From heads-admin at sund.ku.dk Tue Apr 5 16:28:14 2022 From: heads-admin at sund.ku.dk (SUND-CHDS-HeaDS-Admin) Date: Tue, 5 Apr 2022 14:28:14 +0000 Subject: [SocBiN] HeaDS Seminar Series: 'Towards Spatial Transcriptomics: A cell is known by the company it keeps' Message-ID: <5dc7628be74a44b793cc4381c5b2d1f7@sund.ku.dk> Dear SocBin Mailing List, Please find some information about the April installment of our Seminar Series, run by the Center for Health Data Science (HeaDS): --- HeaDS Seminar Series Excited about health data science? Join the HeaDS seminar series for monthly expeditions into new and exciting research at SUND and beyond. Our seminars are aimed towards researchers on all levels. Speaker: Kyoung Jae Won Talk: 'Towards Spatial Transcriptomics: A cell is known by the company it keeps' Date: 21 April 2022 Time: 15:00-16:00 Location: Room 7.15.92 (Foredragssal), Panum There will be refreshments and mingling after the seminar. Everyone is welcome without prior registration. For a description of our previous talks, see here. -- Best wishes, Admin Team Center for Health Data Science (HeaDS) Faculty of Health and Medical Sciences University of Copenhagen https://heads.ku.dk/contact/ Blegdamsvej 3B, 2200 København N. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsten.daub at ki.se Thu Apr 7 09:16:29 2022 From: carsten.daub at ki.se (Carsten Daub) Date: Thu, 7 Apr 2022 07:16:29 +0000 Subject: [SocBiN] Call for abstract and registration: Emerging Systems Medicine 2022 Message-ID: <15A76504-10C4-4A86-8B74-DDC7A588B6C8@ki.se> I would like to bring your attention to the upcoming “Emerging Systems Medicine Conference”, which is highly relevant for us who work with bioinformatics. Best, Carsten Daub [https://reg.akademikonferens.se/app/Data/ProjectImages/18348/Biomedicum_ZIM_680px.jpg] [https://reg.akademikonferens.se/app/Data/ProjectImages/18348/Logga%20ESM%202022_180px.jpg] Emerging Systems Medicine 2022 Conference REGISTER NOW The academic conference Emerging Systems Medicine (ESM 2022) will be held in Stockholm, June 15-17 2022. Systems Medicine aims at understanding and treating complex human diseases, such as cancer, cardiovascular disease, the impact of aging and responses to infection. A central theme in Systems Medicine is to explore complex diseases using a combination of powerful biotechnology-based and computing-based methods. This includes emerging methods such as single cell profiling, gene editing, Big Data/AI, quantitative microscopy and stem cell/organoid technologies. This will ultimately result in a systems level understanding of disease taking into account all the different scales of disease cause and manifestation. ESM 2022 will highlight some of the most exciting emerging developments in systems medicine and how they can be applied to further boost our knowledge. By gathering world-leading and local expertize, ESM 2022 will not only disseminate emerging ideas and technologies, but also serve to cross-fertilize new ideas and technologies and to inspire future advancements in systems medicine. ESM 2022 is to be held at the Karolinska Institutet Solna Campus, and is aimed for 200 attendees. The venue is also in close proximity to SciLifeLab, Stockholm. CALL FOR ABSTRACT The ESM 2022 Organizing Committee invites researchers from around the world to submit an abstract for oral or poster presentation. The abstract submission is open to 20 April 2022. Please see the ESM 2022 website for more information about the conference (including a preliminary program) and for submitting an abstract: https://esm2022.ki.se REGISTRATION The registration to the ESM 2022 Conference is open with an Early bird deadline on 10 May 2022. Register here: https://esm2022.ki.se/registration/ CONFIRMED SPEAKERS Ernest Arenas, Karolinska Institutet, Sweden Sergio Baranzini, UCSF, San Fransisco, USA Andreas Califano, Columbia University, USA Mika Gustafsson, Linköping University, Sweden Gioele La Manno, EPFL, Lausanne, Switzerland Sven Nelander, Uppsala, Sweden Garry Nolan, Stanford University, USA Lucas Pelkmans, University of Zurich, Switzerland Olivier Pertz, University of Bern, Switzerland Joel Selkring, EMBL, Hedielberg, Germany Luis Serrano, CRG, Barcelona, Spain Kristin Swanson, Mayo Clinic, Phoenix, USA Jussi Taipale, University of Cambridge, UK, and Karolinska Institutet, Sweden Andrew E. Teschendorff, Chinese Academy of Sciences, Shanghai, China Anna Överby, Umeå University, Sweden [https://reg.akademikonferens.se/app/Data/ProjectImages/18348/KarolinskaLogo2-203x90.png] [https://reg.akademikonferens.se/app/Data/ProjectImages/18348/LiU_logo_218x90.jpg] [https://reg.akademikonferens.se/app/Data/ProjectImages/18348/UU_logo_118x110.png] Contact: esm2022 at akademikonferens.se Photo: Stefan Zimmerman När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeanette.tangrot at umu.se Thu Apr 7 13:29:33 2022 From: jeanette.tangrot at umu.se (=?iso-8859-1?Q?Jeanette_T=E5ngrot?=) Date: Thu, 7 Apr 2022 11:29:33 +0000 Subject: [SocBiN] =?iso-8859-1?q?SBW2022_in_Ume=E5?= Message-ID: <4b41cea0db7740a8a51e58265bc5034d@umu.se> Mark your calendars! The Swedish Bioinformatics Workshop (SBW) is set to take place the 27-28th October 2022 in Umeå. The two days will be filled with inspiring talks, hands-on workshops, a poster session, and a social event with dinner. Registration will open later this spring and more information will follow. For now, just save the date and we hope to see you there this autumn! Best regards, Jeanette Tångrot On behalf of the SBW 2022 organising committee --------------------------------------------------------------------------------------------------------------- Jeanette Tångrot, PhD NBIS - National Bioinformatics Infrastructure Sweden Institutionen för molekylärbiologi / Department of Molecular Biology Umeå universitet / Umeå University SE-901 87 Umeå, Sweden +46-90-785 67 60 jeanette.tangrot at umu.se, jeanette.tangrot at nbis.se När du skickar e-post till Umeå universitet så innebär detta att Umeå universitet behandlar dina personuppgifter. För att läsa mer om hur detta går till, gå till www.umu.se/gdpr By sending an email to Umeå University, the University will need to process your personal data. For more information, please read www.umu.se/en/gdpr -------------- next part -------------- An HTML attachment was scrubbed... URL: From sermarcue at gmail.com Tue Apr 19 09:00:00 2022 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Tue, 19 Apr 2022 08:00:00 +0100 Subject: [SocBiN] Openings Data Sciences and Quantitative Biology at AstraZeneca Message-ID: Hi all, We have a number of exciting opportunities to join the Data Sciences and Quantitative Biology at AstraZeneca. If you are looking for a move to doing research and development in the biopharmaceutical industry, have a look at the following link: https://pages.beamery.com/astrazeneca/page/quantitativebiology Best wishes, Sergio -------------- next part -------------- An HTML attachment was scrubbed... URL: From ion.petre at utu.fi Tue Apr 19 11:35:07 2022 From: ion.petre at utu.fi (Ion Petre) Date: Tue, 19 Apr 2022 09:35:07 +0000 Subject: [SocBiN] CMSB 2022: last CFP References: <5ff68e99-6b31-43be-a89a-83a6397c80bf@Spark> Message-ID: <873ef669-86c2-44bf-87e0-996554db1cd3@Spark> CMSB 2022: last call for papers ============================== September 14-16, 2022 at the University of Bucharest, Romania CMSB 2022 website: https://fmi.unibuc.ro/en/cmsb-2022/ CMSB series website: https://cmsb.sciencesconf.org/ CMSB, the conference on Computational Methods in Systems Biology, aims to bring together researchers from across the biological, mathematical, computational, and physical sciences, interested in the modelling, simulation, analysis, inference, design, and control of biological systems. IMPORTANT NOTE CONCERNING THE COVID-19 PANDEMIC CMSB 2022 is planned as a physical, in-person event, with certain support for remote presence, both for speakers and for other participants who are unable or unwilling to come. Depending on the COVID-19 pandemic situation, we may have to switch the conference to an online-only mode. This will be decided by the end of June 2022. INVITED SPEAKERS Alessandra Carbone (Sorbonne Université, France) Gabriela Chiosis (Memorial Sloan Kettering Cancer Center, USA) Loïc Paulevé (Laboratoire Bordelais de Recherche en Informatique, France) Alfonso Rodríguez-Patón (Universidad Politécnica de Madrid, Spain) Erik Sonnhammer (Stockholm University, Sweden) IMPORTANT DATES (all dates are AoE) Abstract Submission: extended to May 8, 2022 Paper Submission: extended to May 15, 2022 Notification: June 10, 2022 Camera Ready: June 17, 2022 Poster/highlight talk: July 1, 2022 Conference: September 14-16, 2022 PAPER SUBMISSION CMSB 2022 solicits high quality papers reporting research results and/or tools related to the topics mentioned below. In this call we solicit two types of papers: regular and tool papers (in a later call we will also solicit posters and highlight talks): REGULAR papers should describe original work that has not been previously published and is not under review for publication elsewhere. Accepted regular papers will be published as part of the conference proceedings in the Springer LNBI series. Papers in this category should not exceed 15 pages in the Springer LNBI style (including main figures and tables, excluding references and possible appendices). TOOL papers should present new tools or public websites, new tool components or novel extensions to existing tools or websites supporting biological system modelling, analysis, simulation, or similar. Submissions must include information on methods, tool availability, and selected application results. They should be original and not previously published in a similar form. Accepted tool papers will be published as part of the conference proceedings in the Springer LNBI series. Papers in this category should have 4-6 pages in the Springer LNBI style (including main figures and tables, excluding references and possible appendices). Each paper will undergo a thorough review process. The paper may be supplemented with a clearly marked appendix, which will be reviewed at the discretion of the program committee. Papers must be submitted electronically as PDF files via EasyChair: https://easychair.org/conferences/?conf=cmsb2022 TOPICS * formalisms for modelling biological processes; * methods and tools for biological system analysis, modelling and simulation; * frameworks for model verification, validation, analysis, and simulation of biological systems; * high-performance methods for computational systems biology; * identification of biological systems; * applications of machine learning and data analytics in biology; * network modelling, analysis, inference; * automated parameter and model synthesis; * model integration and biological databases; * multi-scale modelling and analysis methods; * design, analysis, and verification methods for synthetic biology; * methods for biomolecular computing and engineered molecular devices; * data-based approaches for systems and synthetic biology; * optimality and control of biological systems; * modelling, analysis and control of microbial communities. AWARDS CMSB 2022 will offer two awards: the best paper award and the best student paper award. The awards are sponsored by Springer Nature. The winners will be announced at the conference. ORGANIZATION COMMITTEE David Pacioianu, University of Bucharest, Romania Andrei Paun, University of Bucharest, Romania (co-chair) Ion Petre, University of Turku, Romania (co-chair) Nicoleta Siminea, University of Bucharest Joel Sjöberg, University of Turku, Finland PROGRAM COMMITTEE Alessandro Abate – University of Oxford (UK) Paolo Ballarini – Centrale Supélec (France) Daniela Besozzi – University of Milan Bicocca (Italy) Luca Cardelli – University of Oxford (UK) Milan Češka – Brno University of Technology (Czech Republic) Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) Eugen Czeizler – University of Helsinki (Finland) Franck Delaplace – Université Paris-Saclay (France) Jerome Feret – Inria Paris (France) Clémence Frioux – Inria Bordeaux (France) Ashutosh Gupta – IIT Bombay (India) Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) Jane Hillston – University of Edinburgh (UK) Tommaso Mazza – CSS Mendel (Italy) Andrzej Mizera – University of Luxembourg (Luxembourg) Jun Pang – University of Luxembourg (Luxembourg) Nicola Paoletti – University of London (UK) Loïc Paulevé – CNRS, LaBRI (France) Andrei Paun – University of Bucharest, Romania, co-chair Ion Petre – University of Turku, Finland, co-chair Tatjana Petrov – University of Konstanz (Germany) Ovidiu Radulescu – University of Montpellier France) Andre Ribeiro – University of Tampere (Finland) Maria Rodriguez Martinez – IBM Zürich Research Laboratory (Switzerland) Olivier Roux – École Centrale de Nantes (France) David Šafránek – Masaryk University (Czech Republic) Carolyn Talcott – SRI International (USA) Jing Tang – University of Helsinki (Finland) Adelinde Uhrmacher – University of Rostock (Germany) Andrea Vandin – Technical University of Denmark (Denmark) Verena Wolf – Saarland University (Germany) Christoph Zechner – Max Planck Institute of Molecular Cell Biology and Genetics (Germany) TOOL EVALUATION COMMITTEE Georgios Argyris – Technical University of Denmark, Copenhagen (Denmark) Candan Çelik – Comenius University, Bratislava (Slovakia) Anastasis Georgoulas – University College London (UK) Lukrécia Mertová – Heidelberg Institute for Theoretical Studies (Germany) Samuel Pastva – IST Austria (Austria) Misbah Razzaq – Inserm BPH, Bordeaux (France) David Šafránek – Masaryk University (Czech Republic), chair Jakub Šalagovič – KU Leuven (Belgium) Matej Trojak – Masaryk University (Czech Republic) STEERING COMMITTEE Luca Cardelli – University of Oxford (UK) François Fages – INRIA (France) Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) Tomasso Mazza – CSS Mendel (Italy) Satoru Miyano – University of Tokyo (Japan) Ion Petre – University of Turku, Finland Gordon Plotkin – University of Edinburgh (UK) Corrado Priami – University of Pisa (Italy) Carolyn Talcott – SRI International (USA) Adelinde Uhrmacher – University of Rostock (Germany) Alessandro Abate – University of Oxford (UK) Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) Jun Pang – University of Luxembourg (Luxembourg) Loïc Paulevé – CNRS, LaBRI (France) Andrei Paun – University of Bucharest, Romania Tatjana Petrov – University of Konstanz (Germany) Verena Wolf – Saarland University (Germany) CONTACT All questions about the conference should be emailed to the organizers Ion Petre (ion.petre at utu.fi) and Andrei Paun (apaun at fmi.unibuc.ro). -------------- next part -------------- An HTML attachment was scrubbed... URL: From mauno.vihinen at med.lu.se Wed Apr 20 21:21:37 2022 From: mauno.vihinen at med.lu.se (Mauno Vihinen) Date: Wed, 20 Apr 2022 21:21:37 +0200 Subject: [SocBiN] 2 postdoc/research scientist positions in bioinformatics, Lund Message-ID: <9968fe7e-020a-cd61-6a19-9ea1ea724d74@med.lu.se> DO YOU WANT TO MAKE A DIFFERENCE? If so, you may be the person we are looking for. Protein Structure and Bioinformatics Group (http://structure.bmc.lu.se/) develops prediction methods and performs analyses that make a difference. We work on variation (mutation) interpretation, have developed several of the most reliable prediction methods in the world for sorting harmful variants and for predicting the causative mechanisms (at DNA, RNA, protein, structure, function etc levels). We are looking for a fellow to continue this successful research line. Our predictors include e.g. PON-P2, PON-MMR2, PON-Tstab and PON-mt-tRNA. This position requires skills in AI/ML. Another position is more related to bioinformatic data analysis. The positions are for two years and open immediately. The positions are at the Department of Experimental Medical Science, Lund University and located at the Biomedical Center (BMC). More information and instructions for application are available at https://lu.varbi.com/en/what:job/jobID:491543/ https://lu.varbi.com/en/what:job/jobID:497455/ The position is called for assistant researcher (biträdande forskare in Swedish) and equals to a postdoctoral fellow. The application deadlines are April 30th and May 8th. For further information, contact Mauno Vihinen (mauno.vihinen at med.lu.se). -- Mauno Vihinen Professor of Medical Structural Biology Department of Experimental Medical Science Lund University BMC B13 SE-22184 Lund Sweden http://structure.bmc.lu.se tel +46 72 526 0022 ORCID iD 0000-0002-9614-7976 From laurent.guyon at cea.fr Thu Apr 28 17:23:51 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Thu, 28 Apr 2022 15:23:51 +0000 Subject: [SocBiN] Virtual seminar of Isana Veksler-Lublinsky related to microRNA target prediction - 2nd of May, 4pm CET Message-ID: <48290248fbd24f0dbd8d7d1b126e1ef3@cea.fr> 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 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) 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 - 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) 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: