May 2016 - BBClist - maillist.psb.ugent.be

REMINDER: BeMGI 2016-Brussels Meeting, Wednesday-13 April
by Marilou Ramos Pamplona 23 Sep '16

23 Sep '16

Dear BBC colleagues, We would like to remind you of the 2016 Annual Meeting of the Belgian Medical Genomics Initiative (BeMGI) entitled "From predisposing germline and somatic variants to disease-driving mechanisms.," which will feature the two keynote lectures: Genetic basis and mechanisms of Parkinson’s disease. Alexis Brice, MD Brain and Spine Institute Hôpital Pitié Salpêtrière Paris, France Search for predisposing factors in myeloid malignancies. Christine Bellanné-Chantelot, PhD Centre de Génétique Moléculaire et Chromosomique Groupe Hospitalier Pitié-Salpétrière Paris, France This meeting will take place on Wednesday (13 April 2016) from 12h00-17h30 at the Auditoire central 51E of UCLouvain Brussels campus (Avenue Mounier 51, 1200 Bruxelles, www.uclouvain.be/286287.html) The complete meeting info document with directions to the meeting venue, is available via: https://edc.ulg.ac.be/merci/BeMGI2016-Brussels_Meetin_d1f1ea81615957fe5c13_… The online meeting registration (http://bit.do/BeMGI2016register) is available until tomorrow noon (Tuesday, 12-Apr, 12h00). We kindly request all interested meeting participants to either register online by tomorrow noon or to register on site upon arrival at the meeting venue. See you soon in Brussels! Regards, The BeMGI network

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Bioinformatics Post-doctoral position @ INRA, France
by emmanuelle morin 31 May '16

31 May '16

*Postdoctoral Position in Comparative Genomics and Symbiosis Evolution * *Institution*: INRA, Lab of Excellence ARBRE *Location*: Nancy, France *Job Description: * A postdoctoral researcher position is available immediately in the lab of Francis Martin at the Tree-Microbe Interactions Department at INRA in Nancy, France. Martin’s lab uses computational approaches to study how saprotrophic and symbiotic (mycorrhizal) fungi evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying the emergence of the symbiotic mutualism in fungal and tree species by phylogenomics; 2) Characterization of symbiosis-related genes by using comparative transcriptomics; and 3) Deciphering genomic signatures of fungal adaptations to carbon decay and sequestration in forest habitats by metatranscriptomics. More information about Martin’s lab is available at http://mycor.nancy.inra.fr/blogGenomes/?page_id=149. Qualified applicant must have a Ph.D. in bioinformatics, computational biology, computer science, evolutionary biology or a related field with background and strong interest in molecular evolution of Fungi. The ideal candidate will already have some experience working with large genomic data sets from sequenced fungi or plants. This position requires a high level of proficiency in programming skills, and experience applying computational methods to genomic data is highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English (or French). Strong skills in the use of unix-based computer software, critical thinking, problem-solving abilities, and the ability to work semi-independently are also required. The responsibilities will include pipeline development for analyses of next-generation data sets and utilization of high-performance computing facilities. The successful candidate should anticipate contributing to a variety of ongoing collaborative research projects with the Joint Genome Institute, including the 1000 Fungal Genomes project and the Mycorrhizal Genomics Initiative, with teams across France, Europe and the United States. In addition to becoming a part of a vibrant research and educational environment, the incumbent can take advantage of professional development programs offered by Laboratory of Excellence ARBRE (http://mycor.nancy.inra.fr/ARBRE/?page_id=2&lang=en) The initial appointment is for one year with the possibility of renewal for up to two additional years contingent upon performance and funding. Review of applications will begin immediately and continue until the position is filled. Start date is July 1st, 2016 at the latest. *Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Francis Martin at fmartin[at]nancy.inra.fr.* -- Emmanuelle MORIN UMR 1136 INRA/Université de Lorraine F-54280 Champenoux Tel : + 33 3 83 39 41 33 http://mycor.nancy.inra.fr

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Benelearn 2016: last call for abstracts (with deadline extension)
by Yvan Saeys 31 May '16

31 May '16

LAST CALL FOR ABSTRACTS: BENELEARN 2016 September 12-13, 2016. Kortrijk, Belgium http://www.kuleuven-kulak.be/benelearn/ Benelearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. The 25th edition will be co-organised by KU Leuven, UGent and the Flemish Supercomputer Centre, in cooperation with the Dutch Research School for Information and Knowledge Systems (SIKS), at the Katholieke Universiteit Leuven, Campus Kortrijk (KULAK). In contrast to previous editions, the anniversary edition of Benelearn will be organised on two days, where the first day will feature a workshop on Big Data, including keynote speakers, a tutorial session, corporate presentations, and ample opportunity for networking. KEYNOTE SPEAKERS: The following keynote speakers have agreed to speak at the conference: Jeff Ullman (Stanford University) Christian Blum (University of the Basque Country) Greg Tsoumakas (Aristotle University of Thessaloniki) Kristian Kersting (TU Dortmund) Emilia Barakova (Technische Universiteit Eindhoven) Hugo Ceulemans (Janssen R&D) Luc De Raedt (KU Leuven) Isaac Triguero (UGent / University of Nottingham) SUBMISSIONS: The conference solicits abstract contributions (2 pages max.) of original work or work that was recently accepted or published in a peer-reviewed machine-learning journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts will be checked mainly for relevance, rather than receive a full review. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session (with spotlight presentations). Submissions related to Big Data analysis will preferably be presented on the thematic day. All accepted contributions will be published on the Benelearn website, but no copyright will be claimed. For submission instructions, please refer to http://www.kuleuven-kulak.be/benelearn/. SCOPE: Although we particularly encourage submissions related to learning from Big Data, submissions from all topics of interest within machine learning are welcome (non-exhaustive list): Kernel Methods Bayesian Learning Case-based Learning Causal Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Inductive Logic Programming Knowledge Discovery in Databases Online Learning Learning in Multi-Agent Systems Neural Networks Deep Learning Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Learning Learning for Language and Speech Media Mining and Text Analytics Learning and Ubiquitous Computing Applications of Machine Learning Learning from Big Data KEY DATES: Submission deadline (extended): June 7, 2016. Notification of acceptance: July 1, 2016. Conference: September 12-13, 2016. Organizing committee: Celine Vens (KU Leuven) Patrick De Causmaecker (KU Leuven) Yvan Saeys (UGent) Ewald Pauwels (VSC)

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Bioinformatics Internship at Schneider Lab, University of Luxembourg
by ISCBSC announcement 31 May '16

31 May '16

*Bioinformatics Internship at Schneider Lab, University of Luxembourg* *Title:* Developing web resource for enzymes of unknown function *Deadline:* June 18, 2016 The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider Lab at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in August 2016, and it is available to Undergraduate and Masters students in computational biology or related areas from developing nations. To know more about the position, please click on the link below. We strongly encourage all interested applicants to read the entire description as well as the requirements laid out on the page below before attempting to apply. Incomplete applications will not be processed by our submission system. http://career.iscbsc.org For further questions, contact us at internships(a)iscbsc.org. We wish you all the best with your application and we look forward to receiving it. Please forward this message to all who might be interested! Education and Internships Committee ISCB Student Council <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MLSB2016 submission deadline extended to June 10, 2016
by Dijk, Aalt-Jan van 30 May '16

30 May '16

Due to several requests we have decided to extend the MLSB 2016 submission deadline until June 10, 2016, and the notification deadline until July 8, 2016. The workshop webpage (http://www.eccb2016.org/programme/workshops/w1/) has been updated to reflect the changes. As a reminder we have two tracks: Manuscript track with papers published in BMC Bioinformatics and Highlights tracks for abstracts describing computational aspects of work that has been recently published in a journal (or is “in press”) as well as unpublished/on-going work. Best regards, MLSB 2016 organizers Juho Rousu Dick de Ridder Harri Lähdesmäki Aalt-Jan van Dijk

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Computational Cancer Biology Position in Amsterdam
by m.michaut＠nki.nl 24 May '16

24 May '16

Hi all, Still 1 week to apply for the positon in the Computational Cancer Biology group at NKI in Amsterdam. Have a nice day, Magali Integrative modelling to identify therapy resistance mechanisms Project description The purpose of this project is to identify the underlying resistance mechanisms in invasive lobular carcinoma (ILC). ILCs are known as ‘slow killers’ as they grow relatively slowly, but respond poorly to therapy, eventually killing the patient. To unravel the resistance mechanisms, we have generated comprehensive molecular profiles (gene expression, mutational, copy number and (phospho-)proteomics profiles) from matched pairs of sensitive and resistant mouse models of ILCs. We will employ integrative computational (Bayesian) modeling to integrate prior knowledge and the molecular datasets to identify candidate resistance factors. These will be validated in genetic and pharmacological perturbation studies in cultured ILC cell lines and mouse models. Knowledge of these mechanisms will enable us to design combination therapies able to block the development of resistance, leading to improved therapy response. The successful candidate will be responsible for carrying out all the computational analyses, including the complete analysis workflow starting at the basic analyses of the DNA and RNA sequencing and mass spectrometry data up to the more complicated integrative analyses and the Bayesian pathway modelling. He/She will also be expected to coordinate the project and to liaise with the molecular biologists, the animal facility, the genomics core facility and the proteomics facility. The project will be carries out in close collaboration with the groups of Jos Jonkers (mouse models of breast cancer) and Maarten Altelaar (proteomics). Candidate profile We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science or a related discipline. Applicants should be experienced in cancer biology and clinical applications and should be skilled in analysing high-throughput molecular data. Experience in analyses of (phospho)-proteomics data is a plus. The candidate needs to be proficient in common bioinformatics scripting and programming languages (e.g. R, Python). Interested? Please send CV and motivation letter to Magali Michaut (m.michaut(a)nki.nl<mailto:m.michaut@nki.nl>) & Lodewyk Wessels (l.wessels(a)nki.nl<mailto:l.wessels@nki.nl>). Please include a list of publications and the names and contact information of at least two references. See ccb.nki.nl<http://ccb.nki.nl> for further information. Deadline 1 June 2016

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[Gtpb] Course announcement BPBR16 Bioinformatics using Python for Biomedical Researchers
by Pedro Fernandes 23 May '16

23 May '16

ANNOUNCEMENT Applications for BPBR16 - Bioinformatics using Python for Biomedical Researchers with Allegra Via and Vincenza Colonna are open IMPORTANT DATES for this Course Deadline for applications: July 4th 2016 Latest notification of acceptance: July 6th 2016 Course date: July 11th - July 15th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course Description Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: working with DNA and protein sequences data retrieval from files and their manipulation running applications, such as BLAST, locally and from a script finding motifs in sequence parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython ways to find and correct program errors The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course. Target Audience End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way. Course Pre-requisites Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. More details at the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/BPBR16/ Best wishes Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 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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Edinburgh Genomics bioinformatics workshops - Register interest for workshops
by Bert Overduin 20 May '16

20 May '16

Hi all, It is now possible to register your interest for workshops that we are planning to offer in the future, but for which we haven't set a date yet. This helps us to determine whether there is enough interest for a workshop to start organising it. We also will use this information to mail you as soon as registration opens for a workshop you have expressed interest in. At the moment you can register your interest for 5 workshops: Introduction to ChIP-Seq Data Analysis (2 days) Introduction to RAD-Seq Data Analysis (2 days) Introduction to RNA-Seq Data Analysis (2 days) Introduction to Variant Analysis of NGS Data (2 days) Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications (1 day) To register your interest for one or more of these workshops, please go to: https://www.surveymonkey.co.uk/r/3LRCW7D With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Call for abstracts for ESCS 2016
by ISCBSC announcement 20 May '16

20 May '16

Dear colleague, Abstract submission for oral and poster presentations is open for the 4th European Student Council Symposium (ESCS) 2016. ESCS will take place on Saturday 3rd September during ECCB 2016 in The Hague, Netherlands. Please visit http://submit.iscbsc.org/escs to submit your abstract. The ESCS is a biennial interdisciplinary symposium that brings together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium offers you a great opportunity to present your research to an international audience, get insights into hot topics and newly developed methods and build a network within the computational biology community of Europe. We are pleased to announce our three confirmed keynote speakers Kris Laukens (University of Antwerp, Belgium), Yves Van de Peer (Ghent University, Belgium), and Nuria Lopez-Bigas (Universitat Pompeu Fabra, Spain). The symposium includes ice-breaking, oral presentations, keynote talks, poster presentations and an evening social event that offer you the opportunity to get to know fellow young scientists from all over Europe in a casual setting. Please visit our website http://escs2016.iscbsc.org/ regularily as more information will be announced soon. For registration details, please visit http://www.eccb2016.org/registration/. We welcome students and young researchers from all areas of computational biology to join our community. Please help us spread the word by sharing the event flyer (please find it attached), and using the hashtag #ESCS16 on social media. We look forward to welcome you in The Hague! Annika Jacobsen and Kevin Schwahn, chair and co-chair, ESCS 2016 [image: Inline images 1] <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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PhD vacancy at the Center for Medical Genetics of Ghent University
by Katrijn Vannerum 20 May '16

20 May '16

Dear colleagues, We have an exciting opportunity for an enthusiastic PhD candidate in a joint project entitled “Analysis of circulating tumor DNA from patients with cancer for early detection and selection of patients for precision medicine” at the Center for Medical Genetics of Ghent University in collaboration with the Department of Pathology and the Department of Radiology at Ghent University Hospital. The project aims to develop and experimentally validate novel computational methods to identify copy number variants and rare mutations in liquid biopsy samples from patients with cancer. Such methods will not only provide novel insights into the genetic makeup of several cancers, but will also provide new genomic tools for early detection of cancer, prediction of relapse and will enable the selection of patients for precision medicine. We are looking for an ambitious PhD candidate with an MSc degree in bio-engineering, biotechnology or biochemistry. The candidate should have a particular interest in genomics and bioinformatics research. More information about the position and the application procedure can be found in attachment. With kind regards, Björn Menten — Björn Menten, PhD Center for Medical Genetics Ghent University De Pintelaan 185 9000 Gent Belgium +32 9 332 5284 bjorn.menten(a)ugent.be<mailto:bjorn.menten@ugent.be>

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