- BBClist - maillist.psb.ugent.be

TransMed 2016: Translational Medicine Informatics & Applications Meeting ISMB2016, July 8, 2016, Orlando, USA
by Venkata Pardhasaradhi SATAGOPAM 17 May '16

17 May '16

Dear all We are organising a Special Interest Group (SIG) during ISMB 2016. We will be very happy to see you there. TransMed 2016: Translational Medicine Informatics & Applications Meeting ISMB 2016, (Orlando, USA), on July 8, 2016. Knowledge-based translational medicine is a rapidly growing discipline in biomedical research and aims to expedite the discovery of new diagnostic tools and treatments by using a multi-disciplinary, highly collaborative, "bench-to-bedside" approach. Large amounts of multi-omics, imaging (medical and molecular) and clinical data can now be captured for given patient populations. In addition to the challenges of data curation and harmonisation, new computational methods are required to identify molecular signatures that suggest disease subtype. These signatures may be predictive of outcome or progression, and impact on disease management by suggesting personalised therapeutic strategies for patients. Such approaches will further the development of a new taxonomy of disease. In the TransMed SIG meeting, we will explore the current status of computational biology approaches within the field of translational medicine. Keynote Speakers Confirmed: Prof. Russ Altman, Professor of Bioengineering, Genetics, Medicine and Computer Science; Director, Biomedical Informatics Training Program, School of Medicine, Stanford University Prof. Sean Mooney, Professor of Biomedical Informatics and Medical Education, University of Washington; Chief Research Information Officer (CRIO) of UW Medicine Prof. John Overington, Director of Bioinformatics at Stratified Medical, Visiting Professor at the Institute of Cardiovascular Science, University College London and the Farr Institute Key dates: Abstract submissions deadline: May 27, 2016 Poster and Presentation acceptance notifications: May 31, 2016 Final program available: June 10, 2016 TransMed 2016 SIG: July 8, 2016 TransMed2016 SIG web site: http://transmedit.org/Main_Page <http://transmedit.org/Main_Page> Registration: https://www.iscb.org/ismb2016-registration <https://www.iscb.org/ismb2016-registration> Abstract submission: https://easychair.org/conferences/?conf=transmed2016 <https://easychair.org/conferences/?conf=transmed2016> Contact: transmed-coord(a)googlegroups.com <mailto:transmed-coord@googlegroups.com> Best regards, Venkata on behalf of TransMed 2016 SIG organising team -- Venkata P. Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)uni.lu <mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu <http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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job opening at VIB - Bioinformatics Tool Engineer
by Alexander Botzki 17 May '16

17 May '16

Dear colleagues, At VIB, we have a new opening of a Bioinformatics Software Engineer - http://www.vib.be/en/jobs/Pages/Bioinformatics-Tool-Developer.aspx Please forward it in case you know someone who might be interested in applying for this opening at VIB. Thanks a lot and best regards, Alex Alexander Botzki Manager BITS | Training Coordinator ELIXIR-BE VIB - BITS, Rijvisschestraat 126, 9052 GENT | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @bitsatvib<https://twitter.com/bitsatvib> | https://corefacilities.vib.be<https://corefacilities.vib.be/>

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PhD position in Systems Biology
by Sophie de Buyl 13 May '16

13 May '16

Dear Colleagues, I would like to ask you to forward the following announcement to students who might be interested in applying for a PhD position in Systems Biology at VUB in Brussels. Thanks a lot! Sophie de Buyl PhD in Systems Biology — Applied Physics Group (APHY) @ VUB =================================================== We are looking for a highly motivated PhD student with a Master degree in Physics, Mathematics, Bio-Engineering or Biology interested in the development of mathematical and computational models applied to biological systems. Depending on the interest of the applicant, the PhD project could be oriented towards modeling the dynamics of human-associated microbial communities, modeling cellular differentiation or circadian rhythms. More generally, we focus on the dynamics of networks of interactions in biological systems. Knowledge of a programming language is a plus. The Applied Physics research group (http://we.vub.ac.be/aphy/About) is a multidisciplinary group of enthusiastic researchers that use experimental and theoretical methods to address fundamental challenges in biological physics, condensed matter physics, electromagnetism, laser physics and photonics. This combination allows an imaginative, cross-disciplinary and insightful approach to such problems. For example, we focus on the study of metamaterials and nanophotonics, on bio-inspired approaches to machine learning (reservoir computing), on the dynamics of semiconductor lasers, nonequilibrium pattern formation and soliton dynamics, as well as on genetic transcription, cell division & microbial interactions in biological systems. APHY is recognised as a leading and growing research group by the university. For that reason, in 2014 it received a Strategic Research Project “Applied Physics and Systems Biology” (2014-2019). The Vrije Universiteit Brussel (VUB) has been a leading player in the Flemish Higher Education landscape for 40 years. The University numbers 12.000 students and together with its hospital - UZ Brussel – employs more than 6000 people. The Vrije Universiteit Brussel is the largest Dutch speaking employer in the capital. Teaching and research at the VUB are founded on the principle of unfettered inquiry to benefit the progress of mankind. This means rejecting dogmatic positions and guaranteeing the freedom to form opinions without interference; in this way the University aims to ensure the dispersal of the principle of unfettered inquiry throughout society. As an employee of the Vrije Universiteit Brussel your days will be spent in a dynamic, diverse and multilingual environment. Our campus “Etterbeek” is a green oasis on the outskirts of the center of the capital of Flanders, Belgium and Europe. The city center, with all its opportunities, is within your reach by public transport in less than half an hour. To apply, please send your CV including grades, a motivation letter (one page) and one letter of reference (to be sent separately). Your motivation letter should briefly describe your research interests and why you are interested in joining our group. Please send your application material by email to sdebuyl(a)vub.ac.be. The position is open until filled and the expected starting date is September 1, 2016 (or earlier). Also students in their last year expecting to get their Master’s diploma before Sept. 1 may apply. =================================================== ______________ Sophie de Buyl Assistant Professor Applied Physics Group Vrije Universiteit Brussel Theoretical Physics Pleinlaan 2 1050 Brussels Belgium Room: 9F07.b sdebuyl(a)vub.ac.be Tel: +32-2-6292357 Fax: +32-2-6293614

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mark your agenda for the BIG N2N bioinformatics exhibition
by Katrijn Vannerum 13 May '16

13 May '16

Dear colleague, Do you find it difficult to explain your aunt, brother, neighbor,... what you're doing? The free Dutch/English BIG N2N bioinformatics exhibition aims at getting a broad public acquainted with bioinformatics: what is it and what is it used for? When? 14-24/7/2016, so during the Ghent Festival and a few days before, with official opening on 14/7 (more info will follow) Where? Palmarium, Botanical garden UGent, K.L. Ledeganckstraat 35, Gent Spread the word! Welcome, Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [logo_BIG N2N_signature]

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Vacancy for Postdoctoral Researcher at Kris Gevaert lab – Chemical Proteomics, Identification of the Targets of Lead Compounds - erratum
by Katrijn Vannerum 12 May '16

12 May '16

Dear all, this is the correct link to apply: http://www.vib.be/en/jobs/Pages/Postdoctoral-Researcher-%E2%80%93-Chemical-… Excuses. Katrijn Vannerum From: nucleotides2networks-request(a)lists.ugent.be<mailto:nucleotides2networks-request@lists.ugent.be> [mailto:nucleotides2networks-request@lists.ugent.be] On Behalf Of Katrijn Vannerum Sent: 12 May 2016 11:34 To: nucleotides2networks(a)lists.ugent.be<mailto:nucleotides2networks@lists.ugent.be>; bbclist(a)psb.vib-ugent.be<mailto:bbclist@psb.vib-ugent.be> Subject: [N2N] Vacancy for Postdoctoral Researcher at Kris Gevaert lab – Chemical Proteomics, Identification of the Targets of Lead Compounds Description The proteomics lab headed by Prof. Kris Gevaert is hiring a postdoctoral researcher with proven expertise in contemporary proteome research to work in a multidisciplinary project that brings together several academic partners and a Flanders-based biotechnology company. We will use established (e.g., affinity purification-mass spectrometry, AP-MS) technologies and further implement recent developments (i.e., thermal proteome profiling) to identify the protein targets of a range of lead compounds in the area of human health. The selected candidate will have access to the latest mass spectrometry equipment in the VIB’s Proteomics Expertise Center (https://corefacilities.vib.be/pec) housed in the VIB Medical Biotechnology Center, and will work in close collaboration with molecular biologists. Profile Expertise in the field of mass spectrometry driven proteomics, and especially on protein complex purification and analysis is an important asset. How to apply? Interested candidates are asked to apply online through http://www.vib.be/en/jobs/Pages/Postdoctoral-Researcher-%E2%80%93-Chemic.... Please upload your full CV as well as two reference letters to your online application. Contact information: Kris.Gevaert(a)UGent.be<mailto:Kris.Gevaert@UGent.be> Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [logo_BIG N2N_signature]

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Vacancy for Postdoctoral Researcher at Kris Gevaert lab – Chemical Proteomics, Identification of the Targets of Lead Compounds
by Katrijn Vannerum 12 May '16

12 May '16

Description The proteomics lab headed by Prof. Kris Gevaert is hiring a postdoctoral researcher with proven expertise in contemporary proteome research to work in a multidisciplinary project that brings together several academic partners and a Flanders-based biotechnology company. We will use established (e.g., affinity purification-mass spectrometry, AP-MS) technologies and further implement recent developments (i.e., thermal proteome profiling) to identify the protein targets of a range of lead compounds in the area of human health. The selected candidate will have access to the latest mass spectrometry equipment in the VIB’s Proteomics Expertise Center (https://corefacilities.vib.be/pec) housed in the VIB Medical Biotechnology Center, and will work in close collaboration with molecular biologists. Profile Expertise in the field of mass spectrometry driven proteomics, and especially on protein complex purification and analysis is an important asset. How to apply? Interested candidates are asked to apply online through http://www.vib.be/en/jobs/Pages/Postdoctoral-Researcher-%E2%80%93-Chemic.... Please upload your full CV as well as two reference letters to your online application. Contact information: Kris.Gevaert(a)UGent.be Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [logo_BIG N2N_signature]

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Two computational biologist positions in the UK
by Rekin's Janky 11 May '16

11 May '16

For your interest: Two computational biologist positions (£38,000-£56,000) in a UK consulting company to work in Oxfordshire or South Yorkshire. Closing date of 06/06/2016. Best, Rekin’s [Nucleomics Core]<http://www.nucleomics.be> Rekin's Janky, Ph.D. Bioinformatics Address: Herestraat 49, O&N4, Post Box 816, Room nr. 404-24 / 08.428, 3000 Leuven - Belgium Tel: +32 (0)16 376972 Tel: +32 (0)16 373126 Fax: +32 (0)16 373129 Web: www.nucleomics.be<http://www.nucleomics.be/>

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Postdoc opportunities in Metagenomics Group Utrecht Univeristy
by Bas E. Dutilh 11 May '16

11 May '16

https://www.academictransfer.com/employer/UU/vacancy/33839/lang/en/ The Metagenomics Group at Utrecht University (UU) in The Netherlands aims to fully understand microbial ecosystems by analyzing and modeling meta'omics datasets. For example, we identify new microbes and viruses in metagenomes, study their distributions in different environments, and infer their interactions within the underlying microbiomes. Two examples of ongoing projects include modeling the phage-host interaction network in the human gut, and elucidating the metabolic routes used for biodegradation of hydrocarbon contaminations in soil. All projects start from metagenomic datasets and use computers to understand the underlying ecosystem, including phage-host prediction and metabolic network inference in the examples above. We collaborate internationally with wet lab biologists to obtain novel data, and we recycle "big data" from public repositories, where much remains to be discovered by using innovative tools. The group currently has two opportunities for new postdocs who are driven by the challenge of understanding the fundamental ecological and evolutionary mechanisms shaping microbial communities. Candidates will be given the opportunity to manage their own projects within the group, supervise students, write papers, and apply for grants. For more details and an application link, please see https://www.academictransfer.com/employer/UU/vacancy/33839/lang/en/ -- Dr. Bas E. Dutilh Metagenomics Group Theoretical Biology and Bioinformatics, Utrecht University Utrecht Bioinformatics Center +31 (0)30 253 4212 - http://tbb.bio.uu.nl/dutilh

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[Gtpb] Fwd: URGENT: Expressions of interest - Training on 3C-based analysis and modelling...
by Pedro Fernandes 11 May '16

11 May '16

Dear friends and colleagues, Apologies for this mass posting. Some of you have previously expressed interest in our courses for hands-on training on TADbit and TADkit (http://www.3DGenomes.org http://www.3dgenomes.org ). We are about to open a new course in the GTPB programme from the 6th to 9th of June. Additional info on the course can be found at the end of the e-mail. 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding May we ask you to *quickly* inform us if you would be interested in attending, or recommending that your collaborators would attend? We will run the course on those dates but we need to find-out whether or not we should offer it in a later date, November 2016 for example. Best, Pedro -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt >>>>>>>>>>>> Course description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: ? 1D - Map paired-end sequences to generate Hi-C interaction matrices ? 2D - Normalize matrices and identify constitutive domains (TADs, compartments) ? 3D - Generate populations of structures which satisfy the Hi-C interaction matrices ? 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Target Audience The course design is oriented towards experimental researchers and bioinformaticians at the graduate and post-graduate levels. The last edition of this course was attended by people with different backgrounds and interested in the genome organization. Moreover, Hi-C data have recently been used in metagenomics studies to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. It is likely that the participants to this course aim at getting involved in generating Hi-C data for chromosome structure determination or that they just want to be able to correctly interpret and analyse publicly available data. Course Pre-requisites Recommended Linux and basic Python programming skills, graduate level in Life Sciences. Course fee Eur 360.00, lunches and coffee-breaks included. _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Two variant analysis courses at CSC in Finland 13- 17 June 2016
by Celia.vanGelder＠radboudumc.nl 10 May '16

10 May '16

Please note that registration is now open for the following two variant analysis courses at CSC in Finland: Variant analysis workshop 13.-15.6.2016 (www.csc.fi/web/training/-/variant-analysis<http://www.csc.fi/web/training/-/variant-analysis>) This ELIXIR EXCELERATE -funded course covers several aspects of variant analysis including variant annotation and prioritization. It consists of lectures and hands-on exercises which are suitable for everybody, as analysis is performed with easy-to-use graphical tools (the VEP hands-on tutorial on day 2 contains also an optional session for participants with coding experience). Participants can select and combine the following course days according to their needs: 13.6.2016 Introduction to variant analysis from sequencing data -Variant analysis with Chipster 14.6.2016 Variant annotation and effect prediction -Analysing variation data with the Variant Effect Predictor (VEP) -Genome variant annotation and interpretation in a clinical context using omnomicsQ -TBA 15.6.2016 Variant analysis and prioritization -European Genome-phenome Archive (EGA) -RD-Connect genomics analysis platform -Variant prioritization with UMD-Predictor, VarAFT and Human Splicing Finder Variant analysis with GATK 16.-17.6.2016 (www.csc.fi/web/training/-/gatk<http://www.csc.fi/web/training/-/gatk>) This course covers the core steps involved in calling variants with the Broad's Genome Analysis Toolkit (GATK), using the Best Practices developed by the GATK team. It highlights key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq specific processing, and somatic variant discovery using MuTect2. The trainers also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery. The course consists of a lecture day which is suitable for everybody, and an optional hands-on day for which you need to have basic familiarity with the command line environment. Best regards, Eija Eija Korpelainen, Ph.D Product Manager Application services, Bioinformatics CSC - IT Centre for Science P.O.Box 405 02101 Espoo, Finland Phone +358 50 381 9726 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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