From laurent.guyon at cea.fr Mon Jul 4 12:44:23 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Mon, 4 Jul 2022 10:44:23 +0000 Subject: [SocBiN] Virtual seminar of Cynthia Sharma - mechanisms/functions of small RNAs in bacteria, 4th of July - 4pm CET Message-ID: <3bf3838680a54ce78a2c418226f2035a@cea.fr> Dear colleagues, **late cancellation** I am sad to announce that the speaker had to cancel the presentation planned later today. It will be postponed later on, probably in mid-September. The new date will be announced here later on: https://smallrna-bioinformatics.eu/Pages/Seminars/S22_07.aspx The speaker and all the organizers ask you to apologize for this late cancellation independent of our willingness. Best regards, Laurent Guyon for the organizing committee (Rolf Backofen, Ana Eulálio, Bastian Fromm, Laurent Guyon, Andreas Keller, Marie-France Sagot) ____________________________ Laurent GUYON, PhD, HDR - Bioinformatics CEA IRIG (Interdisciplinary Research Institute of Grenoble) UMR 1292 - BioHealth BCI (Biology of Cancer and Infection laboratory) Bât C3 - Bureau 224 (+33)4.38.78.04.53 http://laurent.guyon.phd.free.fr/ De : GUYON Laurent Envoyé : vendredi 24 juin 2022 17:24 À : 'socbin at sbc.su.se' Objet : Virtual seminar of Cynthia Sharma - mechanisms/functions of small RNAs in bacteria, 4th of July - 4pm CET Dear colleagues, 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 Cynthia Sharma related to mechanisms/functions of small RNAs in bacteria. Caution: the seminar will not be recorded this time. More information here and below (including future seminars): https://smallrna-bioinformatics.eu/Pages/Seminars/S22_07.aspx Start Monday July 4th 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/93609306988?pwd=SWdvS1RPc0oxbDRRai9GUmpKN0t0dz09 Link to the YouTube stream: https://www.youtube.com/watch?v=VYIKBJq_coM Main Speaker: Cynthia Sharma, Professor, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Germany (Link) Title: Regulatory RNAs in pathogenic Epsilonproteobacteria Abstract: Non-coding RNAs and RNA-protein (RNP) complexes play central roles in diverse physiological processes in all kingdoms of life. Research in our lab focuses on RNA-based processes in the two pathogenic Epsilonproteobacteria Helicobacter pylori, the cuasative agent of gastric cancer, and the related food-borne pathogen Campylobacter jejuni. We are especially interested in the roles of small, regulatory RNAs (sRNAs) and RNPs in virulence control as well as novel mechanisms of gene regulation. For example, we have discovered new connections between so-called phase-variation at length variable DNA repeats and post-transcriptional regulation. I will present our work on sRNAs from H. pylori and C. jejuni that target variable G-repeats and regulate genes involved in host colonization as well as antibiotic sensitivity. Moreover, we recently identified a sRNA that is itself regulated by a phase-variable repeat and acts as a central regulator of the major virulence factors of H. pylori. Short session speaker (8 minutes long): Fabian König Title: A 3´UTR-derived, processed small RNA modulates flagellar biogenesis by repression of the anti-sigma factor FlgM in Campylobacter jejuni Abstract: In Campylobacter jejuni, as for many pathogens, flagella are a crucial virulence factor, enabling traversal through the viscous mucus layer of the human intestine. Flagellar biogenesis is known to involve hierarchical transcriptional control of each component, with class I genes transcribed from sigma-70-dependent promoters, and class II and class III genes transcribed with the help of alternative sigma factors, RpoN and FliA, respectively. In contrast to transcriptional control, less is known about post-transcriptional regulation of flagellar biosynthesis cascades by small regulatory RNAs (sRNAs). Here, we have characterized a conserved Campylobacter sRNA, CJnc230, encoded downstream of the RpoN-dependent flagellar hook structural protein FlgE, and found that three ribonucleases are involved in sRNA maturation. RNase III cleaves off the sRNA from the flgE mRNA, while RNase Y and PNPase process CJnc230 at its 3´ end. We identified a regulator of flagella-flagella interactions as well as the anti-sigma-28 factor FlgM as targets of CJnc230 repression. CJnc230 overexpression led to de-repression of FliA and subsequent upregulation of class III flagellar genes such as the major flagellin flaA, culminating in an increase in motility and flagellar length. Overexpression of the FliA-dependent sRNA CJnc170 instead led to reduced motility suggesting sRNA-mediated regulation of C. jejuni flagellar biosynthesis through balancing of the hierarchically expressed components. 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/1540352879780892672 YouTube channel (most of the seminars are then shared through this channel, but not this one): https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A Seminars are given at 4pm CET, except in rare cases. - 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) ____________________________ Laurent GUYON, PhD, HDR - Bioinformatics CEA IRIG (Interdisciplinary Research Institute of Grenoble) BioHealth Department - BCI (Biology of Cancer and Infection laboratory) 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 at 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjorn.wallner at liu.se Tue Jul 5 09:45:37 2022 From: bjorn.wallner at liu.se (=?utf-8?B?QmrDtnJuIFdhbGxuZXI=?=) Date: Tue, 5 Jul 2022 07:45:37 +0000 Subject: [SocBiN] Postdoc in ML and Structural Bioinformatics Message-ID: <675A22D5-13CF-4548-B7B8-C5A0F8BC5023@liu.se> Dear all, We have a postdoc position open in Machine Learning and Structural Bioinformatics funded by the Data-Driven Life Science (DDLS) and Wallenberg AI, Autonomous Systems and Software Program (WASP) at Linköping University. Read more and apply here: https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=19565&rmlang=UK If you have any questions shoot me an email: bjorn.wallner at liu.se Please forward this to any candidate you find suitable. Cheers Björn -------------- next part -------------- An HTML attachment was scrubbed... URL: From Rolf.I.Skotheim at rr-research.no Tue Jul 5 14:28:49 2022 From: Rolf.I.Skotheim at rr-research.no (Rolf I. Skotheim) Date: Tue, 5 Jul 2022 12:28:49 +0000 Subject: [SocBiN] Job announcement: Two postdocs in cancer genomics In-Reply-To: <7ca62bf270d640f1a3f7affe1bf7d45e@medisin.uio.no> References: <894c9fa9de544139af04c590b8190e37@medisin.uio.no>, <7ca62bf270d640f1a3f7affe1bf7d45e@medisin.uio.no> Message-ID: <53884856FB6613478340EBDBA97D8B010E1DC459@RHS-EXCHANGE-01.ad.medicalresearch.no> Do you want to work within an interdisciplinary group, combining informatics, biology and medicine in the research of cancer genomes? We are now hiring two postdocs in genomics on hormone dependent cancer (prostate and ovarian cancers) - at the Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet. Please see attached for complete announcement, and apply for the position here, by the deadline of 29 July. The two positions are full-time for two-years, with the possibility of extension. Sincerely, Rolf Skotheim - - Rolf Skotheim, PhD Genome Biology Group Department of Molecular Oncology Institute for Cancer Research Oslo University Hospital-Radiumhospitalet P. O. Box 4953 Nydalen, 0424 Oslo, Norway Tel: +47 2278 1727 http://www.ous-research.no/molecularoncology Biomedical Informatics, Section for Machine Learning and Center for Bioinformatics Department of Informatics University of Oslo, Norway http://www.mn.uio.no/ifi/english/research/groups/bmi -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Two_Postdocs_in_Genomics_on_Hormone_Dependent_Cancer.pdf Type: application/pdf Size: 192038 bytes Desc: Two_Postdocs_in_Genomics_on_Hormone_Dependent_Cancer.pdf URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2021-09-15 15.32.58_GroupPhoto_crop.jpg Type: image/jpeg Size: 770416 bytes Desc: 2021-09-15 15.32.58_GroupPhoto_crop.jpg URL: From phil at seqera.io Fri Jul 8 23:18:55 2022 From: phil at seqera.io (Phil Ewels) Date: Fri, 8 Jul 2022 14:18:55 -0700 Subject: [SocBiN] Nextflow Summit 2022 Message-ID: Hi all, Registration has just opened for the the 2022 Nextflow Summit: https://summit.nextflow.io The event will be in Barcelona and also online, from October 12-14. There's also an associated nf-core hackathon from 10-12 October and free Nextflow and nf-core training online the week before. The call for abstracts is also open, until July 22nd. We're looking for talks in any of the following themes: - Nextflow - central tool, language, and plugins - Community - pipelines, applications, and use cases - Ecosystem - infastructure and environments - Software - containers and tool packaging It should be a lot of fun, shout if you have any questions. I hope to see many of you there! Phil -- Phil Ewels, Ph.D. Lead Developer Advocate Seqera Labs phil at seqera.io - seqera.io Stockholm, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Jul 11 22:56:43 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 11 Jul 2022 22:56:43 +0200 Subject: [SocBiN] Fwd: 3D-BioInfo - ELIXIR Structural Bioinformatics Community - AGM November 2nd - 4th 2022 In-Reply-To: References: Message-ID: Dear All *3D BioInfo Community F2F/hybrid meeting * 2-4 November 2022 | EMBL-EBI, UK (hybrid) Deadline: 31 July 2022 The ELIXIR 3D BioInfo Community is inviting its Community members to participate in and contribute to the 3D BioInfo Community F2F/hybrid meeting (Annual General Assembly). This will be a hybrid meeting with F2F attendance at EMBL-EBI, Hinxton. Funding, including travel, accommodation and (food) expenses is available for a number of ELIXIR Community members. Selection will be based on submitted abstracts. Please send information on the number of years you have undertaken research post PhD and a one page summary of the research you would present. To be eligible for funding you need to be resident in a country that is a registered ELIXIR node or which is an Community Partner. You're receiving this message because you're a member of the 3d-bioinfo-all-contacts group from University College London. To take part in this conversation, reply all to this message. View group files | Leave group | Learn more about Microsoft 365 Groups -------------- next part -------------- An HTML attachment was scrubbed... URL: From francesca.delorenzo at helsinki.fi Tue Jul 12 10:52:01 2022 From: francesca.delorenzo at helsinki.fi (De Lorenzo, Francesca) Date: Tue, 12 Jul 2022 08:52:01 +0000 Subject: [SocBiN] Bioinformatician position at Hematology research Unit Helsinki (University of Helsinki, Finland) Message-ID: Dear all, The Hematology Research Unit Helsinki (HRUH) is a translational research group at the University of Helsinki, led by Professor Satu Mustjoki, which aims at understanding the pathobiology of malignant blood diseases and chronic inflammation. In blood cancers, the responses to immune checkpoint inhibitors have been modest, and there is a significant need for more effective therapies and for better understanding individual resistance and response mechanisms (personalized medicine). In our ongoing projects we aim to discover more effective immunotherapies, and individual resistance and sensitivity mechanisms using unbiased functional screens at the single cell level (e.g. CRISPR-Cas9 screens, high-throughput drug sensitivity assays) and utilizing primary patient immune and cancer cells in the dynamic co-culture models. The Hematology Research Unit is seeking A BIOINFORMATICIAN https://jobs.helsinki.fi/job/Bioinformatician-to-Hematology-Research-Unit/749925502/?feedId=350602&utm_source=CareerSite_UniversityOfHelsinki The deadline for the applications is 14 August 2022. Francesca De Lorenzo, Ph.D. Project Coordinator Translational Immunology Program (TRIMM) Hematology Research Unit University of Helsinki Biomedicum 1, room C407b Haartmaninkatu 8 00290 Helsinki, Finland francesca.delorenzo at helsinki.fi 0294126613 (+358504524919) -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Wed Jul 13 18:30:44 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 13 Jul 2022 18:30:44 +0200 Subject: [SocBiN] Fwd: Assignment DDLS research school director In-Reply-To: References:

Message-ID: Opening in Stockholm (if you have a position already) *Are you or someone you know our new DDLS research school director?* We seek a researcher at associate or full professor level, or an assistant professor or scientist with equivalent experience who is able and interested in directing the planning and the launch of the DDLS research school together with the 11 DDLS partner organizations. It is a 2- year assignment with a possibility of prolongation at about 0,4 FTE (available from mid-October). The director can be assigned to any of the participating DDLS universities or the Swedish Museum of Natural History. Read more here: https://www.scilifelab.se/career/assignment-ddls-research-school-director/ Deadline for application is September 19 2022 Please share this with whom might find it interesting Best regards DDLS Support Team Via Ulrika _________________________________________________________ *Ulrika Wallenquist* | Project coordinator SciLifeLab, Uppsala University Box 3037, 750 03 Uppsala | Husargatan 3 ulrika.wallenquist at scilifelab.uu.se | www.scilifelab.se [image: signature_1537031406] När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image003.png Type: image/png Size: 6014 bytes Desc: not available URL: From sermarcue at gmail.com Fri Jul 15 15:14:06 2022 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Fri, 15 Jul 2022 14:14:06 +0100 Subject: [SocBiN] Associate Principal Bioinformatician/Data Scientist - Hit Discovery - AstraZeneca Message-ID: Excellent opportunity to join the Data Sciences and Quantitative Biology department at AstraZeneca in Cambridge. If interested in developing hit discovery data analytics capabilities at a company committed to lifelong learning, growth and development, apply today! https://astrazeneca.wd3.myworkdayjobs.com/Careers/job/UK---Cambridge/Associate-Principal-Bioinformatician-Data-Scientist---Hit-Discovery_R-142592-2 Deadline for applications *July 19th*! -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Jul 22 22:15:41 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 22 Jul 2022 22:15:41 +0200 Subject: [SocBiN] Fwd: 3D-BioInfo AGM 2022 2 - 4th November EBI Hinxton Hybrid Meeting In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Orengo, Christine Date: Fri, 22 Jul 2022, 21:35 Subject: 3D-BioInfo AGM 2022 2 - 4th November EBI Hinxton Hybrid Meeting To: 3d-bioinfo-all-contacts <3d-bioinfo-all-contacts at live.ucl.ac.uk> Dear All, The 2022 ELIXIR 3D BioInfo F2F/hybrid meeting, the Communities Annual General Meeting takes place from: *2 November 2022, 12:00 GMT to 4 November 2022, 14:00 GMT. * This meeting is planned as a hybrid meeting, with the F2F component at the Wellcome Genome Campus, Hinxton, UK. The meeting will include presentations, workshops and participant engagement and will focus on the five Community activities: 1. 2. FAIR infrastructure for protein 3D-models and associated structural and functional annotations 3. 4. Open resources for sharing, integrating and benchmarking software tools for modelling the Interactome in 3D 5. 6. Development of models for protein-ligand interactions 7. 8. Nucleic Acid Tools: Progress and further plans 9. 10. Protein Engineering More details can be found on the Community website . The agenda will be published soon. This meeting has a limit of 80 in-person attendees, with no-limit on virtual participant numbers. We are inviting submission of abstracts to give a talk or present a poster. A selected number of participants invited to speak or present a poster will be eligible to receive funding to attend the meeting. *Deadline: 12 August 2022 * Click on the "submit an abstract" link below for more information on the abstract submission. *Submit an abstract by 12 August 2022 * We hope you will consider participating in the meeting. Best Wishes Christine Orengo, Sameer Velankar, Shoshana Wodak, Bohdan Schneider, Vincent Zoete, Lynne Regan You're receiving this message because you're a member of the 3d-bioinfo-all-contacts group from University College London. To take part in this conversation, reply all to this message. View group files | Leave group | Learn more about Microsoft 365 Groups -------------- next part -------------- An HTML attachment was scrubbed... URL: From xffhello at gmail.com Sat Jul 23 11:28:11 2022 From: xffhello at gmail.com (Feifei Xu) Date: Sat, 23 Jul 2022 11:28:11 +0200 Subject: [SocBiN] Bioinformatician position in Phillipsons lab at Uppsala University Message-ID: <83F01212-52FE-4E2C-AE4F-7347DFEF1F49@gmail.com> There is a bioinformatician position available in the laboratory of Professor Mia Phillipson (co-director, SciLifeLab) at Uppsala University. The lab today consists of about 15 excellent Postdocs and PhD students. The Phillipson group is mainly focusing on revealing novel functions of immune cells, and to find means to control these functions during e.g. organ development, regulation of homeostasis, tissue regeneration, blood vessel formation and inflammation using intravital imaging, functional studies and multiomics approaches. Among the most important discoveries of the Phillipson group are the alternative roles of immune cells in restoration of blood perfusion following ischemic injury and transplantation, as well as during wound healing. Following their discoveries of how to regulate these immune cell functions, a spin-off company (Ilya Pharma) was founded to develop immunotherapies accelerating healing of wounds in skin and mucosa now in clinical phase 2. The Phillipson lab is now looking for an experienced bioinformatician for analysing data coming from the lab, mainly single cell RNA-seq data but also bulk RNA-seq and metagenomics data. This person will also work on data mining of public databases. The official ad will be out in August, but we are sharing the information here now to attract talents already. If you think you are the right person, please send your CV to Mia Phillipson > and Feifei Xu >. We’ll start the application process in August. Qualifications of this candidate should have/be PhD in bioinformatics or related Substantial experiences with NGS data, transcriptomics analysis Experienced in data management/mining Solid programming skills in Python, R, Bash Familiar with statistical models Familiar with Unix/Linux Operating system Advanced knowledge of spoken and written English Excellent communication skills, high level of motivation and ability to interact constructively with others in the group and workplace are required Independent, take initiative and drive projects Best, Feifei -------------- next part -------------- An HTML attachment was scrubbed... URL: From fcunial at broadinstitute.org Mon Jul 25 16:53:33 2022 From: fcunial at broadinstitute.org (Fabio Cunial) Date: Mon, 25 Jul 2022 10:53:33 -0400 Subject: [SocBiN] Computational scientist position - Algorithms for structural variation discovery from long reads - Broad Institute of MIT and Harvard Message-ID: The Long Reads group, within the Data Sciences Platform at the Broad Institute in Cambridge, MA, is looking for two method developers to join its efforts in discovering structural variants from tens of thousands of long-read samples from human individuals, and in genotyping structural variants on millions of short-read samples. The ideal candidate for the first position has experience in designing algorithms and data structures on sequences, in implementing them at scale, and preferably an appreciation of the complexities of real data and a significant background in computational biology. Previous experience in algorithms/data structures for pangenomes, or in genome assembly, would be very useful. The second position requires expertise in machine learning and statistics, including deep learning, and concrete previous experience in designing and deploying learning algorithms at scale (not necessarily in genomics). Our data comes from the All of Us Research Program (https://allofus.nih.gov) and from several other partnerships with sequencing centers and research groups. Our team tackles methods development needs arising from long-read data across the Broad, and is connected to groups in the Broad community and to clinical and academic researchers worldwide. For more details about the position, see e.g.: https://www.linkedin.com/jobs/view/computational-scientist-long-reads-group-at-broad-institute-of-mit-and-harvard-3163620369 If interested, please send your CV, a list or publications, and a cover letter that explains how your profile fits the position, to Fabio Cunial ( fcunial at broadinstitute.org), or use the application form at the link above. Feel free to contact Fabio for any other questions you might have. -------------- next part -------------- An HTML attachment was scrubbed... URL: