Segway statistics

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Citations per year

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

This map represents all the scientific publications referring to Segway per scientific context
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Associated diseases

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Popular tool citations

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Protocols

Segway specifications

Information


Unique identifier OMICS_06227
Name Segway
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Segway
  • person_outline Michael Hoffman

Publications for Segway

Segway citations

 (53)
library_books

Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast like synoviocytes

2018
Nat Commun
PMCID: 5953939
PMID: 29765031
DOI: 10.1038/s41467-018-04310-9

[…] es could provide a unique opportunity to define the global epigenomic landscape of RA, they also pose a great challenge to analyze in one integrative model. Segmentation methods, such as ChromHMM and Segway can identify functional elements but focus on histone modifications and have not incorporated other data such as DNA methylation. Furthermore, the epigenomic signals in RA and OA FLS mostly dif […]

library_books

Prediction of enhancer promoter interactions via natural language processing

2018
BMC Genomics
PMCID: 5954283
PMID: 29764360
DOI: 10.1186/s12864-018-4459-6

[…] The majority of our datasets were adapted from TargetFinder. Promoter and enhancer regions were identified using ENCODE Segway [] and ChromHMM [] annotations for K562, GM12878, HeLa-S3, and HUVEC cell lines, and using Roadmap [] Epigenomics ChromHMM annotations for NHEK and IMR90 cell lines. Since EPIs could only happe […]

library_books

Patterns of variation in cis regulatory regions: examining evidence of purifying selection

2018
BMC Genomics
PMCID: 5787233
PMID: 29373957
DOI: 10.1186/s12864-017-4422-y

[…] The genome segmentations used in this study were generated by integrating [] two unsupervised chromatin state annotation algorithms, ChromHMM [] and Segway []. The use of unsupervised methods allowed for enhanced discovery of potential functionality in the genome, with less bias toward well characterized regions. With distinct signals of purifying […]

library_books

Genome wide association study in 79,366 European ancestry individuals informs the genetic architecture of 25 hydroxyvitamin D levels

2018
Nat Commun
PMCID: 5772647
PMID: 29343764
DOI: 10.1038/s41467-017-02662-2

[…] I hypersensitivity sites (DHSs and fetal DHSs), obtained as a combination of Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomics data, and processed by Trynka et al.; combined chromHMM and Segway predictions obtained from Hoffman et al., which leverage on many annotations to partition the genome into seven underlying chromatin states (the CCCTC-binding factor (CTCF), promoter-flanking, […]

library_books

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

2017
Genome Biol
PMCID: 5747114
PMID: 29284524
DOI: 10.1186/s13059-017-1379-8

[…] otations were extracted from the GENCODE v14 release [] (June 2012). The promoters for these transcripts were recorded as −300/+100 bp around their annotated TSSs.Chromatin state maps produced by the SEGWAY algorithm [] were downloaded for Gm12878, HepG2, Huvec, and K562 cells from the Ensembl Biomart site (release 67, May 2012) []. The states ‘Predicted Enhancer’ and ‘Predicted Weak Enhancer/Cis- […]

library_books

Deep‐targeted sequencing of endothelial nitric oxide synthase gene exons uncovers exercise intensity and ethnicity‐dependent associations with post‐exercise hypotension

2017
PMCID: 5704084
PMID: 29180482
DOI: 10.14814/phy2.13510

[…] on data for hg19 is based on 25 different chromatin states (including eight different chromatin marks, RNA polymerase II, and CTCF binding) that are used to segment the genome using both ChromHMM and Segway (ENCODE Project Consortium , Hoffman et al. ). […]


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Segway institution(s)
Princess Margaret Cancer Centre, Toronto, ON, Canada; Engineering Physics Program, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Segway funding source(s)
Supported by the Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-03948), the Canadian Institutes of Health Research (384410) and the National Institutes of Health (U41HG007000).

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