- BBClist - maillist.psb.ugent.be

Barcelona Supercomputing Center: Post-doc Researchers in Computer Science and Bioinformatics (R2)
by BSC RRHH 28 Jun '19

28 Jun '19

Post-doc Researchers in Computer Science and Bioinformatics (R2) *Reference:*180_19_LS_ICB_R2 *Job title:*Post-doc Researchers in Computer Science and Bioinformatics (R2) *About BSC* The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, and is a hosting member of the PRACE European distributed supercomputing infrastructure. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 600 staff from 49 countries. Look at the BSC experience: BSC-CNS YouTube Channel <https://www.youtube.com/channel/UC-jQw5yIjnUTRAg4DwOY4aA> Let's stay connected with BSC Folks! <https://www.youtube.com/watch?v=VRkEii7OzRE> *Context And Mission* Professor Nataša Pržulj is looking for several post-docs to work in machine learning and network science. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj. The successful candidates will address developing and applying sophisticated machine learning and network science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining the data for new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitate rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The students will work in a highly sophisticated HPC environment, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas. *Key Duties* * Conduct high-quality research * Publish in high impact journals and conferences * Present research at national and international conferences and meetings * Collaborate with various research groups across Europe and elsewhere * Help supervise PhD and MSc students * Participate in grant writing and organizational activities * Participate in educational and outreach activities MORE INFO & APPLY HERE: https://www.bsc.es/join-us/job-opportunities/18019lsicbr2 http://bsc.es/disclaimer

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Assistant/associate professor position at Wageningen University
by Ridder, Dick de 28 Jun '19

28 Jun '19

Position: assistant/associate professor in bioinformatics or computational biology The Wageningen Bioinformatics Group has a vacancy for an assistant / associate professor in bioinformatics or computational biology. As a candidate, you have a good scientific track record and a drive to develop your own research line. You can attract funding to build and support a group and you are able to set up a strong academic and industrial network. Your research should connect method development to application, be relevant for plant, animal or microbial biotechnology, and complement the current expertise in the group. Relevant areas include (but are not limited to) metagenomics, metabolomics, proteomics and phenomics. You strive to become an enthusiastic and knowledgeable teacher and supervisor in bioinformatics. Finally, you are a collaborative team member, contributing to the organization of the group, the university and the scientific community at large. Wageningen University & Research focuses on food, health and the living environment and is one of the leading organisations in this domain worldwide. The Bioinformatics Group provides a collaborative working environment with young, dedicated staff with expertise in a number of areas, particularly in genomics. Our group is strongly embedded in the Plant Sciences Group and collaborates intensively with Wageningen Research. We maintain extensive computational resources and have the opportunity to teach (advanced) MSc courses and supervise thesis projects in the Master’s Programme in Bioinformatics. We offer a meaningful job with a competitive salary (depending on your experience) and good benefits. The Wageningen tenure-track system provides an excellent opportunity and support for academic development. For more information and an online application form (deadline September 8, 2019), please see https://tinyurl.com/y3ucfwys or contact Dick de Ridder (dick.deridder(a)wur.nl)

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Barcelona Supercomputing Center: Technician at Text Mining Unit (RE2)
by BSC RRHH 28 Jun '19

28 Jun '19

Technician at Text Mining Unit (RE2) Reference: 179_19_LS_TM_RE2 *Context And Mission* The Text Mining Unit of the BSC-CNS (TeMU-BSC) is funded through the Plan de Impulso de las Tecnologías del Lenguaje de la Agenda Digital, by the Secretary of State of Telecommunications and the Information. It is the first publicly funded text mining unit in Spain and has the aim to promote the development of natural language processing and machine translation resources for Spanish and other co-official languages in the area of biomedicine. We search for a technician who will be responsible of the integration of data, applications and search tools, and the maintenance of the servers and other infrastructure of the unit. *Key Duties* * Administration task on servers, operating systems and applications. * Installation of new releases of software/server patches. * Integration of NLP components using IUMA, GATE, OpenNLP, etc. * Development of mechanisms for the integration of resources and a data warehouse. MORE INFO & APPLY VIA: https://www.bsc.es/join-us/job-opportunities/17919lstmre2 http://bsc.es/disclaimer

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Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven
by Riel, N.A.W. van 27 Jun '19

27 Jun '19

We are hiring: Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven: https://jobs.tue.nl/en/vacancy/assistant-professor-artificial-intelligence-… . We seek to appoint a scientist/engineer who is passionate about research as well as teaching. We are looking for a creative and pro-active team player to establish a complementary research line. We work on biomedical systems biology, which ranges from fundamental science to clinical applications. Existing research lines focus on oncology and metabolic disease. We search for candidates with a PhD degree in computational biology, biomedical signal processing, or other relevant discipline to develop a research line on 'Artificial Intelligence for Systems Medicine'. In this Tenure Track position model-based data analysis and signal processing will be developed, combining computer simulation models of the human physiological system, stochastic models of uncertainties and variation in the process, and (biosensor) data, for application in systems medicine. Artificial Intelligence (AI) technology is applied for real-time learning and adaptation of the models, to accurately estimate the current state of the system and to predict its future trajectory. In addition to execution of research and education the candidate is expected to actively setup collaborations and secure research funding. The candidate will play an active role in the new TU/e Artificial Intelligence institute. Kind regards, Prof. dr. ir. Natal van Riel

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job opening Genomics Bioinformatician at BRIGHTcore (the VUB-ULB genomics platform) in Brussels
by Catharina Olsen 27 Jun '19

27 Jun '19

Dear all, We are looking for a Genomics Bioinformatician at BRIGHTcore. Details about the position: https://www.uzbrusselwerkt.be/en/vacatures/viewjob/174860 Best regards, Catharina

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JOB: PhD position in the Thomas More University of Applied Sciences and Hasselt University
by Ziv SHKEDY 27 Jun '19

27 Jun '19

Dear All, As a part of a H2020 European project “NanoInformaTIX” ( http://www.nanoinformatix.eu/) we open a PhD position in Biostatistics/Data science in the Thomas More University of Applied Sciences - Radius group (http://radius.thomasmore.be) and the center of statistics (CenStat), Hasselt University (https://www.uhasselt.be/censtat) The 4 years research project will be focused on nanoparticle toxicity modelling. The PhD candidate will be located in the Thomas More Radius group (3-4 days per week) and UHasselt (1-2 days per week). Strating date of the PhD project: *01/10/2019*. Specific research lines of the PhD project include: · Dose-response modelling of nanoparticle toxicity. · Extrapolation of the (in vitro based) dose-response models to an in vivo setting. · Integrated data analysis of several nanoparticle toxicity databases. Your Profile: · Master in biostatistics/statistics/bioinformatics. · Knowledge of R and SAS (knowledge of Winbugs/JAGS would be an asset). · Good written and excellent communication skills. · Ability to work independently and as a part of multidisciplinary team. · Problem solving skills and team player This PhD position offers a unique opportunity to conduct research as a part of multidisciplinary team in collaboration with several European institutes. If you are interested in the position, please contact by email Geert Verheyen (geert.verheyen(a)thomasmore.be) or Ziv Shkedy ( ziv.shkedy(a)uhasselt.be) Closing date to send an email is 07*/07/2019*

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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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