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A domain sequence approach to pangenomics: applications to Escherichia coli

Lars-Gustav Snipen, David W Ussery
<span title="2013-05-29">2013</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
We use this approach in a pangenome study of the model organism Escherichia coli, the prokaryotic species with the largest set of available genomes.  ...  The data are from the model organism Escherichia coli only, and many of the more specific results cannot be extended to other species.  ...  On page four, in the Methods part of the paper, the authors present a formula for the binomial mixture 7. model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.1-19.v2">doi:10.12688/f1000research.1-19.v2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24555018">pmid:24555018</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3901455/">pmcid:PMC3901455</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ykl6cwu66bdc5mgqjqdc25pvda">fatcat:ykl6cwu66bdc5mgqjqdc25pvda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722025255/https://f1000researchdata.s3.amazonaws.com/manuscripts/1101/631f5c24-573b-4c3c-9a33-218c955bb3c7_120%20-%20snipen%201-19%20v2.pdf?doi=10.12688/f1000research.1-19.v2" 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/5f/a4/5fa4a649460f9d091af57f93376d3cb4f3fb885d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.1-19.v2"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901455" 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 domain sequence approach to pangenomics: applications to Escherichia coli

Lars-Gustav Snipen, David W Ussery
<span title="2012-10-01">2012</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
We use this approach in a pangenome study of the model organism Escherichia coli, the prokaryote species with the largest set of available genomes.  ...  The data are from the model organism Escherichia coli only, and many of the more specific results cannot be extended to other species.  ...  On page four, in the Methods part of the paper, the authors present a formula for the binomial mixture 7. model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.1-19.v1">doi:10.12688/f1000research.1-19.v1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24555018">pmid:24555018</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3901455/">pmcid:PMC3901455</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fgq26rulg5elpnlvcyelbe5fne">fatcat:fgq26rulg5elpnlvcyelbe5fne</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720141912/https://f1000researchdata.s3.amazonaws.com/manuscripts/120/a2b27580-5d6b-4430-b459-6ef85f64b2c0_120%20-%20snipen%201-19%20v1.pdf?doi=10.12688/f1000research.1-19.v1" 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/50/38/50389b2746260a74413c7886e13840c4def06dc3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.1-19.v1"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901455" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Crowdsourcing Emotions in Music Domain

Erion Çano, Maurizio Morisio
<span title="2017-07-30">2017</span> <i title="Academy and Industry Research Collaboration Center (AIRCC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dlcgzkn4cvbevhkswphjjxglsa" style="color: black;">International Journal of Artificial Intelligence &amp; Applications</a> </i> &nbsp;
Recent crowdsourcing approaches such as harvesting social tags, design of collaborative games and web services or the use of Mechanical Turk, are becoming popular in the literature.  ...  In this paper we discuss the viability of various crowdsourcing instruments providing examples from research works.  ...  Computational resources were provided by HPC@POLITO 11 , a project of Academic Computing within the Department of Control and Computer Engineering at Politecnico di Torino.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5121/ijaia.2017.8403">doi:10.5121/ijaia.2017.8403</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qziofuxemfa5jb56pqr34dqvvq">fatcat:qziofuxemfa5jb56pqr34dqvvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724054337/https://iris.polito.it/retrieve/handle/11583/2677905/158245/ErionCanoCrowdMusic.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/a4/1b/a41b121fb0c2eddde2d73cbc953a55719f710164.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5121/ijaia.2017.8403"> <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>

UProC: tools for ultra-fast protein domain classification

Peter Meinicke
<span title="2014-12-23">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Motivation: With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics.  ...  UProC is by three orders of magnitude faster than profile-based methods and in a metagenome simulation study achieved up to 80% higher sensitivity on unassembled 100 bp reads.  ...  Conflict of Interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu843">doi:10.1093/bioinformatics/btu843</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25540185">pmid:25540185</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4410661/">pmcid:PMC4410661</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ykeqts7pcnduvjgzuhdhvlsy4q">fatcat:ykeqts7pcnduvjgzuhdhvlsy4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727003043/https://watermark.silverchair.com/btu843.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb4wggG6BgkqhkiG9w0BBwagggGrMIIBpwIBADCCAaAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMYxv0yBkQt4pfjghuAgEQgIIBcSyTir-CU6OeromrsJfuXs_3pWi8Ay--FZjBx1XcS--cs6Q_li0fINF2VQtajIniOw7XSOhTFzKAdhR5AFy9mv-WNxxum0H6iqm4R8vnjUhdM6Y2Yj_hmiHCI9Xc5cLKWkkTdDWtHH6MJB4WMKixkL0cWli-1lsM6PcZ8NqREq2EnqiqELPLRRjpe8h8ujIl8o30xVAD86M4PpyZzbP3WolJYceezfPjmYnxAXlexpBFv5rMcSPR7MUI1KfQuiarOg6CXXwz6cCf6lpAaA-iC6dxSnEOOaDETJCG_VQNO0VbfnaSQOEIMdVIHfkTjCarZ5wTpilaV_cFTW_rs3jE7UfiYNkLJaXpMFNuk5lSciWevQXpr3-qb8bgzLRwF1mKTBUXAgzJnmWH3SXR3ak4VntomezG3WQXVkueyL3pbPe7BPx2wru_7oqoKlgdyUUiKIf1j-2ylxBTuv_H7mvFBCJbvmH_EEAJOLK3a58o4VGMEg" 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/c5/3dc58410c57be58defdb387d00d6d0f924b8ca07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu843"> <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/PMC4410661" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Knowledge mining of unstructured information: application to cyber-domain [article]

Tuomas Takko, Kunal Bhattacharya, Martti Lehto, Pertti Jalasvirta, Aapo Cederberg, Kimmo Kaski
<span title="2021-09-10">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This constant stream of noisy information requires new tools and techniques if it is to be used for the benefit of analysts and investigators in various organizations.  ...  In this paper we present and implement a novel knowledge graph and knowledge mining framework for extracting relevant information from free-form text about incidents in the cyber domain.  ...  Acknowledgments TT, KB, ML and KK acknowledge research project funding from Cyberwatch Finland.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2109.03848v2">arXiv:2109.03848v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x3yac67kbbe3zefivjphiyt34e">fatcat:x3yac67kbbe3zefivjphiyt34e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210917002749/https://arxiv.org/pdf/2109.03848v2.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/9e/73/9e73d82b71794c260aa1f16589815f9301cad87f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2109.03848v2" 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>

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

Heiner Klingenberg, Kathrin Petra Aßhauer, Thomas Lingner, Peter Meinicke
<span title="2013-02-15">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
As an application example we provide a large-scale analysis of data from the Human Microbiome Project.  ...  model.  ...  Model-based approaches build a taxon-dependent, in most cases organism-specific, feature representation of reference genomes that is used for the analysis of metagenomic sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt077">doi:10.1093/bioinformatics/btt077</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23418187">pmid:23418187</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3624802/">pmcid:PMC3624802</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4et7o4r6vjalfoaard2wt5kngm">fatcat:4et7o4r6vjalfoaard2wt5kngm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130531182739/http://bioinformatics.oxfordjournals.org:80/content/early/2013/02/15/bioinformatics.btt077.full.pdf?papetoc" 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/38/a4/38a454ad92defbf08aff1cb47c28daa7533d3f47.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt077"> <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/PMC3624802" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predicting pathway membership via domain signatures

Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
<span title="2008-08-01">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Results: We present a classification model, which for a specific gene of interest can predict the mapping to a KEGG pathway, based on its domain signature.  ...  The classifier makes explicit use of the hierarchical organization of pathways in the KEGG database.  ...  Funding: National Genome Research Network (NGFN) of the German Federal Ministry for Education and Research (BMBF)grants SMP Bioinformatics (01GR0450, subprojects PFB-S19T10, PBF-S02T11 to T.B. and H.F.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn403">doi:10.1093/bioinformatics/btn403</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18676972">pmid:18676972</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2553439/">pmcid:PMC2553439</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dzd6dw344ba6rpryjzdi65t2uu">fatcat:dzd6dw344ba6rpryjzdi65t2uu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728144810/https://watermark.silverchair.com/btn403.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMvVIB155lGG_WMR_QAgEQgIIBc2HPDu_17hh95PqPffdWx7DcAo53gZ7_8XE6knMOTwsNK-v6pXEfyeCN7Ek1hcWqHoVOR0Re22k0wB98O_4C9syJUM9PJOpAHHHfiDZEDFa5QoqUzFvljzCvpAGJVSIFyV5UPqlX2dpJE3G6sl_gFj5pCLJoPlGQUAqIBqUMdKnR5ySsJcnuC7G1nWvxoc4QjO9xZZoNEcSSt8SIrySnwaqbj8KJh_8k36hpRmLhidfB3O9VYGOnvhbfydFNdmuqEd8T7AwTsntWBNdPxBB5I-C8xLTnLGZAf0zpeStSAKlNSMtqyeAKh9d7ggPKVpLoZ8YdTG1Vn4vQML4RSYa7w8it3ywQC4sGxbkd7l_R-yV0zPkvFyjs9FtghXJaMWrd-A0XCVcuQUJefv1Vx9OlLAwg2RNIZz6qCY4ZTO3UWn2AoB1ILBc28jIEaqfSpV0sdk6yJpEKiVqe3r-6X-VqI_YGTAmNpZU6ae5gg6LjuE6DH18I" 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/24/06/240618d1b21b5a5b8289bd0b2a181dd9363fba8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn403"> <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/PMC2553439" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Reconstruction of highly heterogeneous gene-content evolution across the three domains of life

Wataru Iwasaki, Toshihisa Takagi
<span title="2007-07-01">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Subsequently, this algorithm was applied to an actual data set of nearly 200 genomes to reconstruct the heterogeneous gene-content evolution across the three domains of life.  ...  This method comprises analytically integrable modeling of gene-content evolution, analytical formulation of expectation-maximization and efficient calculation of marginal likelihood using an inside-outsidelike  ...  This work was supported by KAKENHI (Grantin-Aid for Scientific Research) on Priority Areas 'Systems Genomics' from the Ministry of Education, Culture, Sports, Science and Technology of Japan. W.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm165">doi:10.1093/bioinformatics/btm165</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17646301">pmid:17646301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ckhrjy4udjb7nf3ww45djpmmqy">fatcat:ckhrjy4udjb7nf3ww45djpmmqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809003732/https://bioinformatics.cs.vt.edu/~murali/conference-fayfaars/2007-ismb-eccb/ISMBECCB07/Papers/45.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/b7/0b/b70b0aeea54dbcbcc42814f6f4e0ba1cf0237dd4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm165"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

Nicolas Terrapon, Olivier Gascuel, Éric Maréchal, Laurent Bréehélin
<span title="2009-09-28">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Motivation: Hidden Markov Models (HMMs) have proved to be a powerful tool for protein domain identification in newly sequenced organisms.  ...  When sequence information alone is not sufficient to warrant the presence of a particular domain, our method enables its detection on the basis of the presence of other Pfam or InterPro domains.  ...  ACKNOWLEDGEMENT This research was supported by the PlasmoExplore project of the French National Research Agency (ANR-06-CIS6-MDCA-14).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp560">doi:10.1093/bioinformatics/btp560</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19786484">pmid:19786484</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/umejtvcskndv5aj34vnstj3kce">fatcat:umejtvcskndv5aj34vnstj3kce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110524223625/http://hal.archives-ouvertes.fr/docs/00/43/11/71/PDF/article090911.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/d5/93/d5932c3972c3512d9bae7de39257798aa3459eca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp560"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Genome Projects of Model Organisms [chapter]

Alfred Phler, Doris Jording, Jrn Kalinowski, Detlev Buttgereit, Renate Renkawitz-Pohl, Lothar Altschmied, Antoin E. Danchin, Horst Feldmann, Hans-Peter Klenk, Manfred Kroger
<i title="Wiley-VCH Verlag GmbH"> Biotechnology Set </i> &nbsp;
Projects in Model Organisms  ...  For this chapter on genome projects of model organisms, several experts in genome research have been asked to give an overview of specific genome projects and to report on the respective organism from  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/9783527620999.ch1e">doi:10.1002/9783527620999.ch1e</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/csodhfacxndi3hdtjbfcd3257e">fatcat:csodhfacxndi3hdtjbfcd3257e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110814041112/http://www.normalesup.org/~adanchin/PDF_files/articles_05/Enc_subtilis.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/b5/6fb5859503aaabb73f1c2d346c9c7b72c420967d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/9783527620999.ch1e"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
<span title="2021-05-18">2021</span> <i title="Oxford University Press"> <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;
Because of the interconnected nature of its data, the biomedical domain has been one of the early adopters of graph databases, enabling more natural representation models and better data integration workflows  ...  From early graph models to more recent native graph databases, the landscape of implementations has evolved to cover enterprise-ready requirements.  ...  Applications in the omics domain In the last five years, the usage of graph databases to support the integration of genomic, proteomic, metabolomic and phenotypic data has substantially increased.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baab026">doi:10.1093/database/baab026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34003247">pmid:34003247</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8130509/">pmcid:PMC8130509</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xku5npedwzgs3ayzsuvz6iattq">fatcat:xku5npedwzgs3ayzsuvz6iattq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210519002120/https://watermark.silverchair.com/baab026.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArwwggK4BgkqhkiG9w0BBwagggKpMIICpQIBADCCAp4GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMX_DD5iwEOGPvZxqqAgEQgIICb4_phJcj9INNvuo0Rzu3R7CEFU8YzaC2LtJIv8UucXvqwFh9EEV-N3luDQZ9RawocnDJI2FPgFr16dPryoTmF3Nx9e4gCMYZP7Y4NGmTRmQIMbsIPjCTo4DVwyyyxHqJ1-Oh5E_l5mha-ozGMpgrN76PytghreXNKG6a7g3HJN-cqnnrGjZdhdj-J1jmiPEwIpoDyS4xlZrizWJVvt42PnxBOPSOV2wKmflDqBvmZi26N3vzZjW66bpE8VLvp1EXPicUNN_yuTmABY4DbY_8nC9-g3o9m4t3-CsZx7F19Y4n0uHhjF8boD3rEkTOjvt1OFA5tz9Mdf651F_-K7CgC5mi_Ou2WKuGgMjZygtClfb2Yfy7YQIc2zacH6i7E48sTHAz4dUfn57dqZrbPxSli_2AqGHWn9FJ3XNhIPwrrL7BodmvGGbDyNUARi20TccYykpVRfweSFWCvZr-CKHBPbo1VuHyFjPX3JrDY42BGe9JmKmHH-MV-UiJMeeGsl0MREpy1GgMIR6y2CaN3n0tttU3q5KZAg-boV4Xqu52RUGZAUKZlcdoPaKt9nqzScIaherDVsJf0bebDr_IGggeiQWOUZ5z3W-_j5W0N57HrPxhy1ybFSPg4CaZEyp0lrHHYy1-tIQnPJR7oWnpGW8_Wcgpyt67XwKopJ7aFAVLK4KNVefZ3Z60JmGuF00Q5lFX8sPQfGT-H4ANYcZXGPshjGJhjS7lpMOBR680bKCN6tyTATYS7hH1aowbYpdlkvzRFQjPivkIRvgz78gH-iZp9bNFjbAQGBtf9vL9pbKOYqjLdLSXq2QzG0YXjhiRaNor" 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/df/c8/dfc84e033fbe2a429fda6142b19b10a5f1863534.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baab026"> <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/PMC8130509" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum

Nicolas Terrapon, Olivier Gascuel, Éric Maréchal, Laurent Bréhélin
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Hidden Markov Models (HMMs) are a powerful tool for protein domain identification.  ...  In spite of their high specificity, HMMs may lack sensitivity when searching for domains in divergent organisms.  ...  While for P. falciparum the practical interest is limited, this illustrates the potential of such approaches for all genome sequencing projects of organisms from poorly known phyla, with no already sequenced  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-67">doi:10.1186/1471-2105-13-67</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22548871">pmid:22548871</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3434054/">pmcid:PMC3434054</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bf35qdgvjjhfzddp63cogv2ksu">fatcat:bf35qdgvjjhfzddp63cogv2ksu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811210906/https://hal-lirmm.ccsd.cnrs.fr/file/index/docid/701611/filename/Terrapon-_BMC_Bioinformatics_-_2012.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/70/3c/703ccd5211ecd75c7fcfc0c99c6400e73c555c9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-67"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434054" 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 Measurement Ontology Generalizable for Emerging Domain Applications on the Semantic Web

Henry M. Kim, Arijit Sengupta, Mark S. Fox, Mehmet Dalkilic
<span title="">2007</span> <i title="IGI Global"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dc5hhrehbzhk3htmsyonnhxxae" style="color: black;">Journal of Database Management</a> </i> &nbsp;
This article introduces a measurement ontology for applications to Semantic Web applications, specifically for emerging domains such as microarray analysis.  ...  One facet needed to develop Semantic Web ontologies of emerging domains is creating ontologies of concepts that are common to these domains.  ...  In a similar vein, applications such as genomics and GIS's represent emerging domains represented for semantic modeling.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4018/jdm.2007010102">doi:10.4018/jdm.2007010102</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3p7lvau7ffgpre6aljj23lr434">fatcat:3p7lvau7ffgpre6aljj23lr434</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922235854/http://eil2.mie.utoronto.ca/wp-content/uploads/enterprise-modelling/papers/kim-db07.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/b9/80/b980f2c1d949632306b1d85daed0bbda673158d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4018/jdm.2007010102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Life sciences domain analysis model

Robert R Freimuth, Elaine T Freund, Lisa Schick, Mukesh K Sharma, Grace A Stafford, Baris E Suzek, Joyce Hernandez, Jason Hipp, Jenny M Kelley, Konrad Rokicki, Sue Pan, Andrew Buckler (+5 others)
<span title="">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/aapnwtybrvghlc35hfimbtdlom" style="color: black;">JAMIA Journal of the American Medical Informatics Association</a> </i> &nbsp;
The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research.  ...  Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research.  ...  The LS DAM work has and continues to involve stakeholders from NCI's caBIG Ò project, HL7's Clinical Genomics Work Group (HL7 CGWG) 10 and the BRIDG project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/amiajnl-2011-000763">doi:10.1136/amiajnl-2011-000763</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22744959">pmid:22744959</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3486731/">pmcid:PMC3486731</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/esoqtildrfgp5kqjkq5ayyguei">fatcat:esoqtildrfgp5kqjkq5ayyguei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211112529/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3486731&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/a6/41/a6417983e2767f1de41193da5fc0d5b235c5e1be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/amiajnl-2011-000763"> <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/PMC3486731" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

Alejandro Barrera, Ana Alastruey-Izquierdo, María J. Martín, Isabel Cuesta, Juan Antonio Vizcaíno, Christos A. Ouzounis
<span title="2014-07-17">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
In addition, we also investigated which domains could be considered promiscuous in the different organisms.  ...  As an application of this analysis, we explored three different ways to detect potential targets for antifungal drugs.  ...  The likely explanation for this lower coverage is that some of the domains are not found in the traditional model organisms and therefore not included in Pfam.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003733">doi:10.1371/journal.pcbi.1003733</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25033262">pmid:25033262</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4102429/">pmcid:PMC4102429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z5uddlb4zbfzxpa727cg7xdrd4">fatcat:z5uddlb4zbfzxpa727cg7xdrd4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4102429/PMC4102429-journal.pcbi.1003733.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/a7/53/a7532ec4eb35441c31b16e8bd345f02352c8d11a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003733"> <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/PMC4102429" 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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