June 2019 - BBClist - maillist.psb.ugent.be

Job posting: Postdoc in Blue Biotech - second announcement
by Filip Volckaert 27 Jun '19

27 Jun '19

Job posting: Postdoc in Blue Biotech Dear all, Please find attached and at the bottom of this message our latest open position for the Genomics Core and Department of Biology at the KU Leuven. We would appreciate it if you could post this up in your job portals. Please do not hesitate to contact me if in need of further assistance. Thank you! Kind regards Filip Volckaert Professor of marine ecology and evolution Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Ch. Deberiotstraat 32, box 2439 B-3000 Leuven, Belgium Phone: +32 16 32 39 72 Fax: +32 16 32 45 75 Email: filip.volckaert(a)kuleuven.be<mailto:filip.volckaert@kuleuven.be> URL: bio.kuleuven.be/eeb/lbeg Skype: filipvolckaert1 Postdoctoral fellow in Blue Biotech The Department of Biology and The Genomics Core of the KU Leuven are currently looking for a postdoctoral fellow in Environmental genomics & bioinformatics to lead independent population genomic research and develop ESFRI-EMBRC bioinformatics services. The successful candidate will join two international teams that study the molecular evolution of marine organisms and develop analytical tools for NGS data for research purposes, and transitions them to/towards marine scientists. The successful candidate will focus on independent scientific research in evolutionary genomics and the development of bioinformatic toolkits for external users. We also offer the possibility to develop our ongoing consultancy in marine genomics. We are looking for a motivated and scientifically excellent candidate in environmental genomics/ bioinformatics with a problem-solving attitude to work in a collegial environment pervaded with intellectual rigor. Strong communication skills complemented with innovative and analytical thinking are important assets. Applicants must hold a PhD in a related field such as (Applied) Biology, Bioinformatics or Computational Biology. The individual we are looking for will have to be confrontable with common bioinformatics software and programming languages (Python, Perl, Java, R), and be highly motivated to solve biological problems. The successful applicant will also be adapting and implementing existing bioinformatics pipelines in an automated cloud-based analysis platform to make these algorithms available for marine biological and other fundamental biological questions. The candidate will also have an opportunity for the teaching and mentoring of students. We look forward to receiving a motivation letter (max. 1 page), short CV (max. 3 pages), a scientific achievements track-record (max. 2 pages) including a list of your five most important publications, and three names of referees. We offer an initial 18 Months contract (extendable with national or EU funds) a competitive salary and interactive work environment in collaboration with the European Marine Biological Resource Center (www.embrc.eu<http://www.embrc.eu>), a well-established marine research team (bio.kuleuven.be/eeb/lbeg) and the largest Genomics Service core (www.genomicscore.be<http://www.genomicscore.be>) in Belgium. KU Leuven is a research-intensive, internationally oriented university that has been elected Europe's most innovative university by Reuters and consistently ranks and features in Europe's top-15 universities within the Times Higher Education ranking. Leuven is a historic, dynamic and lively city located in the heart of Belgium, within 20 min from Brussels, the capital of the European Union, and less than 2 h from Paris, London and Amsterdam. Working site: Leuven, Belgium Application deadline: The application must be sent as a single PDF by email to conny.coeckelberghs(a)kuleuven.be<mailto:conny.coeckelberghs@kuleuven.be> with as subject 'eGenomics/bioinformatics postdoc position' by midnight June 25th 2019. For further information contact dr. Gregory Maes, phone +32 16 37 25 22, gregory.maes@ kuleuven.be<mailto:gregory.maes@%20kuleuven.be> and/or prof. Filip Volckaert, phone: +32 16 39 72, filip.volckaert(a)kuleuven.be<mailto:filip.volckaert@kuleuven.be>.

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Upcoming BioSB courses: Machine Learning, Algorithms for Genomics, Constraint-based modelling
by Femke Francissen 26 Jun '19

26 Jun '19

Dear colleague, Registration is open for the following courses of the BioSB research school <http://www.biosb.nl> (more detailed information below): - Machine Learning for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-sy…> - 7-11 October 2019, Delft/Amsterdam, the Netherlands - Algorithms for Genomics <https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/> - 14-18 October 2019, Delft, the Netherlands - Constraint-based modelling <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…> - 25-29 November 2019, Leiden, the Netherlands *** Machine Learning for bioinformatics and systems biology, 7-11 October 2019, Delft/Amsterdam, the Netherlands* Modern biology is a data-rich science, driven by our ability to measure the detailed molecular characteristics of cells, organs, and individuals at many different levels. Interpretation of these large-scale biological data requires the detection of statistical dependencies and patterns in order to establish useful models of complex biological systems. Techniques from machine learning are key in this endeavour. Typical examples are the visualization of single-cell RNA-seq data using dimensionality reduction methods, base calling for nanopore sequencing data using hidden Markov models and (recurrent) neural networks, and classification of high-throughput microscopy image data using convolutional neural networks. In this one-week course, the foundations of machine learning will be laid out and commonly used methods for unsupervised (clustering, dimensionality reduction, visualization) and supervised (mainly classification) learning will be explained in detail. Methods will be illustrated using recent examples from the fields of systems biology and bioinformatics. Methods discussed in the morning lectures will be put into practice during the afternoon computer lab sessions. Read more & register <https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-sy…> *** Algorithms for Genomics, 14-18 October 2019, Delft, the Netherlands* Comparative genomics aims to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how comparative genomics is developing is important to shape your own research. In this 5-day course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. Read more & register <https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/> *** Constraint-based modelling: Introduction & advanced topics, 25-29 November 2019, Leiden, the Netherlands* Constraint-based modeling is a powerful modeling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modeling is the use of genome-scale reconstructions that represent particular cellular functions as a biochemical reaction network. In this 5-day course, you will be introduced to: - the principles of constraint-based reconstruction and analysis (COBRA) - the underlying mathematical foundations of constraint-based modeling - methods for integration of omics data with constraint-based models - basic and advanced methods for interrogating models and interpreting results - open source COBRA software, including the COBRA Toolbox - standards for reconstruction and model sharing - example applications to biomedicine and biotechnology The course is structured into both lectures and practical sessions so that theory can be illustrated with biologically motivated computational examples. Read more & register <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…> These courses are part of the BioSB research school course portfolio <https://www.biosb.nl/education/course-portfolio/>. The BioSB research school offers a wide variety of training courses that enable life scientists to apply modelling and computational approaches in addressing scientific challenges. Best regards, Femke Francissen *Femke Francissen* Community manager BioSB Research School *V*isiting address: Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht E-mail: femke.francissen(a)biosb.nl Website: www.biosb.nl

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Postdoc position Bioinformatics: Laboratory of Cancer Epigenetics
by mbizet 26 Jun '19

26 Jun '19

Dear all, A postdoctoral position (see attachment) is available for a highly motivated PhD that wishes to join the Laboratory of Cancer Epigenetics (http://fukslab.ulb.be/ ) headed by Prof. François Fuks (ULB-Cancer Research Center, Brussels). The research goal will be the analysis of transcriptomic and epigenomic changes (/e.g./ DNA methylation, histone modifications) that arise in cancers. Particularly the analysis of next generation sequencing data concerning a novel RNA epigenetic modification, which our lab recently investigated, will be one of the main challenging tasks of the candidate (Delatte et al., Science 2016). He/she will also participate in several projects with high impact factor publication potentials. The host lab is running a Next Generation Sequencing platform (http://epics.ulb.be/) and the candidate will have the opportunity to analyse many types of sequencing methods (RNA-seq, ChIP-seq, RIP-seq, CLIP-seq, Oxford Nanopore, … ), while having a direct interaction with the wet lab biologists generating the data. The host lab is part of the ULB-Cancer Research Center (U-CRC) (http://ucrc.ulb.be/) providing a high profile scientific environment. The candidate will join other experienced bioinformaticians working on transcriptomics and epigenomics, and collaborate with bioinformaticians from our university, as well as with other institutes from Belgium and abroad. The candidate should hold a PhD (or about to be obtained) in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics and programming (/e.g./ R, python). Experience with sequence data, genome-wide data sets (/e.g./ ChIP-seq, RNA-seq ...) or massive datasets analysis will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. The interaction with the biologists in the lab will be key for the success of this project and genuine interest for biology and clinical researches is required. A good biological background will be valuable. This position is funded for 2 years, with the possibility of further renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected (flexible starting date). Please send a motivation letter, a CV and names of two referees to Martin Bizet (mbizet(a)ulb.ac.be) --- Martin Bizet Ph.D. in Bioinformatics Laboratory of Cancer Epigenetics ULB, Brussels, Belgium

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26-28 August 2019: Course Next generation sequencing data analysis, LUMC, Leiden, the Netherlands
by Celia van Gelder 25 Jun '19

25 Jun '19

On behalf of Madeleine Nivard: 26-28 August 2019: Course Next generation sequencing data analysis, LUMC, Leiden The aim of the course is to give a broad overview of the different applications of NGS with a focus on different ways to analyse the data. Presentations will discuss specifically the different choices available for data analysis, why a specific approach was selected and which alternatives are available. The course will, besides discussing and demonstrating some generally applicable tools, not include practical data analysis nor discuss in detail specific algorithms used. To get practical experience participants should, after this general introductory course, follow more specific courses (e.g. a course on RNAseq, de novo assembly, metagenomics, etc.). For more information and registration visit the website <http://www.medgencentre.com/MGC-courses/> or register directly via Boerhaave <https://www.boerhaavenascholing.nl/medische-nascholing/2019/mgc-next-genera tion-sequencing/>

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Proteomics Service Facility Leader
by Andreas Beyer 24 Jun '19

24 Jun '19

Dear all, We are looking for a Proteomics Service Group Leader on a permanent position in our CECAD Excellence Cluster: https://www.nature.com/naturecareers/job/proteomics-service-group-leader-un… Please, forward this to potentially suitable candidates. Best, Andreas Beyer -- Prof. Dr. Andreas Beyer http://cellnet.cecad.uni-koeln.de/ Phone: +49 221-478 84429

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CFP OLA'2019 Int. Conf. on Optimization and Learning @Spain
by El-ghazali Talbi 24 Jun '19

24 Jun '19

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2020 International Conference on Optimization and Learning: Challenges and Applications 17-19 Feb 2020 Cadiz, Spain http://ola2020.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2020 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2020 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Sept 20, 2019 Notification of acceptance Nov 9, 2019 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference SCOPUS indexed Springer book and a special issue in a Journal are planned to be published. Participants will be invited to submit extended versions of their work for consideration. -- *********************************************************************** OLA'2020 Int. Conference on Optimization and Learning 17-19 Feb 2020, Cadiz, Spain http://ola2020.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Fwd: three open position at Computational Science Lab of University of Amsterdam
by Sanne Abeln 20 Jun '19

20 Jun '19

---------- Forwarded message --------- From: Hoekstra, Alfons <A.G.Hoekstra(a)uva.nl> Date: Thu, 20 Jun 2019 at 17:02 Subject: three open position at Computational Science Lab of University of Amsterdam To: Cc: Hoekstra, Alfons <A.G.Hoekstra(a)uva.nl> Dear colleagues, We currently have three open positions in our lab, see below. If you happen to know suitable candidates, please forward these. Thanks a lot, best regards, Alfons Hoekstra == postdoc In silico Stroke Trials https://www.uva.nl/en/content/vacancies/2019/06/19-418-postdoctoral-researc… PhD position on High performance multiscale modeling of blood flows https://www.uva.nl/en/content/vacancies/2019/06/19-404-phd-position-on-high… Scientific Programmer Computational Biomedicine https://www.uva.nl/en/content/vacancies/2019/06/19-405-scientific-programme… -- Computational Science <http://uva.computationalscience.nl> Lab <http://uva.computationalscience.nl> Master Programme Computational Science <http://www.uva.nl/en/shared-content/subsites/graduate-school-of-sciences/en…> -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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A conference to promote women's research in computational biology #AdvCompBio
by Alba Jene 18 Jun '19

18 Jun '19

Dear colleagues, The first <https://www.iscb.org/advcompbio2019> Advances in Computational Biology conference will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology. The conference is open to everyone to attend, but all the speakers will be women, providing an excellent opportunity to share ideas and build research networks. You are invited to register to attend ( <https://www.iscb.org/advcompbio2019-registration> https://www.iscb.org/advcompbio2019-registration) and to submit an abstract for consideration for oral or poster presentations, please see more details here: <https://www.iscb.org/advcompbio2019-call-submissions> https://www.iscb.org/advcompbio2019-call-submissions. Topics included: 1. Learning from Biological Sequences: population genomics, evolutionary genomics, systems biology, transcriptomics, sequence analysis 2. When Computational Biology meets Medicine: biomedical applications, mutational landscapes, clinical genomics 3. Machines Speeding up Research: high performance computing, machine learning in the life sciences, imaging data analysis, dynamic simulations and algorithm development The keynote speakers of the conference are: <https://www.ucl.ac.uk/orengo-group/people/prof-christine-orengo> Christine Orengo, group leader of Orengo Group at University College London, <https://www.bsc.es/przulj-natasa> Natasa Przulj, group leader of the Life Sciences - Integrative Computational Network Biology at the Barcelona Supercomputing Center and <https://www.linkedin.com/in/marie-christine-sawley-70b5534/?originalSubdoma in=ch> Marie-Christine Sawley, director of the Exascale Lab at Intel. Furthermore the participants will have the opportunity to interact personally in round-table informal meetings with women leaders in the fields of IT, academia research and politics that support the conference. Confirmed discussion leads: <https://www.iscb.org/advcompbio2019-other-activities> https://www.iscb.org/advcompbio2019-other-activities. Important dates: Abstract submission opens May 6th, 2019 Abstract submission deadline July 1st, 2019 Poster and oral communication notification September 1st, 2019 Early bird registration deadline September 15th, 2019 The conference is organised by the Barcelona Supercomputing Center <https://www.iscb.org/advcompbio2019> (BSC-CNS), the joint <https://www.imim.es/> IMIM- <https://www.upf.edu/> UPF Research Programme on Biomedical Informatics ( <http://grib.imim.es/> GRIB) and the Universitat Politècnica de Catalunya ( <https://www.upc.edu/en?set_language=en> UPC). It is an affiliate conference of the International Society for Computational Biology ( <https://www.iscb.org/> ISCB). We look forward to meeting you at the #AdvCompBio Conference in Barcelona this November! Best regards, The Organizing Committee Mar Albà (UPF/IMIM) Eva Alloza (BSC-CNS) Rosa Maria Badia (BSC-CNS) Nataly Buslón (BSC-CNS) Osnat Hakimi (UPC) Alba Jené (BSC-CNS) Eva Navarrete (BSC-CNS) María José Rementería (BSC-CNS) <https://www.iscb.org/advcompbio2019> -- Alba Jené Sanz, PhD Bioinformatics Unit Coordinator Barcelona Supercomputing Center (BSC) <https://maps.google.com/?q=C/+Jordi+Girona+29,+08034-Barcelona,+Spain&entry =gmail&source=g> C/ Jordi Girona 29, 08034-Barcelona, Spain Tel: +34 93 413 7572 http://bsc.es/disclaimer

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PhD or Postdoc position: The role of gut microbiota in immune senescence and cardiovascular diseases
by Patrick Deelen 18 Jun '19

18 Jun '19

*PhD or Postdoc position: The role of gut microbiota in immune senescence and cardiovascular diseases* The Departments of Genetics and Pediatrics, at the University Medical Center Groningen, the Netherlands, are looking for a potential PhD student or junior postdoc in the field of bioinformatics to assess the contributions of microbiome-derived signals in the etiology of age- and obesity-related cardio-metabolic diseases through (immune) senescence. The candidate will investigate the role of gut microbiota composition in immune senescence, predisposition to cardiovascular diseases, and its relation to host genome, environment and lifestyle. This project is a part of “Inflammatory Reprogramming by Ageing and Microbiome - Targets for Treatment of Cardiovascular Disease”, a large, national project funded by CVON (CardioVascular Onderzoek Nederland). This project involves multi-omics integration in multiple human cohorts and assesses the impact of the gut microbiota, immunological parameters related to ageing and risk to CVD. What do we need - M.Sc. (or PhD) degree in bioinformatics, computational biology, systems biology or a comparable discipline. The candidate with experiences in microbiome, metabolism and immunity is preferable. - Experience with advanced statistics, biology or biochemistry - Excellent oral and written communication skills - Fluency in English https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/…

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computational biologist position at NeuroDiderot
by Anne-Louise Leutenegger 14 Jun '19

14 Jun '19

Please spread the offer, Twitter <https://twitter.com/andree_delahaye/status/1133758315484372992> : https://twitter.com/andree_delahaye/status/1133758315484372992 LinkedIn <https://www.linkedin.com/feed/update/urn:li:activity:6539522340626157568> : https://www.linkedin.com/feed/update/urn:li:activity:6539522340626157568 https://itneuro.aviesan.fr/index.php?pagendx=751&p=1558 [image: image.png]

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