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NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

M. Hackenberg, G. Barturen, J. L. Oliver
<span title="2010-10-21">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution.  ...  However, no database exists fully addressing such requirements. We propose here NGSmethDB  ...  We therefore propose here NGSmethDB, a database for single-cytosine resolution methylation data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq942">doi:10.1093/nar/gkq942</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20965971">pmid:20965971</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013793/">pmcid:PMC3013793</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rmxn247h4febnlem5vao52hmrq">fatcat:rmxn247h4febnlem5vao52hmrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226052329/http://pdfs.semanticscholar.org/79a6/d0058dbce50593807dc7dd11a1909a348660.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/79/a6/79a6d0058dbce50593807dc7dd11a1909a348660.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq942"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013793" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes

Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg, José L. Oliver
<span title="2013-11-22">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
A next-generation methylation browser allows fast and smooth scrolling and zooming, thus speeding data download/upload, at the same time requiring fewer server resources.  ...  The updated release of 'NGSmethDB' (http:// bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes.  ...  The advent of next-generation sequencing (NGS), together with bisulfite conversion of DNA, allows the generation of whole genome methylation maps at single-cytosine resolution (17) (18) (19) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1202">doi:10.1093/nar/gkt1202</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24271385">pmid:24271385</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3964946/">pmcid:PMC3964946</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6amwg23cfvechfgkjumjx4wujy">fatcat:6amwg23cfvechfgkjumjx4wujy</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3964946/PMC3964946-gkt1202.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b9/0f/b90ff4830c851c6e06da1f7614af04b180c9f877.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1202"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964946" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Advances in Bioinformatics Tools for High-Throughput Sequencing Data of DNA Methylation

Jianzhong Su
<span title="">2012</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3lg7vm6yxvfxxnghvyd2wnmgse" style="color: black;">Hereditary Genetics: Current Research</a> </i> &nbsp;
Recently, Next-generation sequencing (NGS) technologies spurred a revolution in investigating global DNA methylation profiles.  ...  bioinformatics tools and resources for further analysis of DNA methylation.  ...  ac.cn/ [57] PubMeth Database of DNA methylation literature http://www.pubmeth.org/ [99] NGSmethDB Database for DNA methylation data at single- base resolution http://bioinfo2.ugr.es/ NGSmethDB  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2161-1041.1000107">doi:10.4172/2161-1041.1000107</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5ixyr2ionnhgxhryo7hkihujza">fatcat:5ixyr2ionnhgxhryo7hkihujza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426214053/https://www.longdom.org/open-access/advances-in-bioinformatics-tools-for-high-throughput-sequencing-data-of-dna-methylation-2161-1041.1000107.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4f/27/4f274595817f9a33ab4f59543731abce90f27a71.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2161-1041.1000107"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Mining methylome databases

Colm J. O'Rourke, Therese M. Murphy, Donal Hollywood, Antoinette S. Perry
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Similarly, the Next-Generation Sequencing Methylation DataBase (NGSmethDB) offers a repository for the collection and retrieval of methylomic data [4] .  ...  MethylomeDB is currently the only psychiatric-specific methylation database, containing postmortem human and mouse genome-wide brain DNA methylation profiles (at single-CpG resolution), relating to depression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2012.10.015">doi:10.1016/j.tig.2012.10.015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23182652">pmid:23182652</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/372kmdtwjbcqxd523jvx4uvize">fatcat:372kmdtwjbcqxd523jvx4uvize</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814231309/http://www.lenus.ie/hse/bitstream/10147/324065/1/O%27Rourke%20et%20al.%20%28TiG%202013%29.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7c/d8/7cd8241cd9332c759800efc0941d053d6d506b57.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2012.10.015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

Guillermo Barturen, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, José L. Oliver
<span title="">2013</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
The resultingCpGislandEVOdatabase, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.  ...  Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date.  ...  The database, coupled to a powerful genome browser, links together experimental and predicted CGIs, as well as single-cytosine-resolution DNA methylation data from different mammalian species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/709042">doi:10.1155/2013/709042</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24205506">pmid:24205506</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3800598/">pmcid:PMC3800598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kzilxzdjlbcjra6swhfs6lopii">fatcat:kzilxzdjlbcjra6swhfs6lopii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227000053/http://pdfs.semanticscholar.org/795b/d8f1a488570a4ee9db68e6283f778b7d2dff.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/79/5b/795bd8f1a488570a4ee9db68e6283f778b7d2dff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/709042"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800598" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DevMouse, the mouse developmental methylome database and analysis tools

H. Liu, R. Zhu, J. Lv, H. He, L. Yang, Z. Huang, J. Su, Y. Zhang, S. Yu, Q. Wu
<span title="2014-01-09">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Moreover, a configurable MethyBrowser is provided to view the base-resolution methylomes under a genomic context.  ...  Bisulfite sequencing enables profiling of mouse developmental methylomes on an unprecedented scale; however, integrating and mining these data are challenges for experimental biologists.  ...  Acknowledgement The authors thank Dr Yaoping Lei for revising the manuscript. Conflict of interest. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bat084">doi:10.1093/database/bat084</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24408217">pmid:24408217</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3885893/">pmcid:PMC3885893</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vzoee7m56bd3zphzmm7gaznsaa">fatcat:vzoee7m56bd3zphzmm7gaznsaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808185514/https://www.science-open.com/document_file/2ea9fb34-66bf-4756-986a-a2224360cd4d/PubMedCentral/2ea9fb34-66bf-4756-986a-a2224360cd4d.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cc/e2/cce2c052109517bdbd9a458fd96ceee4724a7534.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bat084"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885893" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DNA Methylation Profiling from High-Throughput Sequencing Data [chapter]

Michael Hackenberg, Guillermo Barturen, Jos L.
<span title="2012-03-16">2012</span> <i title="InTech"> DNA Methylation - From Genomics to Technology </i> &nbsp;
In order to attend these needs we developed NGSmethDB , a database for the storage, browsing and data mining of single-base-pair resolution methylation data which has the following main features:  Based  ...  We will conclude the chapter with a brief discussion of NGSmethDB, a database for the storage of single-base resolution methylation maps that can be used to further analyze the obtained methylation maps  ...  DNA Methylation Profiling from High-Throughput Sequencing Data, DNA Methylation -From Genomics to Technology, Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/34825">doi:10.5772/34825</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fls5ec63rnc5ngu2gax2oik3le">fatcat:fls5ec63rnc5ngu2gax2oik3le</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725141707/https://api.intechopen.com/chapter/pdf-download/32798" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1f/1e/1f1e577092cc5024d111b55d427ccba027d45147.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/34825"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A Method for Identification of the Methylation Level of CpG Islands From NGS Data

Leonid A. Uroshlev, Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il'icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor A. Kondrashov, Yury D. Nechipurenko, Sergei L. Grokhovsky
<span title="2020-05-25">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods.  ...  The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.  ...  This work was supported by project no. 0112-2019-0001 and RFFI grants 18-07-00354 А; 17-07-01331 A, program of the Presidium of the Russian Academy of Sciences for Molecular and Cellular Biology no. 01201456592  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-65406-1">doi:10.1038/s41598-020-65406-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32451390">pmid:32451390</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7kqwylehevg3bn3axpho7txnpq">fatcat:7kqwylehevg3bn3axpho7txnpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200609230159/https://www.nature.com/articles/s41598-020-65406-1.pdf?error=cookies_not_supported&amp;code=c5d42fab-114d-4879-9e96-a8e0ad0329da" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/56/e1567d54436f28e660aba167b666aaaf97050d3e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-65406-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

MethylomeDB: a database of DNA methylation profiles of the brain

Yurong Xin, Benjamin Chanrion, Anne H. O'Donnell, Maria Milekic, Ramiro Costa, Yongchao Ge, Fatemeh G. Haghighi
<span title="2011-12-02">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Users can view the methylation data at single-CpG resolution with the option of wiggle and microarray formats. They can also download methylation data for individual samples.  ...  MethylomeDB (http://epigenomics.columbia.edu/ methylomedb/index.html) is a new database containing genome-wide brain DNA methylation profiles.  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Jay Gingrich for making the mouse methylome data available for inclusion Figure 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1193">doi:10.1093/nar/gkr1193</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22140101">pmid:22140101</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245019/">pmcid:PMC3245019</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/smcfmj2heba57cegwomkcroi7e">fatcat:smcfmj2heba57cegwomkcroi7e</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3245019/PMC3245019-gkr1193.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/1f/e61f201404e6f238e20313a30c2e879ec92bb674.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1193"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245019" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

Qiang Song, Benjamin Decato, Elizabeth E. Hong, Meng Zhou, Fang Fang, Jianghan Qu, Tyler Garvin, Michael Kessler, Jun Zhou, Andrew D. Smith, Osman El-Maarri
<span title="2013-12-06">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness  ...  DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes.  ...  Although individual methyl groups can either be present or absent on a cytosine, current WGBS data is not from single cells, and we therefore refer to a methylation ''level'' for each cytosine, interpreted  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0081148">doi:10.1371/journal.pone.0081148</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24324667">pmid:24324667</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3855694/">pmcid:PMC3855694</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/szywcbftprfq5lafk2g2jhbf3i">fatcat:szywcbftprfq5lafk2g2jhbf3i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808065325/http://smithlabresearch.org/papers/Song_PONE_2013.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6f/64/6f6493239a7adf0d77b23b85e34a2f8b9a57f036.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0081148"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855694" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Insight of Regulation Mechanism from DNA Methylation Based on Single Base Resolution Sequencing Data

Zhang M, Wen Y.H, Wang F
<span title="">2015</span> <i title="Sophia Publishing Group, Inc."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5upamhydhjabjlwy3ji5nf6ewi" style="color: black;">Cancer Genetics and Epigenetics</a> </i> &nbsp;
Many differential methylaiton regions were identified based on high-throughput methylation data between tissues, especially normal and tumors.  ...  Here, we reviewed the regulation mechanism and dynamics of DNA methylation and proposed the prospect of DNA methylation pattern polymorphism.  ...  The next generation of high-throughput single nucleotide resolution sequencing data allow the further research of regulatory mechanisms of DNA methylation on a larger scale and unprecedented resolution  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5376/cge.2015.03.0009">doi:10.5376/cge.2015.03.0009</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3duggsjrsrg7jl5xdzv4woruca">fatcat:3duggsjrsrg7jl5xdzv4woruca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719111147/http://biopublisher.ca/index.php/cge/article/download/1901/1661" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/8e/ad8ec59b4fb24ebe1262454f6b4a58cc3d2421d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5376/cge.2015.03.0009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Next-Generation Sequencing: From Understanding Biology to Personalized Medicine

Karen Frese, Hugo Katus, Benjamin Meder
<span title="2013-03-01">2013</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j5h4zct24vcofi5scx6ttoapnq" style="color: black;">Biology</a> </i> &nbsp;
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease.  ...  Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.  ...  Acknowledgements Our research is supported by grants from the German Ministry of Education and Research (BMBF): NGFN-plus 01GS0836, NGFN-Herz-Kreislauf-German Centre for Cardiovascular Research); the University  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology2010378">doi:10.3390/biology2010378</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24832667">pmid:24832667</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4009863/">pmcid:PMC4009863</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zkakkzgc25benbu2zzenhvbjvm">fatcat:zkakkzgc25benbu2zzenhvbjvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130930214509/http://www.mdpi.com:80/2079-7737/2/1/378/pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/19/80/198017fa66aa8b3c36613c371fb41fd4428df476.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology2010378"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009863" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Epigenetic regulation in obesity

C Lavebratt, M Almgren, T J Ekström
<span title="2011-09-13">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t4r7quidordx5nlutsof7zcwfq" style="color: black;">International Journal of Obesity</a> </i> &nbsp;
Future more comprehensive knowledge on epigenetic regulation will complement genome sequence data for the understanding of the complex etiology of obesity and related disorder.  ...  The availability to the DNA strand and the activity of the transcription machinery is crucial for the cell to use the information in the DNA.  ...  However, there are some information on DNA methylation patterns in various tissues in, for example, the Methylation Database (MethDB, www.methdb.de) and Next Generation Sequencing single-cytosine-resolution  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ijo.2011.178">doi:10.1038/ijo.2011.178</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21912396">pmid:21912396</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2zd2hgssmzabhiuo35wyssra7y">fatcat:2zd2hgssmzabhiuo35wyssra7y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200315160523/https://www.nature.com/articles/ijo2011178.pdf?error=cookies_not_supported&amp;code=e1f77000-7441-4478-9afb-a06baf6dae6b" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/15/92/15920c2bb5d77e832916b8f4394eae43df7ad02d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ijo.2011.178"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium [chapter]

Venkateswara R. Sripathi, Ramesh Buyyarapu, Siva P. Kumpatla, Abreeotta J. Williams, Seloame T. Nyaku, Yonathan Tilahun, Venu Kalavacharla, Govind C. Sharma
<span title="2016-07-27">2016</span> <i title="InTech"> Bioinformatics - Updated Features and Applications </i> &nbsp;
In order to achieve this, a functional understanding of bioinformatics resources such as databases, software solutions, and analysis tools is required.  ...  This discourse begins with a description of concurrent advances in high-throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources  ...  Joshua Reid at Alabama A&M University for reviewing this book chapter. Also authors would like to thank Dr. Ibrokhim Abdurakhmonov and Ms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/64325">doi:10.5772/64325</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y4svepemajghfddagn535mvpqy">fatcat:y4svepemajghfddagn535mvpqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501174326/https://cdn.intechopen.com/pdfs/51541.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/07/b2076517d09483bd6b7fc62fe53813afbb0bcd8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/64325"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

DNA Methylation is Associated with an Increased Level of Conservation at Nondegenerate Nucleotides in Mammals

Trees-Juen Chuang, Feng-Chi Chen
<span title="2013-10-24">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a> </i> &nbsp;
DNA methylation at CpG dinucleotides can significantly increase the rate of cytosine-to-thymine mutations and the level of sequence divergence.  ...  Although the correlations between DNA methylation and genomic sequence evolution have been widely studied, an unaddressed yet fundamental question is how DNA methylation is associated with the conservation  ...  I-Ching Wu for their assistance in statistical tests and programming, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/mst208">doi:10.1093/molbev/mst208</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24157417">pmid:24157417</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3907051/">pmcid:PMC3907051</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wxgjlfgnovh7toymyoixhp3n7m">fatcat:wxgjlfgnovh7toymyoixhp3n7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303200603/http://pdfs.semanticscholar.org/bb08/2577f7bf0d9bab8a7fac169d5cdc8f345f16.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bb/08/bb082577f7bf0d9bab8a7fac169d5cdc8f345f16.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/mst208"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907051" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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