- BBClist - maillist.psb.ugent.be

IRIBHM/ULB PhD program - PhD opportunities in Brussels
by DETOURS Vincent 08 Mar '22

08 Mar '22

Dear all, IRIBHM, a major molecular biology lab in Belgium, launches an PhD graduate program. Topics include computational Biology. More about projects and how to apply here: http://iribhmphd.ulb.be<http://iribhmphd.ulb.be/>, All the best, Prof. Vincent Detours, Ph. D. IRIBHM - Université Libre de Bruxelles Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 E-mail: vdetours at ulb.ac.be Prof. Vincent Detours, Ph. D. IRIBHM - Université Libre de Bruxelles Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 E-mail: vincent.detours at ulb.be

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Computational Methods in Systems Biology (14-16.9, Bucharest): 2nd CfP
by Ion Petre 03 Mar '22

03 Mar '22

CMSB2022: International Conference on Computational Methods in Systems Biology University of Bucharest Bucharest, Romania, September 14-16, 2022 Conference website https://fmi.unibuc.ro/en/cmsb-2022/ Submission link https://easychair.org/conferences/?conf=cmsb2022 Call for papers https://easychair.org/cfp/CMSB2022 Abstract registration deadline April 27, 2022 Submission deadline May 4, 2022 CMSB 2022 - Second Call for Papers The 20th conference on Computational Methods in Systems Biology (CMSB 2022, https://fmi.unibuc.ro/en/cmsb-2022/) will take place on September 14-16, in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. CMSB is a well established conference series, whose aim is 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. NEW in the 2nd CfP * Invited speakers confirmed: * 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) * Conference proceedings to be published in the LNBI series of Springer Nature. * Best paper award(s) sponsored by Springer Nature with 1000 EUR. List of 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. Types of contributions to CMSB 2022 * 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). * POSTERS: Extended abstracts should be submitted to propose poster presentation of original unpublished work, or of major results published or accepted in the last year in a high-quality journal or conference. The abstracts should be submitted in Springer LNBI style and should not exceed 4 pages all included. Authors of accepted abstracts will be invited for presentation in a poster sessions and/or for flash presentations. Poster submissions will not be included in the Springer LNBI proceedings. * HIGHLIGHT TALKS: Highlight talk proposals should be submitted in the form of an extended abstract, for possible oral presentation without publication of related material in the conference proceedings. We particularly welcome submission of recently published work. Submitted abstracts summarising the results and their relevance should not exceed 2 pages including references. Extended abstracts will not be included in the Springer LNBI proceedings. The full information for authors on how to prepare and submit their contributions is available at https://fmi.unibuc.ro/en/cmsb-2022/cmsb-2022-call/. Committees Program Committee * Alessandro Abate<https://www.cs.ox.ac.uk/people/alessandro.abate/> – University of Oxford (UK) * Paolo Ballarini<https://sites.google.com/site/pballarini/> – Centrale Supélec (France) * Daniela Besozzi<https://www.linkedin.com/in/daniela-besozzi-3370868/> – University of Milan Bicocca (Italy) * Luca Cardelli<http://www.lucacardelli.name/> – University of Oxford (UK) * Milan Češka<https://www.fit.vut.cz/person/ceskam/.cs> – Brno University of Technology (Czech Republic) * Eugenio Cinquemani<https://team.inria.fr/ibis/eugenio-cinquemani/> – Inria Grenoble-Rhône-Alpes (France) * Eugen Czeizler<https://www.linkedin.com/in/eugenczeizler/?originalSubdomain=fi> – University of Helsinki (Finland) * Franck Delaplace<https://www.ibisc.univ-evry.fr/~delapla/> – Université Paris-Saclay (France) * Jerome Feret<http://www.di.ens.fr/~feret> – Inria Paris (France) * Clémence Frioux<https://cfrioux.github.io/> – Inria Bordeaux (France) * Ashutosh Gupta<https://www.linkedin.com/in/ashutosh-gupta-3b7a63141/> – IIT Bombay (India) * Monika Heiner<https://www-dssz.informatik.tu-cottbus.de/DSSZ/Main/MonikaHeiner> – Brandenburg Technical University Cottbus-Senftenberg (Germany) * Jane Hillston<http://homepages.inf.ed.ac.uk/jeh> – University of Edinburgh (UK) * Tommaso Mazza<http://bioinformatics.css-mendel.it/> – CSS Mendel (Italy) * Andrzej Mizera<https://satoss.uni.lu/members/andrzej/> – University of Luxembourg (Luxembourg) * Jun Pang<https://satoss.uni.lu/members/jun/> – University of Luxembourg (Luxembourg) * Nicola Paoletti<https://nicolapaoletti.com/> – University of London (UK) * Loïc Paulevé<https://loicpauleve.name/> – CNRS, LaBRI (France) * Andrei Paun<https://www.researchgate.net/profile/Andrei-Paun> – University of Bucharest, Romania, co-chair * Ion Petre<https://users.utu.fi/ionpet/> – University of Turku, Finland, co-chair * Tatjana Petrov<https://www.tatjanapetrov.info/> – University of Konstanz (Germany) * Ovidiu Radulescu<https://ovidiu-radulescu.yj.fr/> – University of Montpellier France) * Andre Ribeiro<https://sites.google.com/view/andreribeirolab/home> – University of Tampere (Finland) * Maria Rodriguez Martinez<https://researcher.watson.ibm.com/researcher/view.php?person=zurich-MRM> – IBM Zürich Research Laboratory (Switzerland) * Olivier Roux<https://olivieroux.wordpress.com/> – École Centrale de Nantes (France) * David Šafránek<https://www.fi.muni.cz/~xsafran1/> – Masaryk University (Czech Republic) * Carolyn Talcott<https://www.sri.com/bios/carolyn-talcott/> – SRI International (USA) * Jing Tang<https://researchportal.helsinki.fi/en/persons/jing-tang> – University of Helsinki (Finland) * Adelinde Uhrmacher<https://mosi.informatik.uni-rostock.de/team/staff/prof-dr-rer-nat-adelinde-…> – University of Rostock (Germany) * Andrea Vandin<http://people.compute.dtu.dk/anvan/> – Technical University of Denmark (Denmark) * Verena Wolf<http://mosi.cs.uni-sb.de/verena.html> – Saarland University (Germany) * Christoph Zechner<https://zechnerlab.wordpress.com/> – Max Planck Institute of Molecular Cell Biology and Genetics (Germany) Organizing committee * David Pacioianu, University of Bucharest, Romania * Andrei Paun<https://www.researchgate.net/profile/Andrei-Paun>, University of Bucharest, Romania (co-chair) * Ion Petre<https://users.utu.fi/ionpet/>, University of Turku, Romania (co-chair) * Nicoleta Siminea, University of Bucharest * Joel Sjöberg, University of Turku, Finland Publication The submissions to CMSB 2022 will be fully peer-reviewed. The accepted (regular and tool) articles will be published in the conference proceedings, in the Springer LNBI series. A special issue of a widely recognized international journal is expected to be organized later based on the conference, subject to separate peer-review. A selection of the best papers will be invited to be extended and submitted to this special issue. Important dates * May 4, 2022: regular and tool paper submission deadline (their abstracts submitted by April 27). * June 10, 2022: acceptance notifications. * June 17, 2021: poster and highlight talk abstract submission deadline. * September 14-16, 2021: conference. Venue The conference will be held in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. Contact All questions about submissions should be emailed to the conference organizers Ion Petre (ion.petre(a)utu.fi) and Andrei Paun (apaun(a)fmi.unibuc.ro) -- Prof. Ion Petre Department of Mathematics and Statistics University of Turku, Finland https://users.utu.fi/ionpet/ ion.petre(a)utu.fi

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WIVACE 2022 Call for Papers
by Francesco FONTANELLA 03 Mar '22

03 Mar '22

[image: unnamed.png] *WIVACE 2022* *XVI International Workshop on Artificial Life and Evolutionary Computation * *Gaeta (LT), Italy* *September 14-16, 2022* Web site: http://wivace2022.unicas.it/ The International Workshop on Artificial Life and Evolutionary Computation aims at bringing together researchers working in Artificial Life and Evolutionary Computation to present and share their research in a multidisciplinary context. The workshop provides a forum for the discussion of new research directions and applications in these fields, where different disciplines could effectively meet. It was first held in 2007 in Sampieri (Ragusa), as the incorporation of two previously separately running workshops (WIVA and GSICE). After the success of the first edition, the workshop was organized in the following years in Venice (2008), Naples (2009), Parma (2012), Milan (2013), Vietri (2014), Bari (2015), Salerno (2016), Venice (2017) and Parma (2018). Interested authors are invited to contribute papers on theory and applications of Artificial Life, Evolutionary Computation, and complex smart systems. Contributions solicited cover a variety of topics including but not limited to: - Bioinspired Algorithms - Bioinspired Robotics - Coevolution and Collective Behavior - Complex Systems - Data-driven Self-regulating Systems - Evolutionary Computation - Evolutionary Approaches to Big Data and Big Data Streams - Evolutionary Learning Systems - Evolutionary Agents - Modeling and Simulation of Artificial and Biological Systems - Modeling and Simulation of Social and Economical Systems - Modeling of Business Intelligence Systems - Neural Computers - Neuroevolution: Improving Deep Learning with Evolutionary Computation - Self-organizing Cyber-Physical Systems - Socio-inspired Swarm Intelligence Algorithms - Synthetic and Systems Biology - Systems Chemistry - Theories and Applications of Artificial Life *SUBMISSION DETAILS* Contributions may be submitted in one of the following forms: - Full research papers (up to 12 pages). - Simple Abstracts (1-4 pages). Full research papers should present original unpublished work. Simple abstracts should describe original work in progress or a summary of a full paper. The submissions will be peer-reviewed by at least three members of the program committee. The authors of accepted papers or abstracts will have to improve their papers on the basis of reviewers’ comments and will be asked to send a camera-ready version of their manuscripts. At least one author of each accepted work has to register for the conference, attend the conference and present his work. We have contacted Springer to publish the proceedings of Wivace 2022 in Springer's Communications in Computer and Information Science (CCIS) proceedings series, which is abstracted/indexed in DBLP, Google Scholar, EI-Compendex, Mathematical Reviews, SCImago, Scopus. Accepted abstracts describing unpublished work will be considered for publication of extended versions (up to 12 pages) in the same volume. Submission instructions can be found here: http://wivace2022.unicas.it/submission.html *IMPORTANT DATES* Abstract/paper submission deadline: 1st July 2022 Notification of acceptance: 22nd July 2022 Early Registration: 24th July 2022 *GENERAL CHAIRS* Claudio De Stefano (University of Cassino and Southern Lazio) - destefano(a)unicas.it Francesco Fontanella (University of Cassino and Southern Lazio) - fontanella(a)unicas.it

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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Open roles at AstraZeneca
by Sergio Martinez Cuesta 28 Feb '22

28 Feb '22

Dear all, For those of you reaching your end of contract, the following open positions at AstraZeneca may be of interest: *Senior Bioinformatician for Oligonucleotide Therapeutics* Gothenburg (Sweden) Deadline for applications: February 28th https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Senior Bioinformatics Scientist – Knowledge Graph and Networks* Cambridge (UK) Deadline for applications: March 12th https://careers.astrazeneca.com/job/cambridge/senior-bioinformatics-scienti… *Senior Bioinformatician for Therapeutic Gene Editing* Gothenburg (Sweden) Deadline for applications: March 12th https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Bioinformatician - Proteomics* Cambridge (UK) Deadline for applications: - https://careers.astrazeneca.com/job/cambridge/bioinformatician-proteomics-u… Best wishes, Sergio

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Reminder Research Software Engineers Survey - still one week for submission
by Alexander Botzki 28 Feb '22

28 Feb '22

Dear all, I'd like to send you the link for a survey which a number of international supporters for Research Software Engineering have put together recently. Our effort has been lead by Simon Hettrick from the Software Sustainability Institute. A blog about the results from 2018 is here: https://www.software.ac.uk/blog/2019-02-15-rse-survey-2018-results We would be delighted to have as many as possible answers from persons who write software used in research. So, please have a look at this link for more information and the questions: https://softwaresaved.limequery.com/386272?lang=en The survey will stay open for one more week. Thanks a lot for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore Alexander Botzki – Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [signature_351744268]

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[Could not verify sender] Position for: Postdoctoral researcher in Medical Genetics/Bioinformatics
by Berry Kriesels 24 Feb '22

24 Feb '22

Dear all, We want to draw your attention to our vacancy for a postdoctoral researcher position in Medical Genetics/Bioinformatics. See attached. With kind regards. *Berry Kriesels* - Founder / General director *Omnigen* Bioinformatics research, services and consultancy. Papsouwselaan 119-A 2624AK Delft, 3rd floor b.kriesels(a)omnigen.nl | +31616750561 | www.omnigen.nl

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PhD position in bioinformatics: mechanisms of genetic interactions in pediatric cancer
by Kemmeren-2, P.P.C. (Patrick) 24 Feb '22

24 Feb '22

Dear all, Happy to share that we have an opening for a PhD student in bioinformatics working on understanding mechanisms of genetic interactions in pediatric cancer! Interested in working on this topic and be part of a unique pediatric oncology center with multidisciplinary and dynamic environment, then please apply through the link below: https://werkenbijprinsesmaximacentrum.nl/vacature/phd-student-bioinformatic… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core Princess Máxima Center Associate Professor UMC Utrecht T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_1113111550] [signature_1581634270] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Software engineer - multi-omics data management
by Laurent Gatto 22 Feb '22

22 Feb '22

Dear all, There's a software engineer position open in my group to develop a multi-omics data management platform. The project is in collaboration with Sébastien Jodogne from the EPL (Engineering school at UCLouvain) and a large multi-disciplinary team (including clinicians from the university hospital) at in Brussels. Details and application: https://jobs.uclouvain.be/PersonnelAdministratif/job/Ing%C3%A9nieur%C2%B7e-… Do not hesitate to get in touch if you have any questions. Best wishes, Laurent --- Prof Laurent Gatto Computational Biology Unit (CBIO) de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium Tel: +32 (0)2 764 74 15 http://lgatto.github.io/about

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Open position: Data Governance Bioinformatics (m/f/d)
by Erick Antezana 22 Feb '22

22 Feb '22

*apologies for cross-posting* Become part of our team of highly motivated data science experts (m/f/d) to solve major challenges in modern crop protection by molecular and chemical genetics approaches. In this role you´ll be involved in developing a master data strategy for OMICs data and drive data curation and integration. Join us at Bayer to work on purposeful projects to bring our mission to life: “Health for all and Hunger for none”. YOUR TASKS AND RESPONSIBILITIES - You will develop and implement a data governance strategy for OMICs technologies in coordination with IT and semantics technology experts (m/f/d) - You will manage data maintenance, identify relevant data sources, and ensure data quality in terms of completeness, format, and consistency - You will contribute to product and platform teams in demand planning, prioritization and monitoring the use of services within project requests towards our partner - You will build cross-functional relationships to partner with the business stakeholders (m/f/d) and collaborate with Bayer’s Data Science community to co-develop innovative solutions - You will present your results in compelling stories to various stakeholders (m/f/d) to create both strategic and operational changes in business WHO YOU ARE - You have a PhD or MSc with first experience in bioinformatics, computational biology, computer science, physics or related fields - You are experienced in OMICS data and Meta-data management and able to support innovation and future-oriented data concepts - Molecular and/ or Cellular Biology experience is a plus (preferably in insects, plants and fungi) - You are experienced with relational and/or Graph Databases and proficient in using querying languages such as SQL & SPARQL - You have excellent scripting and programming skills in common Data Science languages such as R, Perl, Python (Django framework) - You have a strategic mindset and a result-oriented, motivated, and proactive personality with proven ability to efficiently work in cross-functional teams reaching joint goals You have good communication skills in English, both written and spoken; a good working knowledge of the German or French language can be beneficial This position is initially limited to two years. https://karriere.bayer.de/en/job/data-governance-bioinformatics-m-f-d--SF55… You can contact me in case of questions.

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