MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Michael Stevens; Jeffrey B. Cheng; Mingchao Xie; Joseph F. Costello; Ting Wang

doi:10.1007/978-3-642-37195-0_23

MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Michael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.

Original language	English
Title of host publication	Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings
Pages	266-268
Number of pages	3
DOIs	https://doi.org/10.1007/978-3-642-37195-0_23
State	Published - Apr 3 2013
Event	17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 - Beijing, China Duration: Apr 7 2013 → Apr 10 2013

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7821 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013
Country/Territory	China
City	Beijing
Period	04/7/13 → 04/10/13

Keywords

Conditional Random Fields
DNA methylation
Epigenomics

Access to Document

10.1007/978-3-642-37195-0_23

Cite this

Stevens, M., Cheng, J. B., Xie, M., Costello, J. F., & Wang, T. (2013). MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. In Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings (pp. 266-268). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7821 LNBI). https://doi.org/10.1007/978-3-642-37195-0_23

Stevens, Michael ; Cheng, Jeffrey B. ; Xie, Mingchao et al. / MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. pp. 266-268 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods",

abstract = "We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.",

keywords = "Conditional Random Fields, DNA methylation, Epigenomics",

author = "Michael Stevens and Cheng, {Jeffrey B.} and Mingchao Xie and Costello, {Joseph F.} and Ting Wang",

year = "2013",

month = apr,

day = "3",

doi = "10.1007/978-3-642-37195-0_23",

language = "English",

isbn = "9783642371943",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

pages = "266--268",

booktitle = "Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings",

note = "17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 ; Conference date: 07-04-2013 Through 10-04-2013",

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Stevens, M, Cheng, JB, Xie, M, Costello, JF & Wang, T 2013, MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. in Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7821 LNBI, pp. 266-268, 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, Beijing, China, 04/7/13. https://doi.org/10.1007/978-3-642-37195-0_23

MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. / Stevens, Michael; Cheng, Jeffrey B.; Xie, Mingchao et al.
Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. p. 266-268 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7821 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods

AU - Stevens, Michael

AU - Cheng, Jeffrey B.

AU - Xie, Mingchao

AU - Costello, Joseph F.

AU - Wang, Ting

PY - 2013/4/3

Y1 - 2013/4/3

N2 - We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.

AB - We introduce MethylCRF, a novel Conditional Random Fields-based algorithm to integrate methylated DNA immunoprecipitation (MeDIP-seq) and methylationsensitive restriction enzyme (MRE-seq) sequencing data to predict DNA methylation levels at single CpG resolution. MethylCRF was benchmarked for accuracy against Infinium arrays, RRBS, whole-genome shotgun-bisulfite (WGBS) sequencing and locus specific-bisufite sequencing on the same DNA. MethylCRF transformation of MeDIP/MRE was equivalent to a biological replicate of WGBS in quantification, coverage and resolution, providing a lower cost and widely accessible strategy to create full methylomes.

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KW - DNA methylation

KW - Epigenomics

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DO - 10.1007/978-3-642-37195-0_23

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SN - 9783642371943

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings

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Stevens M, Cheng JB, Xie M, Costello JF, Wang T. MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. In Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. p. 266-268. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-37195-0_23

MethylCRF, an algorithm for estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods

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