Imperial College London
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DrMikhailSpivakov

Faculty of Medicine, Institute of Clinical Sciences

Honorary Senior Lecturer
 
 
 
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Contact

 

mikhail.spivakov

 
 
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Location

 

ICTEM buildingHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Cairns:2016:10.1186/s13059-016-0992-2,
author = {Cairns, J and Freire-Pritchett, P and Wingett, SW and Várnai, C and Dimond, A and Plagnol, V and Zerbino, D and Schoenfelder, S and Javierre, BM and Osborne, C and Fraser, P and Spivakov, M},
doi = {10.1186/s13059-016-0992-2},
journal = {Genome Biology},
pages = {127--127},
title = {CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data},
url = {http://dx.doi.org/10.1186/s13059-016-0992-2},
volume = {17},
year = {2016}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
AU  - Cairns,J
AU  - Freire-Pritchett,P
AU  - Wingett,SW
AU  - Várnai,C
AU  - Dimond,A
AU  - Plagnol,V
AU  - Zerbino,D
AU  - Schoenfelder,S
AU  - Javierre,BM
AU  - Osborne,C
AU  - Fraser,P
AU  - Spivakov,M
DO  - 10.1186/s13059-016-0992-2
EP  - 127
PY  - 2016///
SN  - 1474-7596
SP  - 127
TI  - CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
T2  - Genome Biology
UR  - http://dx.doi.org/10.1186/s13059-016-0992-2
UR  - http://www.ncbi.nlm.nih.gov/pubmed/27306882
UR  - http://hdl.handle.net/10044/1/51294
VL  - 17
ER  -
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