage distribution map

This map represents all the scientific publications referring to iSAFE per scientific context
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iSAFE specifications

Information


Unique identifier OMICS_20823
Name iSAFE
Alternative name integrated Selection of Allele Favored by Evolution
Restrictions to use None
Input data A binary SNP matrix with each row corresponding to a haplotype and each column to a mutation, and entries corresponding to the allelic state.
Input format hap, vcf
Output data A non-negative iSAFE-score for each mutation, according to its likelihood of being the favored variant of the selective sweep.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.1
Stability Stable
Requirements
numpy, pandas, bcftools
Maintained Yes

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  • person_outline Ali Akbari

Publication for integrated Selection of Allele Favored by Evolution

iSAFE citations

 (10)
library_books

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

2018
Nat Commun
PMCID: 5834599
PMID: 29500350
DOI: 10.1038/s41467-018-03342-5

[…] 114423653–175653680 (the region deviating from the genome-wide ancestry estimate by at least 3 SDs: SD3); chr1: 154764878–161975281 (SD6 region); and chr1: 158934324–160006961 (SD9 region). Finally, Isafe analysis was performed on the 5 Mb region around the SD9 region from 156970642 to 161970642 and using ancestral alleles from ensemble database GRCh37. […]

library_books

Localization of adaptive variants in human genomes using averaged one dependence estimation

2018
Nat Commun
PMCID: 5818606
PMID: 29459739
DOI: 10.1038/s41467-018-03100-7

[…] our priors are made explicit, allowing for clearer interpretation. Future applications of SWIF(r) and other composite sweep-detection frameworks can easily incorporate new summary statistics such as iSAFE, which ranks candidate adaptive mutations in a predefined region under selection (Supplementary Fig. ). Future applications of SWIF(r) can additionally assign variable site-specific prior sweep […]

library_books

A tailored online safety and health intervention for women experiencing intimate partner violence: the iCAN Plan 4 Safety randomized controlled trial protocol

2017
BMC Public Health
PMCID: 5360053
PMID: 28327116
DOI: 10.1186/s12889-017-4143-9

[…] mental health of women exposed to IPV was recently tested in a randomized controlled trial in the United States [], the results of which are pending. Two other variations of this online intervention (isafe and I-DECIDE) are currently being tested in randomized controlled trials in New Zealand [] and Australia [].Drawing on these online interventions and our longstanding history of conducting resea […]

library_books

Participant Recruitment and Engagement in Automated eHealth Trial Registration: Challenges and Opportunities for Recruiting Women Who Experience Violence

2016
J Med Internet Res
PMCID: 5101415
PMID: 27780796
DOI: 10.2196/jmir.6515

[…] of birth, safe email address, any special safety instructions for follow-up communications, and an alternative safe contact to facilitate retention. Women were also asked where they had learned about isafe (source of referral) and the number of children living in their home under the age 18 years that they were responsible for. […]

library_books

Benefit–risk assessment of HMG CoA reductase inhibitors (statins): a discrete choice experiment

2016
BMJ Open
PMCID: 4769438
PMID: 26916689
DOI: 10.1136/bmjopen-2015-009387

[…] ly on the BRA of clinical benefits and risks of drugs while there are other important criteria for drug evaluation and selection that were not included. For instance, other assessment criteria of the ISafE score include the route of administration and frequency or the economic evaluation of drugs includes the cost criterion. However, this study only intended to provide an example of adopting this […]

library_books

A web based intervention for abused women: the New Zealand isafe randomised controlled trial protocol

2015
BMC Public Health
PMCID: 4314812
PMID: 25637195
DOI: 10.1186/s12889-015-1395-0

[…] ove knowledge, create more accurate expectations of possible harms and benefits, increase active decision-making, and reduce the proportion of participants who report being undecided.The New Zealand (isafe) research study is part of an international collaborative and concurrent replication of the USA IRIS trial (NCT01312103) testing the effectiveness of an interactive web-based safety decision aid […]


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iSAFE institution(s)
Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
iSAFE funding source(s)
Supported in part by grants from the NSF (IIS-1318386 and DBI-1458557), and from the NIH (R01GM114362).

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