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<p class="MsoNormal"><span style="font-size:12.0pt">Dear colleagues,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="font-family:"Calibri",sans-serif">In the framework of the <b>small non-coding RNA bioinformatics club</b> (<a href="https://smallrna-bioinformatics.eu/">https://smallrna-bioinformatics.eu/</a>), we are happy to share with you the
<b>seminar of Isana Veksler-Lublinsky related to microRNA target prediction</b>.<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="font-family:"Calibri",sans-serif">More information here and below (including future seminars):
<a href="https://smallrna-bioinformatics.eu/Pages/Seminars/S22_05.aspx">https://smallrna-bioinformatics.eu/Pages/Seminars/S22_05.aspx</a><o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#353535">Start </span><strong><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Monday May 2nd at 4pm</span></strong><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#353535"> (</span><strong><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">CET</span></strong><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#353535">,
Berlin/Paris) (3 pm London/Lisbon, 10am New-York, 7am San Francisco, 5pm Tel Aviv)<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Link to the Zoom conference:</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535"> <a href="https://univ-grenoble-alpes-fr.zoom.us/j/95557401151?pwd=ZEpobUNlWHpNNlFha2k2ZERGN09Vdz09" target="_blank"><span style="color:#0E71EB;border:none windowtext 1.0pt;padding:0cm">https://univ-grenoble-alpes-fr.zoom.us/j/95557401151?pwd=ZEpobUNlWHpNNlFha2k2ZERGN09Vdz09</span></a><o:p></o:p></span></p>
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<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Link to the YouTube stream:</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535"> <a href="https://www.youtube.com/watch?v=Q69h7otui5k" target="_blank"><span style="color:#0E71EB;border:none windowtext 1.0pt;padding:0cm">https://www.youtube.com/watch?v=Q69h7otui5k</span></a><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;background:white;vertical-align:baseline">
<span style="color:#353535"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Main Speaker</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535">: <span style="border:none windowtext 1.0pt;padding:0cm">Isana
Veksler-Lublinsky, Ben-Gurion University of the Negev, Israel (</span><a href="https://bioinfolab.weebly.com/" target="_blank"><span style="border:none windowtext 1.0pt;padding:0cm;background:white">Link</span></a><span style="border:none windowtext 1.0pt;padding:0cm">)</span><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:0cm;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Title: </span></strong><strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#7030A0;border:none windowtext 1.0pt;padding:0cm">miRNA
target prediction through a machine learning lens</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:0cm;background:white;vertical-align:baseline">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Abstract</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535">: MicroRNAs (miRNAs) are small
RNA molecules that hybridize to complementary sequences on target mRNAs and repress their translation to proteins or mediate their degradation. Identifying miRNA target sites on mRNAs is a fundamental step in understanding miRNA function. Novel experimental
methods, which can produce high-throughput, unambiguous interacting miRNA–target datasets, have pushed the field forward in recent years. However, due to technical challenges involved in the application of the experimental methods, there is a constantly increasing
interest in using computational approaches for miRNA target prediction, especially those that are based on machine learning (ML) models. In my talk, I will describe the challenges involved in the application of ML models to miRNA target prediction. In addition,
I will show how we have been using classic and deep learning approaches to investigate whether miRNA-target interaction rules are transferable between species.<br>
<br>
<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Short session speaker</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535"> (8 minutes long): <span style="border:none windowtext 1.0pt;padding:0cm">Shani
Cohen</span> (PhD student)<o:p></o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Title: </span></strong><strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#7030A0;border:none windowtext 1.0pt;padding:0cm">Machine
learning for predicting bacterial small RNA-target interactions</span><span style="color:#7030A0;border:none windowtext 1.0pt;padding:0cm"><o:p></o:p></span></strong></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline">
<span style="color:#353535"><o:p> </o:p></span></p>
<p style="margin:0cm;margin-bottom:.0001pt;background:white;vertical-align:baseline;font-variant-ligatures: normal;font-variant-caps: normal;font-variant-numeric: inherit;font-variant-east-asian: inherit;font-stretch: inherit;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">Abstract</span></strong><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;border:none windowtext 1.0pt;padding:0cm">:
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535;background:white">Bacterial small RNAs (sRNAs) are relatively short non-coding RNA molecules (~50-500 nt) that play a significant role in the regulation of various bacterial
functions, such as virulence, environmental sensing, metabolism, and gene expression. Bacterial sRNAs have a wide variety of regulatory mechanisms, including base-paring with target mRNAs. The two major classes of base-pairing sRNA are commonly called cis-encoded
and trans-encoded. The cis-encoded sRNAs are transcribed from the strand complementary to the mRNA they regulate, whereas the trans-encoded share only a partial sequence complementarity with their targets and thus may regulate multiple genes. Similar to microRNAs
in eukaryotic, the trans-encoded sRNAs modulate the translation, processing, and/or stability of their target mRNAs by short interactions.</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#353535"><br>
<span style="background:white">Although hundreds of sRNAs have already been identified, the characterization of their regulatory mechanism in different bacterial species is still limited and much dependent on the discovery of their bona-fide mRNA targets. We
collected and processed large datasets of E.coli sRNA-mRNA chimeric interactions from recently published high-throughput experiments. We then extracted a variety of features from each interaction and built advanced machine-learning models for predicting sRNA
targets. In this talk, I will share the design of our study, the challenges, and preliminary results.</span></span><span style="font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The club propose seminars every two months. Abstracts and links for the seminars are available here:
<span lang="FR"><a href="https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx"><span lang="EN-US">https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx</span></a></span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Tweet for easy re-transmission: <a href="https://twitter.com/Laurent_Guyon/status/1519691176051363840">
https://twitter.com/Laurent_Guyon/status/1519691176051363840</a><o:p></o:p></p>
<p class="MsoNormal">YouTube channel (most of the seminars are then shared through this channel):
<span lang="FR"><a href="https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A"><span lang="EN-US">https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A</span></a></span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Seminars are given at 4pm CET, except in rare cases.<o:p></o:p></p>
<p class="MsoNormal">- 2 May 2022 - Isana Veksler-Lublinsky - <b>miRNA target prediction</b> through a machine learning lens (+ 8 minute presentation of Shani cohen) -
<span lang="FR"><a href="https://smallrna-bioinformatics.eu/Pages/Seminars/S22_05.aspx"><span lang="EN-US">link</span></a></span><o:p></o:p></p>
<p class="MsoNormal">- 4 July 2022 - Cynthia Sharma - mechanisms/functions of <b>
small RNAs in bacteria</b><o:p></o:p></p>
<p class="MsoNormal">- 10 October 2022 (updated) - Marc Friedländer - <b>miRNA-target interactions in single cells</b><o:p></o:p></p>
<p class="MsoNormal">- 7 November 2022 - Amy Buck - Dr Buck is working in the field of
<b>microRNA-virus interactions</b><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">‘hope to see you virtually in these seminars,<o:p></o:p></p>
<p class="MsoNormal">Laurent Guyon, on behalf of all the organizers (Rolf Backofen, Ana Eulálio, Bastian Fromm, Laurent Guyon, Andreas Keller, Marie-France Sagot)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">PS: Stefan Kirsch seminar related to <b>Single Cell microRNA sequencing</b>: Protocol Comparison, Automation and Application to Clinical Samples is now available in our YouTube channel, more details here:
<a href="https://smallrna-bioinformatics.eu/Pages/Seminars/Seminar-March.aspx">https://smallrna-bioinformatics.eu/Pages/Seminars/Seminar-March.aspx</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:navy">____________________________<br>
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Laurent GUYON, PhD, HDR – Bioinformatics<br>
CEA IRIG (</span><span lang="FR"><a href="http://www.cea.fr/drf/IRIG/english/Pages/Presentation.aspx"><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">Interdisciplinary Research Institute of Grenoble</span></a></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">)<br>
BioHealth Department - BCI (</span><span lang="FR"><a href="http://www.bci-lab.fr/en"><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">Biology of Cancer and Infection laboratory</span></a></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">)<br>
</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">UMR 1292 CEA/Inserm/Université Grenoble Alpes</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"><br>
<br>
</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">CEA Grenoble - Bât C3 – Bureau 224<br>
17 rue des Martyrs - 38054 GRENOBLE Cedex 9 – France<br>
</span><span style="font-size:5.0pt;font-family:"Comic Sans MS",serif;color:navy"><br>
</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Tél : (+33)4.38.78.04.53 - Fax : (+33)4 38 78 50 58</span><span style="font-size:5.0pt;font-family:"Comic Sans MS",serif;color:navy"><br>
</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Email :
</span><span lang="FR"><a href="mailto:laurent.guyon@cea.fr"><span lang="EN-US" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">laurent.guyon@cea.fr</span></a></span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">
- </span><span lang="FR"><a href="http://laurent.guyon.phd.free.fr/"><span lang="EN-US" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">http://laurent.guyon.phd.free.fr/</span></a></span><u><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"><br>
<br>
</span></u><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Interested by small non-coding RNA bioinformatics? Join the
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:#C00000">club</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">!
</span><span lang="FR"><a href="https://smallrna-bioinformatics.eu/"><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">https://smallrna-bioinformatics.eu/</span></a></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"><br>
<br>
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:#C00000">Special issue
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">on small non-coding RNA bioinformatics, submit before the
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:red">15<sup>th</sup> of October</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"> (updated - contact me if you need delay):<br>
</span><span lang="FR"><a href="https://www.mdpi.com/journal/genes/special_issues/Small_RNA_Bioinformatics"><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">https://www.mdpi.com/journal/genes/special_issues/Small_RNA_Bioinformatics</span></a></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"><br>
<br>
Happy to share </span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:#C00000">miRViz
</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">(free to use website to analyze your microRNA datasets):
</span><span lang="FR"><a href="http://mirviz.prabi.fr/"><span lang="EN-US" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">http://mirviz.prabi.fr/</span></a></span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy"><br>
</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Article:</span><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif">
</span><a name="PANISTVisited"></a><a href="https://doi.org/10.1093/nar/gkaa259"><span style="mso-bookmark:PANISTVisited"><span style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue;border:none windowtext 1.0pt;padding:0cm;background:white">https://doi.org/10.1093/nar/gkaa259</span></span><span style="mso-bookmark:PANISTVisited"></span></a><span style="mso-bookmark:PANISTVisited"></span><br>
<span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:navy">Messages of the paper:</span><span lang="EN-GB" style="font-size:7.5pt;font-family:"Comic Sans MS",serif">
</span><span lang="FR"><a href="https://twitter.com/Laurent_Guyon/status/1255487510563651586"><span lang="EN-US" style="font-size:7.5pt;font-family:"Comic Sans MS",serif;color:blue">https://twitter.com/Laurent_Guyon/status/1255487510563651586</span></a></span><span style="font-size:5.0pt;color:navy;mso-fareast-language:JA"><o:p></o:p></span></p>
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