- BBClist - maillist.psb.ugent.be

Call for position: PhD STUDENT ON BIOINFORMATICS FOR EPIGENOMICS
by mbizet 08 Jun '17

08 Jun '17

Hello, A Ph.D. student position on bioinformatics is opening in the "Laboratory of Cancer Epigenetics", ULB, Brussels, Belgium. Job description: ---------------- A position is available for a highly motivated Master student that wishes to realise a Ph.D thesis at the Laboratory of Cancer Epigenetics 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 epigenetic modification, which our lab recently investigated, will also be one of the tasks of the candidate (Delatte et al., Science 2016). The integrative analysis of these different biological levels of information will be one of the main challenging tasks of the candidate, together with the extraction of predictive signatures that may help to improve patient therapy. Working environment: -------------------- The host lab is running a Next Generation Sequencing platform: EPICS (http://epics.ulb.be/) and is part of the ULB-Cancer Research Center (U-CRC), providing a high profile scientific environment. The candidate will join other experienced bioinformaticians working on transcriptomics and epigenomics, and in addition he/she will have to opportunity to interact with other bioinformaticians from the “Interuniversity Institute of Bioinformatics in Brussels” (http://ibsquare.be) Profile/Starting date: ---------------------- The candidate should hold a master in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics and programming (e.g. R, python). Knowledge of sequencing 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 and a taste for interdisciplinary research. 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. The position is associated to a Belgian grant funded for 4 years. Screening of applications begins immediately and continues until an outstanding candidate is selected (flexible starting date). How to apply? ------------- Informal enquiries, a motivation letter, a CV (including grades and ranking) and names of two referees should be sent to: Martin Bizet (mbizet(a)ulb.ac.be) Lab website: http://www.ulb.ac.be/medecine/fukslab Lab NGS platform: http://epics.ulb.be/ Selected publications: ---------------------- - Van Grembergen et al Sci Adv 2016 - Delatte et al. Science 2016 - Boumahdi et al. Nature 2014 - Deplus et al. Cell Rep. 2014 - Dedeurwaerder et al. Briefings in Bioinformatics 2014 - Delatte et al. EMBO J. 2014 - Deplus et al. EMBO J. 2013 - Volkmar et al. EMBO J. 2012 - Dedeurwaerder et al. EMBO Mol Med.2011 - Dedeurwaerder et al. Epigenomics 2011 - Fuks F. Nature 2010 - Villa et al. Cancer Cell 2007 - Viré et al. Nature 2006

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PhD position in Bioinformatics/Computerscience
by Kathleen Marchal 08 Jun '17

08 Jun '17

Dear all, The research group DBN (dataintegration & Biological networks) has an open PhD position in the domain of method development for precision oncology. The goal of the PhD research is to develop and apply systems genetics approaches to identify driver pathways and prognostic biomarkers underlying clinical phenotypes relevant to cancer. Hereto innovative methods need to be developed that integrate genomic information derived from cohorts of tumor samples with clinical information (e.g., therapy outcome). The focus will be on studying the importance of network rewiring during cancer development and on assessing the added value of whole genome sequencing for optimal patient stratification. The research will be performed in close collaboration with clinicians, experts in molecular diagnosis and software engineers to facilitate the transfer of the developed methods to a clinical setting. •You hold a Master degree in Engineering, in Sciences; in Bioinformatics, in Applied Biological Sciences; in Health Sciences or an equivalent degree. Last year students can also apply. •A strong interest in interdisciplinary research •A strong interest in fundamental and/or applied research •Minimal background in biology or molecular biology •Strong background in computer hard- and software systems •Proficiency in programming languages such as Java, Perl or Python, as well as Linux systems. •Fluency in spoken and written English is a strong requirement For more information on how to apply see attachment. Please contact us if you are interested and have more questions. Regards, Kathleen Marchal -- Prof. Kathleen Marchal Dept. of Plant Biotechnology and Bioinformatics, Ghent University Dept. of Information Technology, IDLab, imec, Dept. of Genetics, University of Pretoria, South Africa http://bioinformatics.psb.ugent.be/DBN iGent Toren, Technologiepark 15, 9052 Gent, Belgium

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Introduction to RNA-seq Data Analysis - 21/22 September 2017 workshop open for applications and one place left on 29/30 June 2017workshop
by Bert Overduin 07 Jun '17

07 Jun '17

Dear all, Applications are now accepted for the Introduction to RNA-seq Data Analysis workshop on Thu 21& Fri 22 September 2017. Details and a link to the application form can be found here: http://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis We also have one place left on the workshop on Thu 29 & Fri 30 June 2017. If you're interested in this spot, please fill in the application form you can find at: https://www.surveymonkey.co.uk/r/W63XZDL Other workshops that are currently open for registration / application can be found on the Edinburgh Genomics training page: http://genomics.ed.ac.uk/services/training 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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RSG Student Symposium 2017 - Gent_deadline postponed
by Daniele Parisi 06 Jun '17

06 Jun '17

Dear colleagues, the deadline for abstract submission has been postponed to FRIDAY 2ND JUNE. Don't miss the opportunity of meeting the network of Belgian Master, PhD and Postdoc students in Bioinformatics and Computational Biology. TIME: 8TH JUNE, 14:15 PLACE: TECHNOLOGIEPARK-ZWIJNAARDE 927, 9052 GENT, België KEYNOTE: prof YVES VAN DE PEER NETWORK DRINK AND SOCIAL DINNER follows More info, registration and submission here: https://www.facebook.com/events/1813431575641030/?acontext=%7B%22action_his… Short link to the registration and submission form: https://goo.gl/forms/yRDhXSv54EsVTLpE3 I hope to see you all there Kind regards -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394

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PhD position in Leuven (computer science / statistics)
by Guy Baele 03 Jun '17

03 Jun '17

The Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven; https://rega.kuleuven.be/cev/ecv/) is looking for a motivated PhD student to perform research in a multidisciplinary team. This constitutes an exciting opportunity to work on computational and statistical methods in molecular evolution with applications in infectious diseases. Research group The Evolutionary and Computational Virology Laboratory at the Division of Clinical and Epidemiological Virology (Rega Institute, KU Leuven) focuses on the evolutionary processes that shape viral genetic diversity. This encompasses large-scale epidemic processes, such as population growth and spatial dispersal (a popular topic in phylogeographic and phylodynamics research), as well as small-scale transmission histories and within-host evolutionary processes, including adaptation and recombination. It is our objective to gain better insights into these evolutionary and population genetic processes and to clarify how they relate to epidemic and disease dynamics. To this aim we plan to focus on statistical and computational developments to analyze the increasing amount of data brought about by massive sequencing studies, mainly in a framework of Bayesian phylogenetic inference, for which our research group holds a strong track record. We also aim to explore the applicability of novel models and statistical inference tools, developed as part of our research, in different fields of research. Project This project focuses on new developments in a popular Bayesian phylogenetic inference framework (BEAST: https://github.com/beast-dev/beast-mcmc) and its applications to important evolutionary problems, with a particular focus on infectious diseases. The project involves the development of an integrated web system and database that allows users to register, upload and retrieve sequence data to and from the database. Each user will be able to determine the sharing policy for the data he/she has provided. Such a system should be easily distributed so that other research groups can deploy it on their own server(s) and put it to use without technical interventions. Further, this system will interface with the BEAST software package to analyze the sequence data in an efficient manner. The candidate is expected to design and implement such a system and determine an appropriate strategy to properly distribute the developed system as an easily installed/deployed software package. Additionally, multiple parallelization ideas will be implemented in the BEAST software package. BEAST is mostly written in Java, with its high-performance computational library, known as BEAGLE, being implemented in C/C++. The goal is to develop and implement efficient parallelization strategies from both a computational and a statistical perspective. The computational aspect entails the implementation of popular routines typically used in computer architecture, whereas the statistical aspect entails the development and adaptation of novel transition kernels in a Bayesian phylogenetic inference framework. Profile The candidate for this PhD position should have a strong quantitative background, and preferably holds a master's degree in computer science / informatics (or equivalent through experience), with an interest in statistics/mathematics and (bio)informatics. The candidate hence needs to be experienced in an object-oriented programming language such as Java or C/C++. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel. Offer The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand new facilities of the Rega institute at the University hospital campus, and guided by prolific supervisors. KU Leuven is one of the top universities in Europe and leads the Reuters ranking of Europe’s most innovative universities for the second year in a row. The targeted starting date will be October 1st 2017 and the candidate should obtain his/her master’s degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Additional information, as well as the application procedure, can be found here: https://icts.kuleuven.be/apps/jobsite/vacatures/54182826 Please use the university’s job portal when applying for this position. For more information, contact Guy Baele (guy.baele(a)kuleuven.be) or Philippe Lemey (philippe.lemey(a)kuleuven.be) -- Guy Baele, PhD. Department of Microbiology and Immunology Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Lecture Series in "Translational Bioinformatics and Systems Biomedicine".
by Francisco Azuaje 02 Jun '17

02 Jun '17

Dear Colleagues, This year in Luxembourg ?we begin hosting a Lecture Series in "Translational Bioinformatics and Systems Biomedicine" . Full provisional program is now available at:?? https://files.lih.lu/events/2017/Overview%20translational%20bioinformatics_… Our first lecture (on 19 June) will be given by Prof. Luonan Chen (Director of the Key Laboratory of Systems Biology @ Shanghai Institutes for Biological Sciences): http://tinyurl.com/y95k3bgv? Sincerely, 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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[Gtpb] Reproducible and Open Data Science - a hands-on course
by Pedro L. Fernandes 01 Jun '17

01 Jun '17

ANNOUNCEMENT/REMINDER RODS17 Reproducible and Open Data Science with Rutger Vos and Pedro Fernandes (Instructors) The above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: June 16th, 2017 <=== Course date: June 21st - 23rd 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Description: In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that under-gird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. http://gtpb.igc.gulbenkian.pt/bicourses/RODS17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro Fernandes Bioinformatics Training 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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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen
by Celia van Gelder 30 May '17

30 May '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a <http://biosb.nl/about/members/biosb-membership-information/> member of the BioSB research school. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. 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 has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: · How to set-up a dynamic model to represent biological networks using different interaction mechanisms · To implement, simulate and analyse dynamic network models in different software tools · To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes · To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the <http://biosb.nl/education/course-portfolio-2/> Education Programme of BioSB, 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 <http://www.biosb.nl/> . Beste regards, Femke Francissen Femke Francissen Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: <mailto:femke.francissen@biosb.nl> femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn <http://nl.linkedin.com/in/femkefrancissen> link <http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg>

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C-COMEND: free Training in Translational research, BCRT Oct 9-13th, 2017, Berlin
by Celia van Gelder 30 May '17

30 May '17

Dear all, Please spread the announcement below as you see fit. Best Celia Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht This is to inform you that <https://www.helmholtz-hzi.de/de/aktuelles/veranstaltungen/c_comend/overview…> registration for the next free C-COMEND course is still open. The EU project C-COMEND offers PhD and Postdocs the opportunity to join a course on “Translational Research and Development“ in Berlin from 9th-13th of October 2017. The course consists of an introductory e‑learning (~ 24 hours student investment time) followed by a 5-day face-to-face workshop with speakers from Industry and Academia, including Bob Harris, Professor Immunotherapy, Karolinska Matthias Gottwald, Head of R&D Policy & Networking, BAYER Keith Williams, Director, KW Drug Developments Mike Hardman, former Vice President IMI Collaborations, AstraZeneca Mohamed Abou-El-Enein, Head of Clinical Development Platform, BCRT Participation is free of charge but participants will have to cover their travel costs. Deadline for <https://www.helmholtz-hzi.de/de/aktuelles/veranstaltungen/c_comend/overview/> application is June, 1st. It would be fantastic if you could support us by spreading this information to your colleagues, students and/ or other people in your network that might be interested, either by sharing this email (see also the attached flyer and preliminary program) or via <https://twitter.com/RebeccaLudwig2/status/862210038508773376> twitter, or <https://www.linkedin.com/feed/update/urn:li:activity:6262188458727604224/> LinkedIn and <https://www.facebook.com/photo.php?fbid=1113513968755159&set=gm.12572624210…> facebook. Thank you very much in advance for your time and effort! With kind regards, Rosan Vegter, DVM, PhD C-Comend Training Project Manager cid:image001.png@01D2D928.60139120 EATRIS | European infrastructure for translational medicine rosanvegter(a)eatris.eu | +31 (0)6 15 52 29 34 De Boelelaan 1118 | Room PK 4X 176 1081 HZ Amsterdam | The Netherlands +31 (0)20 4442254 | www.eatris.eu Working days: Monday, Tuesday, Friday <https://twitter.com/EatrisEric> Follow us on Twitter <http://translationalmedicine2017.eu/> cid:image002.png@01D2D928.60139120

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Cytoscape Advanced Tutorial @ ISMB this year
by P. Molenaar 19 May '17

19 May '17

Dear fellow researcher, At ISMB this year, the Cytoscape development team will be staging an all new advanced Cytoscape tutorial. It will be held the afternoon of Friday July 21 at the ISMB site in Prague. This tutorial is especially interesting given the fact that Cytoscape is being transformed as part of a Cytoscape Cyber Infrastructure and will support a full blown REST Api. You can sign up for it on the ISMB web site: https://www.iscb.org/ismbeccb2017-registration (note: the early bird registration ends the 15th of June) The full information is here: https://www.iscb.org/ismbeccb2017-program/tutorials#p4 The brief version is below. Hope to see you there! The Cytoscape development team Network Analysis in Cytoscape: Advanced Topics Intended audience The Advanced Topics tutorial is intended for an audience that has prior experience with at least one of the following: * Cytoscape software * Data integration and analytical methods * Network biology concepts * Bioinformatics analysis pipelines Goals, objectives and motivations By the end of tutorial, you should be able to: * Know when and how to use Cytoscape in your research area * Identify and discriminate relevant source of interactions, networks and datasets * Command programmatic control over Cytoscape * Integrate Cytoscape into your bioinformatics pipelines * Publish, share and export networks online * Generalize network analysis methods to multiple problem domains ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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