In the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/), we are happy to share with you the seminar of Isana Veksler-Lublinsky related to microRNA target prediction.
More information here and below (including future seminars): https://smallrna-bioinformatics.eu/Pages/Seminars/S22_05.aspx
Start Monday May 2nd at 4pm (CET, Berlin/Paris) (3 pm London/Lisbon, 10am New-York, 7am San Francisco, 5pm Tel Aviv)
Link to the Zoom conference: https://univ-grenoble-alpes-fr.zoom.us/j/95557401151?pwd=ZEpobUNlWHpNNlFha2k2ZERGN09Vdz09
Link to the YouTube stream: https://www.youtube.com/watch?v=Q69h7otui5k
Main Speaker: Isana Veksler-Lublinsky, Ben-Gurion University of the Negev, Israel (Link<https://bioinfolab.weebly.com/>)
Title: miRNA target prediction through a machine learning lens
Abstract: 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.
Short session speaker (8 minutes long): Shani Cohen (PhD student)
Title: Machine learning for predicting bacterial small RNA-target interactions
Abstract: 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.
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.
The club propose seminars every two months. Abstracts and links for the seminars are available here: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx
Tweet for easy re-transmission: https://twitter.com/Laurent_Guyon/status/1519691176051363840
YouTube channel (most of the seminars are then shared through this channel): https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A
Seminars are given at 4pm CET, except in rare cases.
- 2 May 2022 - Isana Veksler-Lublinsky - miRNA target prediction through a machine learning lens (+ 8 minute presentation of Shani cohen) - link<https://smallrna-bioinformatics.eu/Pages/Seminars/S22_05.aspx>
- 4 July 2022 - Cynthia Sharma - mechanisms/functions of small RNAs in bacteria
- 10 October 2022 (updated) - Marc Friedländer - miRNA-target interactions in single cells
- 7 November 2022 - Amy Buck - Dr Buck is working in the field of microRNA-virus interactions
'hope to see you virtually in these seminars,
Laurent Guyon, on behalf of all the organizers (Rolf Backofen, Ana Eulálio, Bastian Fromm, Laurent Guyon, Andreas Keller, Marie-France Sagot)
PS: Stefan Kirsch seminar related to Single Cell microRNA sequencing: Protocol Comparison, Automation and Application to Clinical Samples is now available in our YouTube channel, more details here: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminar-March.aspx
____________________________
Laurent GUYON, PhD, HDR - Bioinformatics
CEA IRIG (Interdisciplinary Research Institute of Grenoble<http://www.cea.fr/drf/IRIG/english/Pages/Presentation.aspx>)
BioHealth Department - BCI (Biology of Cancer and Infection laboratory<http://www.bci-lab.fr/en>)
UMR 1292 CEA/Inserm/Université Grenoble Alpes
CEA Grenoble - Bât C3 - Bureau 224
17 rue des Martyrs - 38054 GRENOBLE Cedex 9 - France
Tél : (+33)4.38.78.04.53 - Fax : (+33)4 38 78 50 58
Email : laurent.guyon@cea.fr<mailto:laurent.guyon@cea.fr> - http://laurent.guyon.phd.free.fr/
Interested by small non-coding RNA bioinformatics? Join the club! https://smallrna-bioinformatics.eu/
Special issue on small non-coding RNA bioinformatics, submit before the 15th of October (updated - contact me if you need delay):
https://www.mdpi.com/journal/genes/special_issues/Small_RNA_Bioinformatics
Happy to share miRViz (free to use website to analyze your microRNA datasets): http://mirviz.prabi.fr/
Article: https://doi.org/10.1093/nar/gkaa259
Messages of the paper: https://twitter.com/Laurent_Guyon/status/1255487510563651586
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