From leo.lahti at utu.fi Mon Mar 6 13:46:10 2023 From: leo.lahti at utu.fi (Leo Lahti) Date: Mon, 6 Mar 2023 12:46:10 +0000 Subject: [SocBiN] Design and Control of Microbial Communities Leuven summer school 11 - 13th Sep 2023 In-Reply-To: <05743db37d82402d926942c50ab70ece@cea.fr> References: <05743db37d82402d926942c50ab70ece@cea.fr> Message-ID: Registrations are open to Summer School: Design and Control of Microbial Communities 11 - 13th Sep 2023 Leuven, Belgium In this summer school, we want to introduce students at the Master and PhD level to different computational methods to manipulate microbial communities to shift them towards a desired composition or function. In addition, we want to broaden the horizon of our students with a couple of research talks on the latest developments in the field. Beyond the educational purposes, we also hope to initiate a scientific exchange between speakers and students. More information and registrations: http://msysbiology.com/microbedesign/ on behalf of the organizers, Leo Lahti From ion.petre at utu.fi Tue Mar 7 11:19:05 2023 From: ion.petre at utu.fi (Ion Petre) Date: Tue, 7 Mar 2023 12:19:05 +0200 Subject: [SocBiN] Special issue of TCS/C on Foundations of SysBio References: <6c9589bc-3aa8-4656-a660-6eb11621e57a@Spark> Message-ID: Special issue of Theoretical Computer Science (track C) on Foundational Methods in Systems Biology Submission: continuous, cut-off date May 15, 2023 ================================================================= Dear Colleague, With this email we would like to invite you to submit a paper to the special issue of the Theoretical Computer Science journal (series C: Natural Computing) on “Foundations of Systems Biology”. This special issue is aligned with the conference series on “Computational Methods in Systems Biology (CMSB)” and shares its topics of interests. We look for original research articles on foundational aspects of systems biology and their applications. Topics of interest include, but are not limited to: • 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; • network modelling, analysis, inference; • automated parameter and model synthesis; • 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; • machine learning for systems biology. Submitted papers should not be under consideration for publication elsewhere. Extended versions of manuscripts that have been published in conference proceedings (CMSB or other conferences) can be submitted to this special issue if they have been extended by at least 30% and the differences between the two versions are explained in the introduction. The manuscripts should include all content in the article, rather than in appendices or in supplementary information. Please prepare your article in LaTeX in the Elsevier journal paper format (https://www.elsevier.com/authors/author-schemas/latex-instructions) and submit it using the editorial manager (https://www.editorialmanager.com/TCS/default.aspx). The tile of the special issue is “Foundations of Systems Biology” (short title VSI: FoundSysBio). In order to properly assign your submission to the special issue we are preparing, it is crucial to select VSI: FoundSysBio twice, as Article Type (starting the submission procedure) and Requested Editor (in Review Preferences). All papers for the special issue will be reviewed following the standard refereeing procedure for Theoretical Computer Science. Submissions will be reviewed on a continuous basis, with a cut-off date set for May 15, 2023. We suggest an upper limit of 40 pages on the length of the paper in the LaTeX style of the journal; please contact us if you need more pages for your manuscript. To keep track of the papers, please inform us of after the submission with an email to ion.petre at utu.fi and apaun at fmi.unibuc.ro. With best wishes, Ion Petre and Andrei Paun Guest editors of the special issue of TCS/C on Foundations of Systems Biology -------------- next part -------------- An HTML attachment was scrubbed... URL: From ansikuso at gmail.com Tue Mar 7 14:19:42 2023 From: ansikuso at gmail.com (Dr. Sudhanshu Singh) Date: Tue, 7 Mar 2023 18:49:42 +0530 Subject: [SocBiN] Special issue of TCS/C on Foundations of SysBio In-Reply-To: References: <6c9589bc-3aa8-4656-a660-6eb11621e57a@Spark> Message-ID: Thanks and sure On Tue, 7 Mar, 2023, 3:49 pm Ion Petre, wrote: > Special issue of Theoretical Computer Science (track C) on Foundational > Methods in Systems Biology > Submission: continuous, cut-off date May 15, 2023 > ================================================================= > > Dear Colleague, > > With this email we would like to invite you to submit a paper to the > special issue of the Theoretical Computer Science journal (series C: > Natural Computing) on “Foundations of Systems Biology”. This special issue > is aligned with the conference series on “Computational Methods in Systems > Biology (CMSB)” and shares its topics of interests. We look for original > research articles on foundational aspects of systems biology and their > applications. Topics of interest include, but are not limited to: > > - 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; > - network modelling, analysis, inference; > - automated parameter and model synthesis; > - 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; > - machine learning for systems biology. > > Submitted papers should not be under consideration for publication > elsewhere. Extended versions of manuscripts that have been published in > conference proceedings (CMSB or other conferences) can be submitted to this > special issue if they have been extended by at least 30% and the > differences between the two versions are explained in the introduction. The > manuscripts should include all content in the article, rather than in > appendices or in supplementary information. > > Please prepare your article in LaTeX in the Elsevier journal paper format ( > https://www.elsevier.com/authors/author-schemas/latex-instructions) and > submit it using the editorial manager ( > https://www.editorialmanager.com/TCS/default.aspx). The tile of the > special issue is “Foundations of Systems Biology” (short title *VSI: > FoundSysBio*). In order to properly assign your submission to the special > issue we are preparing, it is crucial to select *VSI: FoundSysBio* twice, > as Article Type (starting the submission procedure) and Requested Editor > (in Review Preferences). > > All papers for the special issue will be reviewed following the standard > refereeing procedure for Theoretical Computer Science. Submissions will be > reviewed on a continuous basis, with a cut-off date set for May 15, 2023. > We suggest an upper limit of *40 pages* on the length of the paper in the > LaTeX style of the journal; please contact us if you need more pages for > your manuscript. > > To keep track of the papers, please inform us of after the submission with > an email to ion.petre at utu.fi and > apaun at fmi.unibuc.ro . > > With best wishes, > Ion Petre and Andrei Paun > Guest editors of the special issue of TCS/C on Foundations of Systems > Biology > _______________________________________________ > SocBiN mailing list > SocBiN at lists.su.se > https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Mar 17 15:52:47 2023 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 17 Mar 2023 15:52:47 +0100 Subject: [SocBiN] Fwd: [Call for Applications] NTU Presidential Postdoctoral Fellowship 2023 In-Reply-To: References: <639812bf612e44bf988844841f5109d4@gov.se> <47a572afea234593a74b7be415ab157f@su.se> Message-ID: *Från: *Director, Office of International Engagement *Datum: *tisdag 14 mars 2023 2:45 em *Ämne: *[Call for Applications] NTU Presidential Postdoctoral Fellowship 2023 Dear partners and friends of NTU Singapore, Greetings from NTU Singapore. I am delighted to be able to share with you details of the prestigious NTU Presidential Postdoctoral Fellowship (PPF) scheme, which is open to outstanding early career researchers from around the world. The scheme provides the opportunity for early career researchers to conduct independent investigations in any discipline. Full details, including eligibility criteria, can be found below. We hope that you can bring this opportunity to the attention of promising and brilliant researchers at your institution – it would be wonderful to receive their applications and deepen the links between our institutions. Thank you in anticipation. Kind regards, Wanda Preiser [image: Graphical user interface Description automatically generated] Young and research-intensive, Nanyang Technological University (NTU Singapore) is ranked 19th globally and placed among the world’s best young universities. NTU has a vibrant research ecosystem with a high proportion of early career researchers. It has a healthy environment for interdisciplinary research collaboration and the research is well-funded. NTU invites outstanding early-career researchers to apply for appointment as a *NTU Presidential Postdoctoral Fellow*. The PPF aims to provide the opportunity for outstanding early career researchers from Singapore and around the world, to conduct independent investigations in any discipline at NTU. This Fellowship provides research funding over two years. There are personal development opportunities coupled with mentorship in an established research group. These conditions will empower the Fellows to strive for research excellence and impact and enable them to meet their ambitions as global research leaders. *PPF BENEFITS* The Presidential Postdoctoral Fellowship provides: - A two-year tenure with a salary of SGD 80,000 per year. - A research grant of up to SGD 100,000 per year. - A housing grant of SGD 18,000 per year with eligibility for subsidized apartment accommodation (subject to availability). - Relocation expenses of up to SGD 4,000 (if eligible). - Mentorship and support in an established research group. - Opportunity to work with faculty in mentoring graduate students. - Exposure to the most dynamic and diverse global growth regions. *Eligibility Criteria* - Within 5 years of obtaining PhD or equivalent degree. - Demonstrable intellectual excellence. - Maturity and capacity to begin an independent research career. - Desire and potential to develop as a future academic leader. - Submit a thoughtful and realistic research proposal - Be available to take up the position no later than 31 Dec 2023. *How to apply* The application is open from 10 February 2023 to *30 April 2023* (Singapore Time, UTC+8). Applications must be submitted in *electronic format *via *NTU Online Application Portal*. *Checklist* The following supporting documents have to be attached to the online application form: 1. Cover Letter 2. Comprehensive CV (with full publication list) 3. Official transcript or Degree Certificate in English (PhD’s degree) 4. Research proposal (in no more than 2 pages, template for download ) 5. Contact information of two referees (one must be a PhD Supervisor) 6. Top 3 publications (in PDF) and any other supporting documents (scanned copy) Interested applicants are advised to have them ready before applying online. Late or incomplete applications will not be considered. For more information on the Presidential Postdoctoral Fellowship 2023, please click here . Queries about the application can be directed to ntuppf at ntu.edu.sg. *Ms Wanda PREISER* Head, Office of International Engagement President’s Office 50 Nanyang Avenue, ADM-02-02, Singapore 639798 *T* 65-6592-2529 d-oia at ntu.edu.sg www.ntu.edu.sg [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/line.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_fb.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_tw.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_yt.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_is.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_li.jpg] [image: http://www3.ntu.edu.sg/cits2/CITS_web_resources/signature/img/icon_rs.jpg] Classification: Restricted ------------------------------ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image010.png Type: image/png Size: 5076 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image011.jpg Type: image/jpeg Size: 370 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image012.jpg Type: image/jpeg Size: 1424 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image013.jpg Type: image/jpeg Size: 1642 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: image003.png Type: image/png Size: 22029 bytes Desc: not available URL: From ingemar.andre at biochemistry.lu.se Tue Mar 21 15:23:12 2023 From: ingemar.andre at biochemistry.lu.se (=?utf-8?B?SW5nZW1hciBBbmRyw6k=?=) Date: Tue, 21 Mar 2023 14:23:12 +0000 Subject: [SocBiN] Postdoctoral position in machine learning applied to protein folding In-Reply-To: References: Message-ID: <36DB3D96-E8F9-42E9-95E5-3810B87E9D8C@biochemistry.lu.se> Dear all, The lab of Ingemar André is looking for a talented postdoctoral researcher in bioinformatics and machine learning at Lund University. The candidate is expected to develop computational methods to understand the relationship between codon usage and protein folding by developing machine learning data to analyze experimental and protein structure data. For more information, visit https://jobrxiv.org/job/lund-university-27778-postdoctoral-position-in-machine-learning-applied-to-protein-folding/ and/or andrelab.lu.se. Best wishes, Ingemar Ingemar André Biochemistry & Structural Biology Lund University PO Box 124 221 00 Lund tel: +46 46 222 4470 email: ingemar.andre at biochemistry.lu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From Tatiana.Starikovskaya at ens.fr Thu Mar 23 14:27:29 2023 From: Tatiana.Starikovskaya at ens.fr (Tatiana Starikovskaya) Date: Thu, 23 Mar 2023 14:27:29 +0100 Subject: [SocBiN] CPM Summer school on bioinformatics and combinatorics on words, June 24-25 2023, ENS Paris Message-ID: ================================================================== CPM Summer school on bioinformatics and combinatorics on words June 24-25 2023, ENS Paris https://cpm2023.u-pem.fr ================================================================== Before this year's edition of the Annual Symposium on Combinatorial Pattern Matching (CPM 2023), there will be a two-day summer school on bioinformatics and combinatorics on words at ENS Paris. The goal of the school is to provide an opportunity for PhD students and postdocs working in either area to become acquainted with the other, and present their research. The school will be comprised of two courses: 1. "Under the hood: the role of string algorithms in contemporary biological research" by Karel Břinda (Inria/IRISA Rennes) 2. "Structural analysis of approximate pattern matching and algorithmic applications" by Panagiotis Charalampopoulos (Birbeck, University of London) As part of the event, there will be a poster session on June 24 in the afternoon. Registration is free but mandatory: please register at https://forms.gle/PRVJa4U1fxQKGjCJA before June 19. Accommodation grants available for poster presenters, see https://cpm2023.u-pem.fr for more details. On behalf of the organisers, Tatiana Starikovskaya From laurent.guyon at cea.fr Tue Mar 28 10:59:48 2023 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Tue, 28 Mar 2023 08:59:48 +0000 Subject: [SocBiN] Virtual seminar this Monday about small RNAs in bacteria (Cynthia Sharma) Message-ID: <743f4f1a6f354f0fa1e5732ce8779f61@cea.fr> Dear colleagues, In the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/), we are reprogramming the virtual seminars of Cynthia Sharma and Fabian König about *small RNAs in bacteria*. *Monday the 3rd of April at 4pm (Berlin/Paris time)* Links to connect (you can choose zoom, which enables questions, or YouTube): https://smallrna-bioinformatics.eu/Pages/Seminars/S22_07.aspx The club proposes seminars every two months. Stay tuned and inscribe to the mailing list (rare emails): https://smallrna-bioinformatics.eu/Pages/_PAGES/Mailing-List.aspx See you virtually very soon! Laurent Guyon PS: tweet for easy retransmission: https://twitter.com/Laurent_Guyon/status/1640638028916899843 ____________________________ Laurent GUYON, PhD, HDR - Bioinformatics CEA IRIG (Interdisciplinary Research Institute of Grenoble) BioHealth laboratory UMR 1292 CEA/Inserm/Université Grenoble Alpes CEA Grenoble - Bât C3 - Bureau 304c 17 rue des Martyrs - 38054 GRENOBLE Cedex 9 - France Tél : (+33)4.38.78.36.91 - 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/ **Post-doc position available in 2023** for a project in bioinformatics related to microRNA in cancer at the single cell level. Feel free to contact me for more information. 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 abhishekniroula7 at gmail.com Thu Mar 30 10:10:04 2023 From: abhishekniroula7 at gmail.com (Abhishek Niroula) Date: Thu, 30 Mar 2023 10:10:04 +0200 Subject: [SocBiN] Fwd: Postdoctoral position in computational cancer genomics In-Reply-To: References: Message-ID: Dear all, We are looking for a bioinformatics postdoc in our new data-driven life science (DDLS) funded research group at Sahlgrenska Academy, University of Gothenburg. The candidate will analyse genomic data from non-cancer donors to study clonal hematopoiesis - a pre-cancerous condition, and cancer development. For more information, see https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=29632 I appreciate it if you can spred the news in your network. Best wishes Abhishek -- Abhishek Niroula Assistant Professor (DDLS Fellow) Institute of Biomedicine, University of Gothenburg -- Best Regards, Abhishek Niroula -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_position_AN.pdf Type: application/pdf Size: 98560 bytes Desc: not available URL: