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DDBJ launches a new archive database with analytical tools for next-generation sequence data

Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
<span title="2009-10-22">2009</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;
Moreover, a new archive for sequencing data from next-generation sequencers, the 'DDBJ Read Archive' (DRA), was launched.  ...  Concurrently, for read data registered in DRA, a semi-automatic annotation tool called the 'DDBJ Read Annotation Pipeline' was released as a preliminary step.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of DDBJ for data collection, annotation and release and for software development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp847">doi:10.1093/nar/gkp847</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19850725">pmid:19850725</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808917/">pmcid:PMC2808917</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2yd7lgivcjdunjkd66kshsexim">fatcat:2yd7lgivcjdunjkd66kshsexim</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219212652/http://pdfs.semanticscholar.org/1ad0/aa6c1344b78657dfe36cd5e96eb46913bb93.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/1a/d0/1ad0aa6c1344b78657dfe36cd5e96eb46913bb93.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp847"> <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/PMC2808917" 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 DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments

Y. Kodama, J. Mashima, E. Kaminuma, T. Gojobori, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
<span title="2011-11-22">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;
DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers.  ...  The DNA Data Bank of Japan (DDBJ; http://www .ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of DDBJ for data collection, annotation and release and for software development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr994">doi:10.1093/nar/gkr994</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22110025">pmid:22110025</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3244990/">pmcid:PMC3244990</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kbjrao6jw5hnrc4tcpq767mgsi">fatcat:kbjrao6jw5hnrc4tcpq767mgsi</a> </span>
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DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
<span title="2015-11-17">2015</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;
The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DB-CLS) in Japan.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1105">doi:10.1093/nar/gkv1105</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26578571">pmid:26578571</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702806/">pmcid:PMC4702806</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dsvzn2iivjb7jhqnqhoehswhtu">fatcat:dsvzn2iivjb7jhqnqhoehswhtu</a> </span>
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DDBJ progress report: a new submission system for leading to a correct annotation

Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
<span title="2013-11-04">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;
DDBJ launched a new nucleotide sequence submission system for receiving traditional nucleotide sequence.  ...  In addition, DDBJ has started a new service, the Japanese Genotypephenotype Archive (JGA), with our partner institute, the National Bioscience Database Center (NBDC).  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Keiichi Nagai and all members of DDBJ for their assistance in data collection, annotation, release and software development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1066">doi:10.1093/nar/gkt1066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24194602">pmid:24194602</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3964987/">pmcid:PMC3964987</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vc62xknuzret3iehrzgxhzqhve">fatcat:vc62xknuzret3iehrzgxhzqhve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729072229/https://watermark.silverchair.com/gkt1066.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaEwggGdBgkqhkiG9w0BBwagggGOMIIBigIBADCCAYMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMBbCsq61GHkNLTrg0AgEQgIIBVMKgVHHVDoM-OC_p7Hu1GTdUDjZoblSPF4-zgFd8ENaOGrbnzp9zzjgJq7l2J5M9v3s_JTH9QCAaHwjhc5aRLt7jHg_FfpcFCF8f2aD530gj-XknOfHwiOy_gbJ6JyH0ZWDpfUjPBqtObpFzQEn776LbsXVlYAVNTryBXjUewDc_G9SEK87QAiC-Ncou5SNqp_tYSrzvpiWZ3tCkSfVh1hd6O738pFCXQcwceudBbgz7VadooVrCvDbvh0tWIvlzM07gbkvW7ZGn8zB8eSOt0Jbe_Jj5gSsi5y96xzyz7JeVARmKjWFHBnCEo45gJVWhnmGpG1CkELRAVWGsLdbBewf-mwrQk8bSp_FakKt5fLvX-NwGrBCMfPh5PXcHTvTmPNQpeSlimWeKoR-RB_HbDmPaoJWp0oXzn3V5zs7WQ6oQiKggBpmY8Ic4MyNtLCotMzg5-d0" 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/90/c0/90c0394fc55fabf8d1d5aeb135cd2dbb01a0b3e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1066"> <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/PMC3964987" 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 DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
<span title="2014-12-03">2014</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;
The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science.  ...  Nakazato, Yuki Naito and Tazro Ohta of DBCLS for database search tools linked from the DDBJ websites; Hideki Nagasaki, Yasuhiro Tanizawa and Shota Morizaki for the DDBJ pipeline updates; Jerven Bolleman  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1120">doi:10.1093/nar/gku1120</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25477381">pmid:25477381</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383935/">pmcid:PMC4383935</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tcpa3elm3zglbo5lauuatx3nca">fatcat:tcpa3elm3zglbo5lauuatx3nca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220192430/http://pdfs.semanticscholar.org/2824/8f0713bd2dd97171ea8c4b3e4b16070dd487.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/28/24/28248f0713bd2dd97171ea8c4b3e4b16070dd487.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1120"> <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/PMC4383935" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

Takako Mochizuki, Yasuhiro Tanizawa, Takatomo Fujisawa, Tazro Ohta, Naruo Nikoh, Tokurou Shimizu, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura (+1 others)
<span title="2017-02-24">2017</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;
With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed.  ...  This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority.  ...  We also thank Shota Morizaki and DDBJ members for system development, Manami Kuruma for supporting to analyze the DNA polymorphisms, Yoshiaki Harushima for helpful comments, and Kimiko Saka for manual  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0172269">doi:10.1371/journal.pone.0172269</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28234924">pmid:28234924</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5325239/">pmcid:PMC5325239</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hcxwu5p2cvastpyys7ernqcksi">fatcat:hcxwu5p2cvastpyys7ernqcksi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171012081914/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0172269&amp;type=printable" 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/1e/cb/1ecb5ed84f90f1b2bf976503194eff346120dbf0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0172269"> <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/PMC5325239" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics: scope and challenges in aquaculture research of Bangladesh- a review

KMS Rana, K Ahammad, MA Salam
<span title="2021-01-21">2021</span> <i title="Bangladesh Journals Online (JOL)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3ckpbbdl3bb4fouiznmbs7ezni" style="color: black;">International Journal of Agricultural Research, Innovation and Technology</a> </i> &nbsp;
By default, these software tools mine and analyze a vast biological data set using the available databases.  ...  However, aquaculture scientists can use bioinformatics for genomic data manipulation, genome annotation and expression profiling, molecular folding, modeling, and design as well as generating biological  ...  database. ✓ Sequence Read Archive (SRA) Submission-stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina, Life Technologies AB SOLiD System.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3329/ijarit.v10i2.51587">doi:10.3329/ijarit.v10i2.51587</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2rq6a6cpmrgpbobg5ydkpqw54a">fatcat:2rq6a6cpmrgpbobg5ydkpqw54a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210203142756/https://www.banglajol.info/index.php/IJARIT/article/download/51587/36752" 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/67/ba/67ba3f8cadb58e315c07905548abb6fec14a8bc0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3329/ijarit.v10i2.51587"> <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>

The Universal Protein Resource (UniProt) 2009

<span title="2009-01-01">2009</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;
be launched directly from any page, and the output of these tools can be combined, filtered and browsed like normal database searches.  ...  New and updated sequences are loaded on a daily basis, cross-referenced to the source database accession number and provided with a sequence version that increments upon changes to the underlying sequence  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn664">doi:10.1093/nar/gkn664</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18836194">pmid:18836194</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2686606/">pmcid:PMC2686606</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4nz73vlhq5f7fbcyreyxbtse6a">fatcat:4nz73vlhq5f7fbcyreyxbtse6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730204128/https://watermark.silverchair.com/gkn664.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMIM_EnM7B-_bXGDVwAgEQgIIBXaV0TiEIzWG6rSuqoa11z4bakmcvTWrRAEV_zFGp1p8RS-8YKH5mPp3zB329S5cspgK_d33B5G5LhjCeYypy9N75MzpDTEx6B_m7BOgaW6W4n-o9P2S6juuH3S-75GQ9JrV_KKja03guevK-MOfL8RgFomK5spiOl8uTsMBhiSPcPWBkxg_lzhLrCXshJiSPG7cAoCrO7Fujx2PH5ztNb4xW5LX8Qrk0kgCnf5s2iV9m8uDYTEpxtctHwC4-xLFszQKhZ1N1APoL4AKtyD4qWv0DPu9uIfvK2ivvkxhtdtfoJBZZNrEOM5LfFVoH2_2ABtfSr76TLPBgKgObj_BXlRbkTkJH-8gMJ3kasLdzvcWWa1rti2uaU7OI8TF1OtfBMOZWjtRjK-q-Z7CpgbQg7fpIaUKAAIJpmIb4z6KiKziINqv7VOvvrPI9Vg-tDzBNM6dcRzpfv9RUk9MgPvo" 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/b6/b2/b6b2a97b9b0feac9df70b16afa7dc9afe3211362.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn664"> <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/PMC2686606" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recent advancement in Next Generation Sequencing techniques and its computational analysis [article]

Khalid Raza, Sabahuddin Ahmad
<span title="2017-03-24">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society.  ...  The algorithms in group, act as a tool in analysing the NGS data.  ...  LANL HIV-DB Next Generation Sequence Archive It is a repository for next-generation lenti-virus sequence data sets containing HIV, SIV and anti-HIV/SIV antibody ultra-deep sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1606.05254v2">arXiv:1606.05254v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ruu3lkfca5fetkzfg5vywzx2su">fatcat:ruu3lkfca5fetkzfg5vywzx2su</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191016221406/https://arxiv.org/pdf/1606.05254v2.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/3d/dd/3ddd2d820df97b0f24c65ac2124c327a911f48d8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1606.05254v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

The landscape for epigenetic/epigenomic biomedical resources

Kabita Shakya, Mary J. O'Connell, Heather J. Ruskin
<span title="2012-09-07">2012</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lkovtdud7bactlc5fb4ffvecii" style="color: black;">Epigenetics</a> </i> &nbsp;
Generation of enormous amounts of data has driven the need for more advanced storage solutions and shared access through a range of public repositories.  ...  This paper attempts a general overview of currently available resources, together with remarks on their data mining and analysis capabilities.  ...  epigenetic mechanisms, develop new epigenetic analytics, generate a repository and long-term data archive, standardize procedures and practices in epigenomics and support new technologies for these.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/epi.21493">doi:10.4161/epi.21493</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22874136">pmid:22874136</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3515018/">pmcid:PMC3515018</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rx6yymd6vzfgdicsxxcfvqdyzq">fatcat:rx6yymd6vzfgdicsxxcfvqdyzq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191019180608/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3515018&amp;blobtype=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/49/67/4967b8c3addeb0cfbbae41acc803f18ce098f571.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4161/epi.21493"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515018" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatic tools for cancer geneticists

Karmen Stankov
<span title="">2005</span> <i title="National Library of Serbia"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oj5szgm6dfhs5nc3yvreii2gpm" style="color: black;">Archive of Oncology</a> </i> &nbsp;
Early detection is essential for the control and prevention of many diseases, particularly cancer, which is the reason why the need for new disease markers with improved sensitivity and specificity continues  ...  Utilization of sophisticated bioinformatic tools enables the increased specificity and a relatively large quantity of high quality assays for any gene of interest.  ...  EMBL, NCBI, and DDBJ automatically update each other every 24 hours with the new sequences they collected or updated.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2298/aoo0502069s">doi:10.2298/aoo0502069s</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f4p7fkaxtrcbxbfbnghz4d2md4">fatcat:f4p7fkaxtrcbxbfbnghz4d2md4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810162726/http://www.onk.ns.ac.rs/archive/Vol13/PDFVol13/V13n2p69.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/7e/fe/7efe2d57b06bc7c8c94cadcb4a35f5978735400a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2298/aoo0502069s"> <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>

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform [article]

Thomas C Matthews, Franklin R Bristow, Emma J Griffiths, Aaron Petkau, Josh Adam, Damion Dooley, Peter Kruczkiewicz, John Curatcha, Jennifer Cabral, Dan Fornika, Geoffrey L Winsor, Melanie Courtot (+20 others)
<span title="2018-07-31">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping  ...  hypothesis generation in epidemiological investigations.  ...  IRIDA is also capable of submitting sequence data and metadata to NCBI's sequence read archive (SRA), which is synchronized daily with EBI-EMBL's ENA and Japan's DDBJ.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/381830">doi:10.1101/381830</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/erbxafldgfg73ow6djqctuiawy">fatcat:erbxafldgfg73ow6djqctuiawy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504064230/https://www.biorxiv.org/content/biorxiv/early/2018/07/31/381830.full.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/e5/28/e5280662a0d93d917774fa1b5b1a45c40253e43d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/381830"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

K. Mochida, K. Shinozaki
<span title="2011-12-01">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qyzgzqbtjbd3xewtgies5bhl2e" style="color: black;">Plant and Cell Physiology</a> </i> &nbsp;
Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications.  ...  Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged.  ...  The authors also thank Daisuke Saisho of Okayama University for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcr153">doi:10.1093/pcp/pcr153</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22156726">pmid:22156726</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3233218/">pmcid:PMC3233218</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5p4m7xlrknflrfbjfb4pwdug4u">fatcat:5p4m7xlrknflrfbjfb4pwdug4u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228183213/http://pdfs.semanticscholar.org/8ff4/917fa8e5fb04ec4c5a0e2a3d09d6904f50d1.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/8f/f4/8ff4917fa8e5fb04ec4c5a0e2a3d09d6904f50d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcr153"> <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/PMC3233218" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, Maria Luisa Chiusano
<span title="2019-10-11">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ec2qn47apbbfjgxx4e2oivikr4" style="color: black;">Marine Drugs</a> </i> &nbsp;
a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas.  ...  As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies  ...  , and the DDBJ sequence Read Archive (DRA) [96] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/md17100576">doi:10.3390/md17100576</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31614509">pmid:31614509</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6835618/">pmcid:PMC6835618</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jch7dwrhgrhipihvf42zr6bljm">fatcat:jch7dwrhgrhipihvf42zr6bljm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200216105956/https://res.mdpi.com/d_attachment/marinedrugs/marinedrugs-17-00576/article_deploy/marinedrugs-17-00576.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/6d/50/6d50a5e2f33a44bcc651b36467ac73729c51fe7a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/md17100576"> <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/PMC6835618" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
<span title="2019-09-23">2019</span> <i title="F1000 ( Faculty of 1000 Ltd)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining.  ...  Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences.  ...  Database Center (NBDC) and the Database Center for Life Science (DBCLS).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.18238.1">doi:10.12688/f1000research.18238.1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdt6bijqlveanplh4bmca5towu">fatcat:mdt6bijqlveanplh4bmca5towu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715103036/https://repository.kaust.edu.sa/bitstream/handle/10754/667841/d641b67c-4e85-42b4-91d7-02098a169622_18238_-_toshiaki_katayama.pdf;jsessionid=3596FE4053F2D8703C9F2EDEFC8E69B3?sequence=1" 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/3e/80/3e807c38ea052f76aa1ddfbee43dd39a56f1d08b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.18238.1"> <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>
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