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‎index.html

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<!DOCTYPE html>
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<html lang="en-us">
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<head>
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<meta charset="UTF-8">
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<title>Mirtop.GitHub.io by miRTop</title>
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<link rel="stylesheet" type="text/css" href="stylesheets/normalize.css" media="screen">
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<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
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<link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
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<link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
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</head>
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<body>
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<section class="page-header">
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<h1 class="project-name">Mirtop.GitHub.io</h1>
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<h2 class="project-tagline">project for small RNA standard annotations</h2>
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</section>
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<section class="main-content">
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<h2>
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<a id="mirna-transcriptomic-open-project-mirtop" class="anchor" href="#mirna-transcriptomic-open-project-mirtop" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>miRNA-Transcriptomic Open Project (miRTOP)</h2>
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<p>The main goal of this project is to create a reflection group on metazoan miRNAs, open to all interested researchers, to identify blockages and develop standards and guidelines to improve miRNA research, resources and communication. This can go through the use of standardized file formats, gene and variants nomenclature guidelines, and advancements in miRNA biology understanding.
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The group will eventually also aim at expanding its breadth to the development of novel tools, data resources, and best-practices guidelines to benefit the scientific community by providing high confidence validated research and analysis strategies, regardless the expertise in this field.</p>
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<p>The motivation and emergence of this group came from the simultaneous publication of two articles from two independent groups and addressing the question of miRNA diversity, origins, evolution, and annotation:</p>
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<ul>
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<li>Desvignes, T., Batzel, P., Berezikov, E., Eilbeck, K., Eppig, J. T., McAndrews, M. S., Singer, A., Postlethwait, J. H. (2015). miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends in Genetics : TIG, 31(11), 613–626. <a href="http://doi.org/10.1016/j.tig.2015.09.002">http://doi.org/10.1016/j.tig.2015.09.002</a>
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</li>
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<li>Fromm, B., Billipp, T., Peck, L. E., Johansen, M., Tarver, J. E., King, B. L., Newcomb J., Sempere L. F., Flatmark K., Hovig E., Peterson, K. J. (2015). A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annual Review of Genetics. <a href="http://doi.org/10.1146/annurev-genet-120213-092023">http://doi.org/10.1146/annurev-genet-120213-092023</a> (<a href="http://mirgenedb.org">http://mirgenedb.org</a>)</li>
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</ul>
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<p>In addition, plants miRNA research is facing the same problems. The different origin of plant and metazoan miRNA systems, however, make the creation of a unified “plant &amp; metazoan” pattern hazardous. Nevertheless, tentative standardization on specific aspects is a future goal of the group.</p>
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<ul>
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<li>Budak, H., Bulut, R., Kantar, M., &amp; Alptekin, B. (2015). MicroRNA nomenclature and the need for a revised naming prescription. Briefings in Functional Genomics, elv026–. <a href="http://doi.org/10.1093/bfgp/elv026">http://doi.org/10.1093/bfgp/elv026</a>
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</li>
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</ul>
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<p>If you work in relation with the miRNA field, and want to take part in this reflection group, please <a href="https://github.com/miRTop/miRTOP.github.io/issues/1">join us</a> and share your ideas in order to create a large community working together to improve the study and analysis of miRNA data.</p>
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<p>Current projects:</p>
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<ul>
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<li><p>Establishment of a unified Nomenclature system:
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Two novel miRNA nomenclature systems have been simultaneously proposed by independent teams, in addition to the schemes proposed by previous groups. One focused on evolutionary conservation and clear orthology establishment to provide phylogenetically informative names based on Human annotation (Fromm and Peterson’s group), while the other envisioned a system for sequence variation analysis following nomenclature guidelines in use for coding-genes (Desvignes and Postlethwait group). The aim of this project is thus to establish a convergent framework, incorporating the strengths of each proposed system, to finalize a unified and persistent nomenclature system.</p></li>
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<li><p>IsomiRs nomenclature:
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IsomiRs have proven to be bona fide variants of miRNA expression and could in some cases be functionally important and having different target sets than the reference miRNA they vary from. Because of functional importance of isomiRs, it appears crucial to be able to refer to a given one in a non-ambiguous way. The aim of this project is thus to formulate a standardized format for isomiR referencing and offer tools to apply them in an easy and general way.</p></li>
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</ul>
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<p>Future projects and discussions:</p>
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<ul>
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<li>What is the biological relevance of moRNAs? How to detect and annotate them?</li>
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<li>Any other ideas or problems?</li>
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</ul>
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<p>Citation: zenodo citation link.</p>
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<p>Contributors:</p>
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<ul>
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<li>Lorena Pantano. Harvard TH Chan School of Public Health, Boston, USA</li>
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<li>Thomas Desvignes, Institute of Neuroscience, University of Oregon, Eugene, OR, USA</li>
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<li>John H. Postlethwait, Institute of Neuroscience, University of Oregon, Eugene, OR, USA</li>
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<li>Karen EIlbeck. University of Utah, Biomedical Informatics.</li>
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</ul>
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<footer class="site-footer">
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<span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span>
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</footer>
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</section>
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</body>
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</html>

‎params.json

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{"name":"Mirtop.GitHub.io","tagline":"project for small RNA standard annotations","body":"## miRNA-Transcriptomic Open Project (miRTOP) \r\n\r\nThe main goal of this project is to create a reflection group on metazoan miRNAs, open to all interested researchers, to identify blockages and develop standards and guidelines to improve miRNA research, resources and communication. This can go through the use of standardized file formats, gene and variants nomenclature guidelines, and advancements in miRNA biology understanding. \r\nThe group will eventually also aim at expanding its breadth to the development of novel tools, data resources, and best-practices guidelines to benefit the scientific community by providing high confidence validated research and analysis strategies, regardless the expertise in this field.\r\n\r\nThe motivation and emergence of this group came from the simultaneous publication of two articles from two independent groups and addressing the question of miRNA diversity, origins, evolution, and annotation:\r\n\r\n* Desvignes, T., Batzel, P., Berezikov, E., Eilbeck, K., Eppig, J. T., McAndrews, M. S., Singer, A., Postlethwait, J. H. (2015). miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends in Genetics : TIG, 31(11), 613–626. http://doi.org/10.1016/j.tig.2015.09.002\r\n* Fromm, B., Billipp, T., Peck, L. E., Johansen, M., Tarver, J. E., King, B. L., Newcomb J., Sempere L. F., Flatmark K., Hovig E., Peterson, K. J. (2015). A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annual Review of Genetics. http://doi.org/10.1146/annurev-genet-120213-092023 (http://mirgenedb.org)\r\n\r\nIn addition, plants miRNA research is facing the same problems. The different origin of plant and metazoan miRNA systems, however, make the creation of a unified “plant & metazoan” pattern hazardous. Nevertheless, tentative standardization on specific aspects is a future goal of the group.\r\n\r\n* Budak, H., Bulut, R., Kantar, M., & Alptekin, B. (2015). MicroRNA nomenclature and the need for a revised naming prescription. Briefings in Functional Genomics, elv026–. http://doi.org/10.1093/bfgp/elv026\r\n\r\nIf you work in relation with the miRNA field, and want to take part in this reflection group, please [join us](https://github.com/miRTop/miRTOP.github.io/issues/1) and share your ideas in order to create a large community working together to improve the study and analysis of miRNA data.\r\n\r\nCurrent projects:\r\n\r\n* Establishment of a unified Nomenclature system:\r\n\tTwo novel miRNA nomenclature systems have been simultaneously proposed by independent teams, in addition to the schemes proposed by previous groups. One focused on evolutionary conservation and clear orthology establishment to provide phylogenetically informative names based on Human annotation (Fromm and Peterson’s group), while the other envisioned a system for sequence variation analysis following nomenclature guidelines in use for coding-genes (Desvignes and Postlethwait group). The aim of this project is thus to establish a convergent framework, incorporating the strengths of each proposed system, to finalize a unified and persistent nomenclature system.\r\n\r\n* IsomiRs nomenclature: \r\n IsomiRs have proven to be bona fide variants of miRNA expression and could in some cases be functionally important and having different target sets than the reference miRNA they vary from. Because of functional importance of isomiRs, it appears crucial to be able to refer to a given one in a non-ambiguous way. The aim of this project is thus to formulate a standardized format for isomiR referencing and offer tools to apply them in an easy and general way.\r\n\r\nFuture projects and discussions:\r\n\r\n* What is the biological relevance of moRNAs? How to detect and annotate them?\r\n* Any other ideas or problems?\r\n\r\nCitation: zenodo citation link.\r\n\r\nContributors:\r\n\r\n* Lorena Pantano. Harvard TH Chan School of Public Health, Boston, USA\r\n* Thomas Desvignes, Institute of Neuroscience, University of Oregon, Eugene, OR, USA\r\n* John H. Postlethwait, Institute of Neuroscience, University of Oregon, Eugene, OR, USA\r\n* Karen EIlbeck. University of Utah, Biomedical Informatics.\r\n","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}

‎stylesheets/github-light.css

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/*
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Copyright 2014 GitHub Inc.
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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See the License for the specific language governing permissions and
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limitations under the License.
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