(Q38215486)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

Methodological aspects of whole-genome bisulfite sequencing analysis (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

main subject

whole genome sequencing

1 reference

based on heuristic

inferred from title

author

Swarnaseetha Adusumalli

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Touati Benoukraf

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

author name string

Mohd Feroz Mohd Omar

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Richie Soong

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

publication date

27 May 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

Briefings in Bioinformatics

19 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

volume

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

page(s)

369-379

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

5-Methylcytosine DNA demethylation: more than losing a methyl group

19 March 2020

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Methylation adjacent to negatively regulating AP-1 site reactivates TrkA gene expression during cancer progression

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Methylation of adjacent CpG sites affects Sp1/Sp3 binding and activity in the p21(Cip1) promoter

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DNA methylation presents distinct binding sites for human transcription factors

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The DNA methylation paradox

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Down-regulation of PU.1 by methylation of distal regulatory elements and the promoter is required for myeloma cell growth.

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DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas.

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Highly integrated single-base resolution maps of the epigenome in Arabidopsis

21 January 2018

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

21 January 2018

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Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

21 January 2018

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Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome

21 January 2018

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Global epigenomic reconfiguration during mammalian brain development

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DNA methylation: a timeline of methods and applications

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Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues

21 January 2018

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Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis--a personal account

21 January 2018

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BIGpre: a quality assessment package for next-generation sequencing data

21 January 2018

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BSeQC: quality control of bisulfite sequencing experiments

21 January 2018

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HTQC: a fast quality control toolkit for Illumina sequencing data

21 January 2018

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NGS QC Toolkit: a toolkit for quality control of next generation sequencing data

21 January 2018

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PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

21 January 2018

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QC-Chain: fast and holistic quality control method for next-generation sequencing data

21 January 2018

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SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

21 January 2018

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RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

21 January 2018

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WBSA: web service for bisulfite sequencing data analysis

21 January 2018

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BRAT: bisulfite-treated reads analysis tool

21 January 2018

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BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

21 January 2018

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BSMAP: whole genome bisulfite sequence MAPping program

21 January 2018

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BS Seeker: precise mapping for bisulfite sequencing

21 January 2018

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

21 January 2018

1 reference

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SOAP: short oligonucleotide alignment program

21 January 2018

1 reference

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BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

21 January 2018

1 reference

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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

21 January 2018

1 reference

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BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

21 January 2018

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MethylCoder: software pipeline for bisulfite-treated sequences

21 January 2018

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MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment

21 January 2018

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PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads

21 January 2018

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A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics

21 January 2018

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DMEAS: DNA methylation entropy analysis software

21 January 2018

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GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data.

21 January 2018

1 reference

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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

21 January 2018

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Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

21 January 2018

1 reference

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The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

21 January 2018

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SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

21 January 2018

1 reference

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Trimmomatic: a flexible trimmer for Illumina sequence data

21 January 2018

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Base-calling of automated sequencer traces using phred. I. Accuracy assessment

21 January 2018

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 January 2018

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Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

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Mapping short DNA sequencing reads and calling variants using mapping quality scores

21 January 2018

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Analysing and interpreting DNA methylation data

21 January 2018

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Updates to the RMAP short-read mapping software

21 January 2018

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Fast mapping of short sequences with mismatches, insertions and deletions using index structures

21 January 2018

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The Sequence Alignment/Map format and SAMtools

21 January 2018

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Establishing, maintaining and modifying DNA methylation patterns in plants and animals

21 January 2018

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Nucleosome deposition and DNA methylation at coding region boundaries

21 January 2018

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Relationship between nucleosome positioning and DNA methylation

21 January 2018

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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

21 January 2018

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Effects of DNA methylation on nucleosome stability

21 January 2018

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Principles and challenges of genomewide DNA methylation analysis

21 January 2018

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Dynamic changes in the human methylome during differentiation

21 January 2018

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'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

21 January 2018

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Genome-wide quantitative assessment of variation in DNA methylation patterns

21 January 2018

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The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

21 January 2018

1 reference

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 January 2018

1 reference

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Circos: an information aesthetic for comparative genomics

21 January 2018

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GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data

21 January 2018

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Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

21 January 2018

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The DNA methylome of human peripheral blood mononuclear cells

21 January 2018

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Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

21 January 2018

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Gene body-specific methylation on the active X chromosome

21 January 2018

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Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

21 January 2018

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DNA methylation profiling of human chromosomes 6, 20 and 22

21 January 2018

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Developmental programming of CpG island methylation profiles in the human genome

21 January 2018

1 reference

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DNA methylation dynamics in health and disease

21 January 2018

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Tobacco-smoking-related differential DNA methylation: 27K discovery and replication

21 January 2018

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Mammalian genomic imprinting.

21 January 2018

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Monoallelic gene expression and its mechanisms

21 January 2018

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Imprinted genes and their role in human fetal growth.

21 January 2018

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Mechanisms regulating imprinted genes in clusters.

21 January 2018

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21 January 2018

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Genomic landscape of human allele-specific DNA methylation.

21 January 2018

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A high-throughput DNA methylation analysis of a single cell

21 January 2018

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The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

21 January 2018

1 reference

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Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

21 January 2018

1 reference

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Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.

21 January 2018

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Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU016

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU016

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA.

21 January 2018

1 reference

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Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

21 January 2018

1 reference

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Annotation of functional variation in personal genomes using RegulomeDB

21 January 2018

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AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

21 January 2018

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21 January 2018

Identifiers

DOI

10.1093/BIB/BBU016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24867940%20AND%20SRC:MED&resulttype=core&format=json

journals/bib/AdusumalliOSB15

19 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference