February 2020 - BBClist - maillist.psb.ugent.be

PhD or post-doc position in the Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven)
by Guy Baele 25 Feb '20

25 Feb '20

The Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven) is looking for a motivated PhD student or postdoctoral researcher with a background in bioinformatics/computer science to perform research in a multidisciplinary team. The candidate for this position should have a strong quantitative background, and preferably hold a master's degree (with distinction/cum laude) and/or PhD in computer science / (bio-)informatics (or equivalent through experience). The candidate hence is preferably experienced in an object-oriented programming language such as Java, although KU Leuven offers courses in object-oriented programming (among others) which the candidates can take if necessary. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel. Full description at KU Leuven's job site: https://www.kuleuven.be/personeel/jobsite/jobs/55574468?hl=en&lang=en Apply here: http://www.kuleuven.be/eapplyingforjobs/light/55574468 Project description This project focuses on new developments in a popular Bayesian phylogenetic and phylodynamic inference framework (BEAST: https://github.com/beast-dev/beast-mcmc) and its applications to important evolutionary problems, with a particular focus on infectious diseases. BEAST is mostly written in Java, with its high-performance computational library, known as BEAGLE, being implemented in C/C++ with CUDA C and C++, the C/C++ interface to the CUDA parallel computing platform. The first part of the project involves the continued development of an online Bayesian phylodynamic inference approach that allows incorporating novel data into an ongoing analysis. As such, the current implementation of such an approach in BEAST (https://arxiv.org/abs/2002.00245) will need to be extended towards more complex models with varying dimensionality and evaluated in terms of its statistical and computational performance. Other approaches to increase the performance of Bayesian phylodynamic inference can also be investigated, such as through parallelization (and interfacing with the BEAGLE library) and the design of novel transition kernels (e.g. Hamiltonian Monte Carlo) aimed at exploring (posterior) distributions of interest in a more efficient manner. In a second part of the project, useful software applications that complement Bayesian phylogenetic and phylodynamic inference will need to be designed and implemented. The main goal is to focus on assessing and interpreting the exploration of tree space, and think of useful and easy-to-interpret visualizations to do so. Novel approaches to visualizing the results of phylodynamic analyses altogether, along with the associated uncertainty on all parameters of interest and accompanying metadata, are also an important aspect of the position, with our group having previous experience in this area (for example, in developing SPREAD and SpreaD3). To this end, web-based applications can also be developed, and knowledge of JavaScript and/or Python is also considered a plus. The topics proposed are not carved in stone however, and we are certainly open to exploring new ideas and concepts. The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand-new facilities of the Rega institute at the Gasthuisberg University hospital campus, and guided by prolific supervisors. The candidate will be able to contribute to the continued development of the BEAST software package - used by many researchers in the fields of phylogenetics, phylodynamics and molecular evolution - and collaborate with top researchers in the field. Additionally, at the Division of Clinical and Epidemiological Virology, the candidate will be able to interact with several top researchers in the field of epidemiology, virology and metagenomics, and work on important infectious disease problems from an evolutionary perspective. The targeted starting date will be June/July 1st 2020, although both earlier and later starting dates can be negotiated, and the candidates should obtain his/her master’s and/or PhD degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Funding is available for 4 years to perform a PhD, and between 2-3 years in case a post-doctoral researcher is selected. The position will remain open until a suitable candidate has been selected. -- Guy Baele, Assistant Professor Department of Microbiology, Immunology and Transplantation Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Open position at Janssen Belgium
by Joke Reumers 25 Feb '20

25 Feb '20

Dear all, Janssen Belgium has an open fixed position in R&D IT. The position would be very suited for a (junior) bioinformatics researcher with a strong interest in the technical aspects of the job (machine learning, cloud operations). The full job description can be found here<https://jobs.jnj.com/jobs/2005800870W?lang=en-us&previousLocale=en-US>. Prior industry experience is not required. Best regards, Joke Reumers Joke Reumers, PhD Team Lead Computational Biology @ Discovery Sciences Janssen Pharmaceutica, Beerse -- +32 14 60 33 24

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Containers & Workflow pipelines course
by Tuur Muyldermans 25 Feb '20

25 Feb '20

Dear, On Monday 11 and Tuesday 12 May 2020 ELIXIR Belgium and VIB are organizing a 'Containers and Workflow Pipelines for reproducible and automated data analysis<https://training.vib.be/containers-and-workflow-pipelines-reproducible-and-…>' course in Ghent. For this two day course we invited the Bioinformatics core of the Centre for Genomic Regulation, Barcelona! The first day is dedicated to Containers (Docker & Singularity) which are great tools for code portability and analysis reproducibility. You will learn how to build a container from scratch, share it with others and how to re-use and modify existing containers. On the second day, you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. With the rising interest in these topics, we hope this might be of interest to you. We start from scratch, however will build up fast and expect prior bioinformatics & programming knowledge. The full program is online and registrations are open via this link<https://training.vib.be/containers-and-workflow-pipelines-reproducible-and-…>. Best, Tuur Muyldermans On behalf of the ELIXIR Belgium team Tuur Muyldermans - ELIXIR Bioinformatics Trainer ELIXIR Belgium | VIB Bioinformatics Core Rijvisschestraat 126, 9052 Ghent | +32 9 248 16 01 www.elixir-belgium.org<https://www.elixir-belgium.org/> | https://corefacilities.vib.be<https://corefacilities.vib.be/> Subscribe to our mailing list<http://eepurl.com/cl-xOX> [ELIXIR logo]

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FW: Global BioImaging - Training Programme Manager
by Alexander Botzki 18 Feb '20

18 Feb '20

From: Training-coordinators <training-coordinators-bounces(a)elixir-europe.org> On Behalf Of Gabriella Rustici Sent: Tuesday, 18 February 2020 12:24 To: training-coordinators(a)elixir-europe.org Subject: [Training-coordinators] Global BioImaging - Training Programme Manager Dear All, Global BioImaging is looking for a Training Programme Manager. This is a great community to work with so please disseminate this opportunity within your networks!!!!!! See attached document for more details Regards Gabry -- Gabriella Rustici, PhD Associate Director of Training, HDR UK Head of Bioinformatics Training, University of Cambridge Department of Genetics Downing Street Cambridge CB2 3EH United Kingdom Email: gr231(a)cam.ac.uk<mailto:gr231@cam.ac.uk> Tel: +44 (0)1223 333614 URL: http://bioinfotraining.bio.cam.ac.uk

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advanced bachelor programme bioinformatics in Bruges (Belgium) (60 ECTS)
by Demeyere Mieke 18 Feb '20

18 Feb '20

Dear Madam/Sir HOWEST University of Applied Sciences starts in September 2020 with a remote bioinformatics study programme! Advanced bachelor of Bioinformatics ... a small summary. Why? Bioinformatics is an emerging field, adding this extra degree to your curriculum, will have an added value to your resume. Aim? Teaching dry-lab skills to people with a molecular biological background in order to function as a fully trained bioinformatician. Content? · Working with databases (build them, retrieve, access and store data in it) · High throughput analysis (working on pipeline, data analysis in R) · Construction of a bioinformatics tool (using php for web application, writing python scripts) · Other: comparative genomics analysis, data mining, structural analysis in pymol, ... For more detailed information please access: http://bioinformatictools.howest.be/programme.pdf For Who? We recruit everyone who holds a diploma of higher education stating sufficient knowledge of molecular biology on (minimal) bachelor level (e.g. Bachelor biomedical Laboratory Technology, bachelor biochemistry, bachelor biotechnology, ...) also relevant Master and PhD degrees are eligible. Duration? One year in daytime education Two year in remote education (starts in September 2020) Want more information? Contact us: Bit(a)howest.be<mailto:Bit@howest.be>, visit our website<https://www.howest.be/en/programmes/advanced-bachelor/bioinformatics> or watch our video<https://www.youtube.com/watch?v=THTK1S-LH34> or presentation in attachment. With kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie/Programme coordinator Advanced Bachelor of Bioinformatics [cid:image001.png@01D5E67B.A4D954D0] Howest University of Applied Sciences Campus Brugge Station Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> en https://www.howest.be/nl/opleidingen/banaba/bio-informatica Bekijk onze navormingen en opleidingen via deze link<https://www.howest.be/nl/opleidingen/navormingen/biomedische-laboratoriumte…>. Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

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IRIBHM/ULB PhD program
by Vincent Detours 18 Feb '20

18 Feb '20

Dear all, IRIBHM, a major molecular biology lab in Belgium, launches an international graduate programme. Topics include computational Biology. More here: http://iribhmphd.ulb.be All the best, Vincent Detours, Ph. D. https://iribhm.org/v-detours/ 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 Skype: vdetours E-mail: vdetours at ulb.ac.be

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Job vacancy applied bioinformatics
by Warris, Sven 17 Feb '20

17 Feb '20

Dear reader, We are looking for a Bioinformatics Assistant to join our research team in Applied Bioinformatics. The group combines wet-lab and bioinformatics expertise. We focus on innovative approaches to genomics analyses, with projects on genome reconstruction, gene annotation, comparative genomics and tool development. Applied Bioinformatics is part of Bioscience, one of the business units of the Wageningen Research foundation of the Plant Sciences Group. Wageningen Research, together with Wageningen University forms Wageningen University & Research. At Bioscience, we study at the molecular level the regulation of metabolic and developmental processes of plants and plant genomics to meet the needs of our growing society. We are developing tools that allow to efficiently use plant genetic resources. Wageningen UR is an internationally renowned research institute in the fields of life sciences and sustainable production. More information: https://www.wur.nl/en/vacancy/Bioinformatics-Research-Assistant.htm Best, Sven Warris Wageningen University & Research

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CFP: AIHA 2020 – International Workshop on Artificial Intelligence for Healthcare Applications
by Nicole Dalia CILIA 17 Feb '20

17 Feb '20

[image: logoAHIA.PNG] *CALL FOR PAPERS* International Workshop on Artificial Intelligence for Healthcare Applications (AIHA 2020) http://lia.unicas.it/AIHA2020 The workshop will be held in conjunction with *ICPR 2020* <https://www.micc.unifi.it/icpr2020/> (25th International Conference on Pattern Recognition, Milan, Italy, 13-18 September 2020). The increased availability of medical data collected from healthcare systems has enabled a number of artificial intelligence applications. Specifically, machine learning can generate insights to improve the discovery of new therapeutic tools, to support diagnostic decisions, to help in the rehabilitation process, just to name a few. Bringing together the advances of this wide and multidisciplinary subject, the aim of this workshop is to present recent advances in artificial intelligence techniques for healthcare applications. *TOPICS* Topics include but are not limited to the following: - Biomedical image analysis - Data analytics for healthcare - Automatic disease prediction - Automatic diagnosis support systems - Genomic and proteomic data analysis - Artificial intelligence for personalized medicine - Machine Learning as a tool to support medical diagnosis and decisions - Machine learning on handwriting and eye-tracking traces for diagnosis and rehabilitation - Decoding of neural signals for diagnosis assistance - Physiological signals processing - Gait analysis - Therapy selection - Brain-computer interface for healthcare - Biomechatronics for medicine - Neuromotor rehabilitation *INVITED SPEAKER * Nico Karssemeijer <http://lia.unicas.it/AIHA2020/invited.html>, Co-chair of DIAG <http://diagnijmegen.nl/index.php/Home> at Radboud UMC, Founder of ScreenPoint <https://screenpoint-medical.com/> Co-founder of Volpara <https://www.matakina.com/> Professor of Computer-Aided Diagnosis, Radboud University Nijmegen, Netherlands. *DATES * Paper Submission: April 15th, 2020 Notification of Acceptance: June 1st, 2020 Camera-ready Submission: July 1st, 2020 *SUBMISSIONS * Submission instructions are available here <http://lia.unicas.it/AIHA2020/submission.html>. *CHAIRS * Alessandro Bria, Nicole Dalia Cilia, Francesco Fontanella, Claudio Marrocco University of Cassino and Southern Lazio, Italy *PROCEEDINGS AND SPECIAL ISSUE* Accepted papers will be published by Springer in the Lecture Notes in Computer Science series (LNCS). We are negotiating with major international journals the publication of a special issue for selected papers presented at the workshop. Contact Information: Nicole Dalia Cilia, nicoledalia.cilia(a)unicas.it

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postdoc position at Sciensano
by Denis BAURAIN 15 Feb '20

15 Feb '20

Dear colleagues, We have a 2-year postdoc position for a bioinformatician specialized in genomics of microorganisms. Expected starting date is April 1st, 2020. Context Sciensano and the BCCM/IHEM collection ensure the general coordination of the BCCM GEN-ERA project. This project aims to answer several scientific questions through the analysis of the genome of different microorganisms. These are preserved in the BCCM collections and include bacteria (including mycobacteria and cyanobacteria), yeasts and molds. The aim is also to implement genomic analysis tools within the BCCM collections. Duties - You work in close collaboration with each of the partner BCCM collections in order to adapt the analyses according to the scientific questions asked and the type of microorganism/genome. - You are responsible for the deployment of pipelines and interfaces for genomic data analysis, as well as the development of additional bioinformatics tools required by the project. - You are responsible for training BCCM collection scientists to use these additional pipelines, interfaces and tools. - You ensure the secure management of the data generated during the project. - You participate in the drafting of scientific reports and publications. - You participate in meetings related to the project, as well as in the general organization of the project, in collaboration with the coordinator (Dr. Pierre Becker). Profile - PhD in Science (bioinformatics). - Experience in analyzing genomic data is essential, preferably on both prokaryotic and eukaryotic genomes. - Knowledge of microbiology and interest in taxonomy of microorganisms is an asset. - Technical skills: Genome assembly (especially expertise in Illumina and MinION data analysis), phylogenomics, functional genomics, interest in traceability of data and analyses. - Computer skills: Linux, high-performance computing (HPC), scripting languages (Python or Perl) and statistics (R). - Generic skills: analytical skills; autonomous and results driven; good organizational and communication skills. More information here: <https://wiv-isp.hr-technologies.com/content/jobpage.asp?a=DETAIL&jdkid=588&…> <https://wiv-isp.hr-technologies.com/content/jobpage.asp?a=DETAIL&jdkid=588&…> Best regards, Denis -- Prof. Denis BAURAIN Head of the Dept of Life Sciences University of Liège InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics Sart Tilman, Quartier Vallée 1 Chemin de la Vallée 4, Bât. B22 4000 Liège Belgium

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Share your research at SMRT Leiden – April 28-29
by A.Mahfouz＠lumc.nl 13 Feb '20

13 Feb '20

Dear all, You are cordially invited to attend the 5th annual SMRT Leiden Scientific Symposium. Feel free to share this information with others who may be interested in attending. We look forward to seeing you at these exciting events! Best regards, Ahmed Mahfouz Ahmed Mahfouz, PhD | Assistant Professor, Department of Human Genetics Leiden University Medical Center | Dept. of Human Genetics | P.O. Box 9600, 2300 RC Leiden | Postal zone S4-P Room R-04-022 | Phone +31 71 52 69274 Please join us at the 5th annual SMRT Leiden Event at Leiden University Medical Center, Leiden, Netherlands from April 28-30 2020, bringing together the SMRT community for three days of engaging science and networking. [https://www.pacb.com/wp-content/uploads/smrt-leiden-2020-artwork_email_hdr.…] Dear all, Please join us at the 5th annual SMRT Leiden Event at Leiden University Medical Center, Leiden, Netherlands from April 28-30 2020, bringing together the SMRT community for three days of engaging science and networking. [http://programs.pacificbiosciences.com/l/1652/2016-09-16/3ptljp/1652/181830…]<https://programs.pacificbiosciences.com/e/1652/Leiden-index-html-registrati…> Share your research! Our scientific advisory committee is reviewing abstracts for presentations and posters for the event. If you are interested, please submit your abstract<mailto:tkerelska@pacificbiosciences.com?subject=Abstract%20Submission%20-%20SMRT%20Leiden%20Conference> by March 31. The Best Abstract Award will be chosen by SMRT Leiden participants. SMRT Scientific Symposium: Changing the World, One Molecule at a Time! — April 28-29 SMRT Scientific Symposium: Changing the World, One Molecule at a Time! is a two-day symposium featuring key experts and opinion leaders sharing scientific discoveries and novel analytical achievements using PacBio Sequencing platforms. SMRT Informatics Developers Conference — April 30 SMRT Informatics Developers Conference is a collaborative event focused on learning, in-person brainstorming and idea exchange about using, developing, and improving analytic tools for PacBio SMRT Sequencing data. Keynote speakers: * Erich Jarvis, Ph.D., Rockefeller University, USA * Ana Conesa, Ph.D., University of Florida, USA * Hagen Tilgner, Ph.D., Weill Medical College of Cornell University, USA * Jennifer Ong, Ph.D., New England Biolabs, USA * Sergey Koren, Ph.D. National Institutes of Health, USA * Kevin Fengler, Ph.D., Corteva Agriscience, USA These events are free and open to all members of the scientific community. We look forward to seeing you in Leiden! Best Regards, The SMRT Leiden Scientific Committee [Forward This]<https://programs.pacificbiosciences.com/e/1652/-unique-lng-en-us-pubid-Soci…>[Tweet This]<https://programs.pacificbiosciences.com/e/1652/his-unique-lng-en-pubid-Soci…>[Send to Linkedin]<https://programs.pacificbiosciences.com/e/1652/his-unique-lng-en-pubid-Soci…>[Send to Facebook]<https://programs.pacificbiosciences.com/e/1652/his-unique-lng-en-pubid-Soci…>[View more services]<https://programs.pacificbiosciences.com/e/1652/50-addthis-unique-pubid-Soci…> [http://programs.pacificbiosciences.com/l/1652/2015-08-27/3dd9ph/1652/174604…]<https://programs.pacificbiosciences.com/e/1652/footer-utm-content-logo-foot…> Pacific Biosciences of California, Inc. 1305 O'Brien Dr., Menlo Park, CA 94025 For Research Use Only. Not for use in diagnostic procedures. © Copyright 2020 by Pacific Biosciences of California, Inc. All rights reserved. Update Profile<https://programs.pacificbiosciences.com/emailPreference/e/epc/1652/p1EsztQ2…> | Unsubscribe<https://programs.pacificbiosciences.com/unsubscribe/u/1652/425dcfb8a3b3531f…> | Legal & Trademarks<https://programs.pacificbiosciences.com/e/1652/gal-and-trademarks-site-usag…> [http://programs.pacificbiosciences.com/l/1652/2016-12-06/3rc6w3/1652/183568…]<https://programs.pacificbiosciences.com/e/1652/pacbio/41mbmx/549153087?h=xD…> [http://programs.pacificbiosciences.com/l/1652/2016-12-06/3rc6vy/1652/183564…] <https://programs.pacificbiosciences.com/e/1652/company-pacific-biosciences/…> [http://programs.pacificbiosciences.com/l/1652/2016-12-06/3rc6w5/1652/183570…] <https://programs.pacificbiosciences.com/e/1652/user-PacificBiosciences/41mb…>

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