July 2017 - BBClist - maillist.psb.ugent.be

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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vacancy bioinformatician
by Demeyere Mieke 04 Jul '17

04 Jul '17

Dear all Here<https://www.howest.be/documenten/vacatures/2017093%20Praktijk%20Lector%20on…> you can find a vacancy for a bioinformatician. Thank you for sending to who's interested! Enjoy the holidays! With kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie [http://innovatiebeurs.be/assets/files/made/assets/files/partners/howest.be_…] Howest University of Applied Sciences Campus Rijselstraat Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

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PhD opportunity in Bioinformatics or Computational Biology
by Francisco Azuaje 04 Jul '17

04 Jul '17

Dear colleagues, We are seeking candidates for a PhD research position at LIH: https://www.lih.lu/jobs/detail/phd-student-in-the-area-of-bioinformatics-or…. Please share this information with potential candidates. Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator Proteome and Genome Research Unit Department of Oncology Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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