Epistasis tools

Main content

Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt

Two-locus association mapping in subquadratic runtime

Summary

We have developed efficient algorithms and GPU implementations for genome-wide epistasis screens, that is, genome-wide SNP x SNP interaction search.

Code

Please find our published code for genome-wide SNP x SNP interaction screens in our GitHub repository here.

Reference

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Panagiotis Achlioptas, Bernhard Schölkopf and Karsten Borgwardt
Two-locus association mapping in subquadratic runtime,
Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2011). (Online)

@inproceedings{Achlioptas_Two-locus_2011,
author = {Achlioptas, Panagiotis and Sch\"{o}lkopf, Bernhard and Borgwardt, Karsten},
title = {Two-locus {A}ssociation {M}apping in {S}ubquadratic {T}ime},
booktitle = {Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
series = {KDD '11},
year = {2011},
isbn = {978-1-4503-0813-7},
location = {San Diego, California, USA},
pages = {726--734},
numpages = {9},
url = {http://dx.doi.org/10.1145/2020408.2020521},
doi = "10.1145/2020408.2020521",
publisher = {ACM},
address = {New York, NY, USA},
}

Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok and Karsten M. Borgwardt

GLIDE: GPU-based linear regression for detection of epistasis

Summary

We have developed efficient algorithms and GPU implementations for genome-wide epistasis screens, that is, genome-wide SNP x SNP interaction search.

Code

Please find our published code for genome-wide SNP x SNP interaction screens in our GitHub repository here (as C und CUBA implementation) and here (as Python implementation).

Reference

Keyboard navigation between tabs via Alt arrow keys as well as Home and End.

Tony Kam-Thong, Chloé-Agathe Azencott, Lawrence Cayton, Benno Pütz, Andre Altmann, Philipp G. Sämann, Bernhard Schölkopf, Bertram Müller-Myhsok and Karsten M. Borgwardt
GLIDE: GPU-based linear regression for detection of epistasis
Human Heredity, 2012;73:220-236. (Online)

@article{kam-thong_glide_2012,
    title = {{GLIDE}: {GPU}-{B}ased {L}inear {R}egression for {D}etection of {E}pistasis},
    volume = {73},
    issn = {0001-5652},
    url = {http://www.karger.com/DOI/10.1159/000341885},
    doi = "10.1159/000341885",
    number = {4},
    journal = {Human Heredity},
    author = {Kam-Thong, T. and Azencott, C.-A. and Cayton, L. and P\"{u}tz, B. and Altmann, A. and Karbalai, N. and S\"{a}mann, P.G. and Sch\"{o}lkopf, B. and M\"{u}ller-Myhsok, B. and Borgwardt, K.M.},
    year = {2012},
    pages = {220--236}
}

Contact  Karsten Borgwardt for questions.

 
 
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Sat Jun 24 05:31:56 CEST 2017
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