- BBClist - maillist.psb.ugent.be

EMBL-EBI Workshop - Finding Evidence in Research Publication
by Dayane Araujo 29 Jul '19

29 Jul '19

Dear all, Workshop: Finding Evidence in Research Publications Venue: EMBL-EBI, Hinxton, Cambridge, UK Dates: 10th - 11th September 2019 You will learn how to search and locate publicly-available open-access datasets from the scientific literature by using advanced search tools and programmatic access via APIs, which are freely available in Europe PMC <https://europepmc.org/>. Who is the workshop aimed at? The workshop is aimed at life science scientists interested to learn how to: I. Extract data and evidence from the research literature. II. Identify cited datasets for reuse, further analysis and background research. III. Apply literature analysis / text-mining in their own research. For more information and how to register: http://bit.ly/FindingEvidenceWorkshop <http://bit.ly/FindingEvidenceWorkshop> Application deadline: Friday 23 August 2019 We look forward to welcoming you! Best Regards, Dayane Araújo Dayane Araújo Technical Outreach Officer, Europe PMC email: dayane(a)ebi.ac.uk

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Upcoming BioSB courses, September-December 2019
by Femke Francissen 29 Jul '19

29 Jul '19

Dear researcher, BioSB <https://www.biosb.nl> is the Bioinformatics and Systems Biology community in the Netherlands. We are committed to train the next generation of computational life scientists. Our challenging and inspiring education programme covers essential topics in bioinformatics and systems biology, taught by teams of experts. *Upcoming BioSB courses* Registration is open for the following BioSB courses: - Machine Learning for bioinformatics and systems biology - 7-11 October 2019, Delft/Amsterdam, the Netherlands (fully booked) - 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 - Modelling and optimization for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/> - 9-13 December 2019, Wageningen, the Netherlands More information about the courses can be found below. A flyer with more information about the BioSB education programme can be found here <https://www.biosb.nl/wp-content/uploads/2019/07/BioSB-education-flyer-2019.…> . ________________________________ *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* The course is fully booked. If you want to be placed on a spare list, please send an email to education(a)biosb.nl. You can pre-register for next year's edition via the pre-registration form <https://www.biosb.nl/education/enrollment/pre-registration-courses/>. *Algorithms for Genomics <https://www.biosb.nl/archive-courses/course-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. *Constraint Based Modelling: Introduction & advanced topics <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…>25-29 November 2019, Leiden, the Netherlands* Constraint-based modelling 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 modelling 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. *Modelling and Optimization for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/>9-13 December 2019, Wageningen, the Netherlands* In this course the participants learn how to describe the dynamic behavior of biological systems, and how to use optimization techniques to solve a variety of problems in bioinformatics and systems biology. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. This course also provides you with the main ideas underlying optimization, and to get you acquainted with the optimization techniques that are nowadays available and widely used. Examples of optimization problems in life sciences will be presented and discussed. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The course is completed with assignments in the form of practical exercises as homework afterwards. *Courses planned for 2020 (preliminary)* - Algorithms for Biological Networks - Machine Learning - Managing and Integrating Information in the Life Sciences - Metagenomics - Modeling and Optimization - Statistics for Omics Data Analysis - Systems Medicine Find more information on our course portfolio page <https://www.biosb.nl/education/course-portfolio/>. If you want to stay up to date, please register for our newsletter <https://www.biosb.nl/newsletter/>! Best regards, Femke Francissen Community manager BioSB Research School

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PhD position in high-dimensional data analysis
by Brandt, B.W. 25 Jul '19

25 Jul '19

Dear all, We have a PhD position available. If you are interested, you can find more information via the link below. You can apply via the application button on that web page until 19 August 2019. PhD position in high-dimensional data analysis in relation to Oral Health https://workingat.vu.nl/ad/phd-position-in-high-dimensional-data-analysis-i… Kind regards, Bernd Brandt Academic Centre for Dentistry Amsterdam | Department of Preventive Dentistry | Gustav Mahlerlaan 3004 | 1081 LA Amsterdam | The Netherlands | www.acta.nl<http://www.acta.nl> ACTA is the collaborative Faculty of Dentistry of the University of Amsterdam and the VU Amsterdam

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Upcoming Training Sessions
by ELIXIR Belgium 25 Jul '19

25 Jul '19

ELIXIR Belgium's training calendar Fall 2019! No Images? Click here https://email.vibconferences.be/t/r-e-jiuludtd-uhtudkhjjk-n/ Training Events - Fall 2019 Train the Trainer This course aims to improve your teaching skills and is made up of four sessions: Learning principles and how they apply to trainingTraining techniques to enhance learner engagement and participationAssessment and feedback in trainingSession, course, and materials design Date: 29 & 30 August Location: Hogeschoollaan 1, Breda Trainers: Patricia Palagi (SIB Swiss Institute of Bioinformatics) & Mateusz Kuzak (Dutch Techcentre for Life Sciences) Info & registration [https://www.eventbrite.co.uk/e/elixir-excelerate-train-the-trainer-event-ti…] Protein Properties Prediction In this workshop, we address how to predict features of proteins from their sequence only, using Python scripts to access APIs of web services available online. We will introduce single-sequence based predictions of biophysical characteristics of proteins, methods that use multiple sequence alignments, and methods that determine the difference between a protein and its mutant form. Date: 10 September Location: U-Residence, Brussels Trainers: Wim Vranken & Niloofar Shirvanizadeh Info & registration [https://training.vib.be/bioinformatics-tools-predict-protein-properties-seq…] Galaxy Training: Using Galaxy for RNA-seq This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. You'll also learn how to perform filtering and quality control of reads, mapping to reference genomes and variant calling. Date: 8 October Location: Clemenspoort, Gent Trainers: Lieven Sterck & Tuur Muyldermans Info & registration [https://training.vib.be/galaxy-training-using-galaxy-rna-seq] Functional Plant Bioinformatics (PLAZA) This two-day workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. You will have a good understanding of the organization of plant genomes, the evolution of plant gene families, the different systems used to describe gene functions and extract relevant biological information from -omics gene sets. Date: 21 & 22 October Location: UGent-VIB Research Building FSVM, Gent Trainers: Klaas Vandepoele & Michiel Van Bel Info & registration [https://training.vib.be/functional-plant-bioinformatics-plaza] ELIXIR Belgium on behalf of VIB You receive this email because you work at VIB or you have expressed interest in our Bioinformatics training sessions. Feel free to forward this email to interested colleagues. If you do not want to receive this email anymore, you can unsubscribe here below. Preferences https://bits.updatemyprofile.com/r-jiuludtd-DCA2A3C5-uhtudkhjjk-p | Unsubscribe https://email.vibconferences.be/t/r-u-jiuludtd-uhtudkhjjk-x/

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COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

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Postdoctoral position in computational biology and bioinformatics
by Marianne Rooman 22 Jul '19

22 Jul '19

Postdoctoral position in computational biology and bioinformatics The Computational Biology and Bioinformatics group (3BIO-BioInfo) of the Brussels University (ULB) is seeking candidates for a postdoctoral position. Research context: Maintaining the stability and interactions of structured proteins is a necessary condition for them to function properly. Designing variants with optimized stability or affinity is a way to create new functional proteins that are stable in various conditions, even outside their physiological range. On the other hand, interpreting the molecular effect of genetic variants is a fundamental step in understanding the pathogenesis processes and a prerequisite to set up personalized drugs and therapies. Considering that experimental techniques are slow and costly, the challenging development of efficient bioinformatics tools, capable of predicting the change in protein stability and interactions upon mutations, could guide and limit the experiments that must be performed to identify relevant mutants. Such tools, usually based on combinations of physics-based and machine-learning approaches, possess a large series of applications in the biotechnological sectors from food to biofuel industry, as well as in the biomedical sector focused on genetic diseases. They also present a fundamental interest as they shed some light on the relationship between protein sequence, structure and function, a longstanding problem in protein science, as well as on the genotype-phenotype relationship. Furthermore, understanding how natural evolution guided protein mutations and led from ancient to current proteins, and what exactly drives this evolution, is another motivating issue. Although stability and natural evolution are obviously linked, their exact relation is complex and far from known. Objective: Design, develop and apply dedicated software for predicting and gaining understanding of protein stability and interactions, of disease-causing variants, and/or of evolutionary pressure. Offer: A full time postdoctoral position for 12 months starting between September and December 2019, financed by the FNRS Fund for Scientific Research, with the possibility of extension through an FNRS postdoctoral research grant or a Marie Curie EC grant. Required: - PhD degree in Sciences (Bioinformatics, Bioengineer, Physics, Chemistry, Informatics). - Excellent programming and computer science skills. - Excellent communication skills in English. - Excellent publication record. Desirable: - Experience in the area of protein structural bioinformatics, physics-based approaches and machine learning. Contact: Please submit to Marianne Rooman (mrooman(a)ulb.ac.be <mailto:mrooman@ulb.ac.be>): (1) a cover letter detailing your background and interest in the position, (2) a full CV and (3) two references (with name, email, address, phone number). Application deadline: Please submit your application by September 15, 2019.

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ELIXIR Train-the-Trainer event in Breda, the Netherlands, 29-30 August 2019, registration open.
by Celia van Gelder 21 Jul '19

21 Jul '19

Dear all, ELIXIR-NL and ELIXIR-CH are pleased to announce an ELIXIR Train the Trainer course. It will take place on 29-30 of August in Breda. The registration for the event is free of charge. Train-the-Trainer courses are for scientists: * with some to little or no teaching experience, * who want to become a teacher or a better one, and * who believe teaching is - or may become - a relevant aspect of their professional development. The course is made up of four sessions, covering * Learning principles and how they apply to training * Training techniques that can be used to enhance learner engagement and participation * Assessment and feedback in training * Session, course, and materials design The workshop format is very interactive and hands-on. The registration and agenda with more details available here <https://www.eventbrite.co.uk/e/elixir-excelerate-train-the-trainer-event-ti…> . For ELIXIR members there is a Travel Grant Schema in place. Please check here <https://elixir-europe.org/intranet/travel-grant-scheme> for more details (ELIXIR Intranet login needed). The deadline for the applications for the Travel Grant is 30 days before the start of the event. Please feel free to contact mateusz.kuzak(a)dtls.nl <mailto:mateusz.kuzak@dtls.nl> or celia.van.gelder(a)dtls.nl <mailto:celia.van.gelder@dtls.nl> with any questions. Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl <mailto:celia.van.gelder@dtls.nl> websites: https://www.dtls.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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BSC: Researcher in Artificial Intelligence applied to life sciences (RRE)
by BSC RRHH 19 Jul '19

19 Jul '19

Researcher in Artificial Intelligence applied to life sciences (RRE) *Reference:*173_LS_AI_RRE *Context And Mission* The Life Sciences Department at the BSC integrates the independent research of senior scientists that work on various aspects of computational biology, ranging from bioinformatics for genomics to computational biochemistry and text mining. The Computational Biology group is involved in multiple projects in collaboration with experimental groups generating state-of-the-art genomics and epigenomics datasets, actively participating in the International Human Epigenome Consortium and with the general aim of enabling new approaches in personalized medicine. Current efforts involve integration of different types of omics data, with a particular emphasis on epigenomics. We are establishing methods to study genome architecture exploiting interdisciplinary tools such as machine learning and network theory. The mission of the Computer Science Department at the BSC is to influence the way machines are built, programmed and used: computer and system architecture, programming models and performance tools, resource management, Big Data and artificial intelligence. The HPAI (High Performance Artificial Intelligence) research group is part of the Computer Science department, and it performs research in Artificial Intelligence, focused on the solutions, problems and infrastructure provided by High Performance Computing. The group actively collaborates with researchers from other fields, with the goal of applying machine learning to challenging problems in a wide variety of domains. HPAI has active collaborations with several large tech companies, pursuing lines of research of common interest. The group is also involved in multiple research projects, both European and national. Although the HPAI is open to all aspects of AI, currently its main lines of research are deep neural networks and graph analytics. The post holder will collaborate with the Life Sciences department and the HPAI research group in the Computer Science department, with the goal of finding AI solutions to life sciences challenges. This will include working closely with researchers from both areas, programming, testing and dissemination of the research. The candidate will be able to develop an independent research programme within the broad topics mentioned above. The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at the local and international levels. *Key Duties* * Development of AI solutions, with special emphasis on machine learning methods, for the analysis and interpretation of biological data * Use predictive computational methods based on statistical and inference approaches to model complex biological processes * Integration of heterogeneous data sources using advanced data mining techniques MORE INFO & APPLY HERE:https://www.bsc.es/join-us/job-opportunities/173lsairre <https://www.bsc.es/join-us/job-opportunities/173lsairre> http://bsc.es/disclaimer

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PhD student position in machine learning / cancer biology
by Patrick Deelen 17 Jul '19

17 Jul '19

https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/…

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The Swedish Elixir node is looking for a Data Steward
by Bengt Persson 15 Jul '19

15 Jul '19

Dear all, The Swedish Elixir node is looking for a Data Steward. Deadline is 10 September. More details are available at: https://www.uu.se/en/about-uu/join-us/details/?positionId=277048 All the best, Yours, Bengt Persson Head of Node Elixir-SE -- Bengt Persson, M.D., Ph.D. Professor of Bioinformatics Director of NBIS (National Bioinformatics Infrastructure Sweden) Science for Life Laboratory Uppsala University & Karolinska Institutet Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bpn(a)icm.uu.se, bpn(a)nbis.se, bengt.persson(a)ki.se Addresses: Uppsala University | Karolinska Institutet SciLifeLab | SciLifeLab ICM -- Department of | MBB -- Department of Medical Cell and Molecular Biology | Biochemistry and Biophysics BMC, room C10:308c | House Gamma, level 6, G6613 Box 596 | Box 1031 S-751 24 Uppsala, SWEDEN | S-171 21 Stockholm, SWEDEN När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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