- BBClist - maillist.psb.ugent.be

ELIXIR Innovation and SME Forum "Data-Driven Innovation in Food, Nutrition and Microbiome"
by Kim De Ruyck 19 Jul '17

19 Jul '17

Dear, I would like to inform you on a meeting that is being organized by ELIXIR. Please find information below. You are welcome to spread information to interested parties. [ https://www.elixir-europe.org/events/elixir-innovation-and-sme-forum-data-d… | ELIXIR Innovation and SME Forum ] on " Data-Driven Innovation in Food, Nutrition and Microbiome”, Brussels, 9-10 October 2017 . This Innovation and SME Forum brings together companies active in the probiotics, food and health sectors to stimulate interaction between companies and academic partners. The event is organized as a series of interactive sessions on "Data Sources", "Tools and Analysis" and "Integration Challenges" enabling microbiome research and innovation. It will showcase a selection of free data resources and services available through ELIXIR as well as examples of innovative companies already using public data in their business. Participants will also learn about the training opportunities on food, nutrition and microbiome resources available through ELIXIR. Companies and SMEs will have the opportunity to present their activities and explore possible collaborations through a dedicated flash-talk session. Confirmed speakers include Wim Haentjens (European Commission, DG Research & Innovation – Agri-food unit), Peer Bork (Group Leader, European Molecular Biology Laboratory) and Silvia Miret Catalan (Director Nutrition & Health Discover at Unilever). More information on the event can be found here: [ https://www.elixir-belgium.org/events/SMEforum_91017 | events page ] – [ https://drive.google.com/file/d/0B8in1NtGRloYTi1VVGgxWF92NFk/view | program ] - [ https://www.eventbrite.co.uk/e/data-driven-innovation-in-food-nutrition-and… | registration ] . Contacts: Kim De Ruyck (ELIXIR Belgium Coordinator, kim.deruyck(a)elixir-belgium.org) and Pablo-Roman Garcia (ELIXIR Industry Officer, pablo.roman(a)elixir-europe.org) This ELIXIR event runs back-to-back with the international workshop on " [ http://www.ewi-vlaanderen.be/evenementen/personalised-nutrition-better-heal… | Personalised nutrition for better health - targeting the microbiome ] " which is organized by OECD and the Department of Economy, Science and Innovation (EWI) of the Flemish government and takes place on 10-11 October 2017 . This workshop will address policy needs to develop this area. Contact: Kathleen D'Hondt (Policy Analyst, kathleen.dhondt(a)ewi.vlaanderen.be) Kind regards, Kim De Ruyck -- Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 Gent | +32 (0)9 33 13 694 [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ] [ https://www.elixir-belgium.org/events/SMEforum_91017 ]

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Training Course on Best practices for RNA-Seq data analysis Salerno Italy
by Celia van Gelder 19 Jul '17

19 Jul '17

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested (apologies if you have already received this announcement) ELIXIR-IIB, in collaboration with University of Salerno, Italy, is pleased to announce the upcoming training course on "Best practices for RNA-Seq data analysis". IMPORTANT DATES: Course date: 27-29 September 2017 Deadline for applications: 11 September 2017 Selection will start on July 20th and those with an adequate profile will be accepted immediately, until we reach 25 participants. VENUE: Campus di Fisciano, University of Salerno, Via Giovanni Paolo II n. 132, 84084 Fisciano (SA), Italy. Full details at: https://elixir-iib-training.github.io/website/2017/09/27/RNA-seq-Salerno.ht… COURSE DESCRIPTION: The aim of this course is to get a deeper understanding of RNA-Seq experiments, providing a theoretical introduction to the data processing steps, together with practical sessions illustrating the use of the most popular data analysis tools. Starting from the raw sequenced data coming from different phenotypical samples (e.g disease vs healthy control samples), genes which are differentially expressed between the two conditions are determine. COURSE OBJECTIVES Students will gain an understanding of: - experimental design - quality control - theoretical principles of RNA-Seq data analysis process - how to identify differentially regulated genes - how to identify alternative splicing events - how to identify gene fusion events - multiple testing correction - biological interpretation of RNA-seq data Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training(a)gmail.com <mailto:elixir.ita.training@gmail.com> ) and/or the local organiser Dr. Anna Marabotti (amarabotti(a)unisa.it <mailto:amarabotti@unisa.it> ). Thank you for your interest, the Organisers and the ELIXIR Training Team Anna Marabotti (ELIXIR Training Team and University of Salerno, Italy) Loredana Le Pera (ELIXIR Training Team and IIT, Italy) Allegra Via (ELIXIR Training Coordinator, CNR-IBPM, Italy)

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Vacancy post-doc bioinformatics
by Christian.Gilissen＠radboudumc.nl 17 Jul '17

17 Jul '17

Dear all, We are looking for a post-doc in bioinformatics/genomics: The genome bioinformatics research group at the department of Human Genetics is looking for an experienced bioinformatics postdoc for the Vidi project entitled "Integrating Metabolomics and Genomics for understanding human Disease". The identification of disease-causing errors in the DNA is difficult and provides us with limited insights into the workings of the disease. Through bioinformatics methods and data integration of metabolite and DNA data we will improve the identification of genetic causes of disease and find novel leads for therapies. Your tasks will be to (1) develop and implement methods for the combined analysis of metabolomics and genetics data to improve patient diagnostics, (2) co-supervise existing PhD students and (3) develop your own research topic within the genome bioinformatics group. Profile You have a PhD in bioinformatics/genomics or related subject and have experience in performing bioinformatics research. You are practical, goal-oriented and a team-player with experience in programming (java/python), linux and statistical methods (R). You are interested in genetics and genomics, have experience in writing scientific publications and are motivated to develop your own research topics. Organization The genome bioinformatics group develops novel bioinformatics methods to improve the interpretation of genome variation, and implements and applies bioinformatics methods for large-scale genomics data to identify novel genetic causes of disease and the mechanisms behind them. The genome bioinformatics group is part of the Department of Human Genetics, which is one of the largest genetics departments in the Europe with more than 300 employees. The Genome Research division has >100 employees, who work under the umbrella of 20 individual research groups. Our research, which is strong in the areas of genomics, methods development, cell and animal models, as well as the investigation of mechanisms leading to monogenic and multifactorial diseases, is regularly published in high-ranking journals. See https://www.radboudumc.nl/en/vacancies/postdoc-bioinformatics Or contact Christian Gilissen (Christian.gilissen(a)radboudumc.nl<mailto:Christian.gilissen@radboudumc.nl>) for more information. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Summerschool: R2 - Genomics analysis and visualization platform
by r2-support 13 Jul '17

13 Jul '17

Dear Researcher, This summer we are organizing a summerschool covering the essentials of working with genomics data in R2. This will be an excellent opportunity to learn how to use this versatile tool. Save the date: Monday the 14th of August 2017 (09:30-17:00). R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. Every participant will receive a printed tutorial book. Coffee / tea and a simple lunch will be provided during the workshop. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). The workshop is provided free of charge, however, we will have to charge 25 euro (for administration, lunch, printing costs) in case of a no show on the workshop. Best regards, ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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BioInformatician vacancy VUmc Amsterdam
by Bessem, Mark 13 Jul '17

13 Jul '17

Dear all, We're looking for a new Bio-informatician at the Clinical Genetics department of the Vrije Universiteit Medical Centre (VUmc) in Amsterdam. As a Bioinformatician in the Laboratory for Genome Diagnostics your primary tasks will entail the smooth operation of Next-Generation Sequencing data analyses (i.e. validating and running pipelines, troubleshooting, database management, etc…) and transfer of results to research analysts and laboratory specialists. Secondary tasks include optimizing databases/workflows and developing new software and pipelines. For more details, check out https://www.werkenbijvumc.nl/vacatures/bioinformatician/. Kind regards, Mark Bessem

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Workshop: Functional Plant Bioinformatics, 14-15 Sept, Ghent BE
by Klaas Vandepoele 13 Jul '17

13 Jul '17

*Workshop FUNCTIONAL PLANT BIOINFORMATICS* Organised by ELIXIR Belgium and the VIB Bioinformatics Core Date: 14-15 September 2017 Location: Ghent, Belgium *Goals* This workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Both plant biologists and geneticists with an interest in bioinformatics, data analysis, and comparative & regulatory genomics should attend this training. After this workshop, you will have a good understanding of the organization and evolution of plant gene families and know how to extract relevant biological information from -omics gene sets. *Summary* DAY 1 Introduction plant comparative genomics (genes, gene families, synteny analysis) + introduction PLAZA platform Functional characterization of plant genes (Families, GO, InterPro) DAY 2 Gene set analysis for different plant -omics data sets: - functional interpretation of RNA-Seq and ChIP-Seq genes using the PLAZA Workbench - co-expression and Transcription Factor analysis *Prerequisites* basic knowledge of genes, genomes, transcript profiling, BLAST, homology, Gene Ontology (no programming skills are required). More info and registration: click here <http://www.vib.be/en/training/research-training/courses/Pages/Functional-Pl…> -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium --------------------------------------------------------- Lab website: http://bioinformatics.psb.ugent.be/cig/ BIG N2N: http://www.bign2n.ugent.be/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Gtpb] Large-scale bioinformatics for Immuno-Oncology - Course announcement for Sept 2018
by Pedro L. Fernandes 10 Jul '17

10 Jul '17

IO17 Large-scale bioinformatics for Immuno-Oncology with Francesca Finotello and Federica Eduati IMPORTANT DATES for this Course Deadline for applications: Aug 30th 2017 Course dates: Sept 20th - Sept 22nd 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description: The immuno-oncology approach leverages on the unique capability of the immune system to recognize and kill tumour cells. This action is hampered by escape mechanisms put in place by tumour cells like, for instance, the engagement immune checkpoints, i.e. inhibitory molecules that modulate the amplitude and duration of immune responses. Immunotherapies that block checkpoint molecules are amongst the most promising approaches in immuno-oncology for the enhancement of antitumour immunity. Thanks to high-throughput technologies, such as next-generation sequencing (NGS) and proteomics, we have now access to large-scale tumour data that can be used to investigate the interplay between tumour and immune cells and the role of the immune system in tumour progression and response to therapy. In this course, you will learn to use bioinformatics tools and mathematical modelling techniques operating on high-throughput tumour data, in order to extract features that can be used to characterise this complex tumour-immune cell interface, such as: - tumour antigens recognized by T cells - tumour-infiltrating immune cells - deregulated signalling pathways in cancer and immune cells A fully practical, hands-on approach will ensure that the newly acquire skills can be used with a great deal of autonomy. Additional details here: http://gtpb.igc.gulbenkian.pt/bicourses/IO17/ We hope that this training course will meet your interests, Pedro Fernandes -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] Introductory BIOSTSTISTICS for Biologists - course announcement for Sept 2018
by Pedro L. Fernandes 10 Jul '17

10 Jul '17

ANNOUNCEMENT IBSTATB17 Introductory Biostatistics for Biologists with Ana Luisa Papoila and Fernanda Diamantino. The GTPB is proud to announce that the above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: Aug 30th 2017 Course dates: Sept 11th - Sept 15th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course Description: This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. Detailed description here: http://gtpb.igc.gulbenkian.pt/bicourses/IBSTATB17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Registration open: BioSB Course Pattern Recognition (5th edition) - 25-29 September 2017
by Femke Francissen 06 Jul '17

06 Jul '17

*BioSB Course Pattern Recognition (5th edition)* *Date: 25-29 September 2017* *Location: AMC, Amsterdam* *Course Coordinator: Perry Moerland (AMC)* Website: http://biosb.nl/education/course-portfolio/pattern-recognition/ Registration: http://biosb.nl/education/course-portfolio/pattern-recognition/enrollment/ Please note that this course is free of charge for PhDs who are or become a member of the BioSB research school <http://biosb.nl/about/members/biosb-membership-information/>. *Description* Many problems in bioinformatics require classification: prediction of the class to which a certain object (i.e. a gene, protein, cell, patient, …) belongs. This calls for algorithms that can assign the most likely label (discrete output) to an object, given one or more measurements on that object. For most interesting problems, the underlying physics are too complex to explicitly design such an algorithm. In such cases, often a machine learning approach is taken: an algorithm is constructed, with parameters that are tuned based on an available dataset of training examples. The algorithm should predict the labels for these examples as well as possible, yet still generalize, i.e. perform well on objects not seen before. Some examples of classification problems in bioinformatics are gene finding (sequence in, gene presence out), diagnostics (gene expression data in, diagnosis out), data integration (measurements in, probability of interaction out), etc. In this course, we will introduce basic techniques from the fields of pattern recognition and machine learning to solve such problems. We will introduce the pattern recognition pipeline: measuring, feature extraction and selection, classification and evaluation. The course is a mixture of theory sessions and lab courses. During the lab courses Matlab will be used and a brief introduction to Matlab will be provided. The course has to be completed afterwards with a 5-10 page report describing the analysis of a biological dataset using some of the methods taught in the course. The structure of the course is as follows: - *Monday *(Introduction; Marcel Reinders): Introduction to pattern recognition: measurements, features, classification. Supervised vs. unsupervised learning, relation to regression. Bayesian framework: risk, cost; evaluation: ROCs, cross-validation. Density estimation: histograms, nearest neighbour, Parzen, Gaussian Bayesian classification. - *Tuesday* (Classification; Perry Moerland): Parametric classifiers: (D)LDA, (D)QDA. Nonparametric classifiers: k-NN, Parzen. Discriminant analysis: LDA, logistic regression. Decision trees and random forests. - *Wednesday* (Feature selection and extraction; Lodewyk Wessels): Feature selection: criteria, search algorithms (forward, backward, branch & bound). Sparse classifiers: Ridge, LASSO. Feature extraction: PCA, Fisher. Embeddings: MDS. - *Thursday* (Clustering and HMMs; Perry Moerland): Hierarchical clustering. Agglomerative clustering. Model-based clustering: mixtures-of-Gaussians, Expectation-Maximization. Hidden Markov models. - *Friday* (Selected advanced topics; Marcel Reinders): Artificial neural networks. Support vector machines. Classifier ensembles. Complexity and regularisation. Deep learning. *Target audience * The course is aimed at PhD students with a background in bioinformatics, computer science or a related field, life sciences. Participants from the private sector are also welcome. A working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. *Learning objectives* After having followed this course, the student has a good understanding of basic pattern recognition and machine learning techniques and is able to recognize what method is most applicable to data analysis problems (s)he encounters in bioinformatics applications. This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl. ** ** *Femke Francissen* Community manager BioSB Research School *NEW V*isiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht *NEW **Postal address *(as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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looking for Phd student for computational design of a receptor protein.
by Arnout Voet 05 Jul '17

05 Jul '17

Dear All, At the laboratory for biomolecular modelling and design we are currently looking for a PhD student (or non-eu postdoc) for a project dealing with the computational design of a novel protein receptor as a building block for synthetic biology. This projects deals with the biomolecular modelling methods, structural bioinformatics, and combines both computer aided drug design methods with computer aided protein design methods. For more information please consult the job offer at : https://icts.kuleuven.be/apps/jobsite/vacatures/54249555?lang=en or contact me Kindest Regards, Arnout Voet Assistant-Professor Laboratory of biomolecular modelling and design Celestijnenlaan 200G 3001 Heverlee Belgium Tel: +3216324496 https://www.chem.kuleuven.be/lbmd/index.html

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