- BBClist - maillist.psb.ugent.be

Postdoc position in the area of biomedical data visualization in disease maps.
by Venkata Pardhasaradhi SATAGOPAM 09 Sep '16

09 Sep '16

Dear all, The Luxembourg Centre of Systems Biomedicine (LCSB), University of Luxembourg has the following Postdoc position in the area of biomedical data visualization in disease maps. Please refer the URL for more details: http://emea3.mrted.ly/16ij4 <http://emea3.mrted.ly/16ij4> Best regards, Venkata -- 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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Fwd: Postdoc position in Cryptomeria genomics at FFPRI
by "Yao-Cheng Lin (林耀正)" 08 Sep '16

08 Sep '16

FYI > Begin forwarded message: > > From: Saneyoshi Ueno <saueno(a)ffpri.affrc.go.jp> > Subject: Postdoc position in Cryptomeria genomics at FFPRI > Date: September 8, 2016 at 1:45:21 PM GMT+8 > To: Yao-Cheng Lin <yao-cheng.lin(a)psb.vib-ugent.be> > > Dear Yao-Cheng, > > Hello, how are you? > > A post-doc position is available in our laboratory. > Please see attached a PDF file for detailed information. > Forwarding this message to interested staff and students is welcome. > > Yours sincerely, > > Saneyoshi UENO > > -- > Saneyoshi UENO Ph.D > Department of Forest Molecular Genetics and Biotechnology > Forestry and Forest Products Research Institute > 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan > Email: saueno(a)ffpri.affrc.go.jp > Tel: +81-29-829-8261 > Fax: +81-29-874-3720 > > -- > 〒305-8687　茨城県つくば市松の里１ > 国立研究開発法人　森林総合研究所 > 林業研究部門　樹木分子遺伝研究領域 > 上野真義 <saueno(a)ffpri.affrc.go.jp> > TEL: 029-829-8261, FAX: 029-874-3720 Yao-Cheng Lin (林耀正) Bioinformatics and Computational Genomics Agricultural Biotechnology Research Center Biotechnology Center in Southern Taiwan Academia Sinica Tainan, Taiwan TEL: +886(6)510 30 70 E-mail: yalin(a)sinica.edu.tw <mailto:yalin@sinica.edu.tw>

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Biostatistician position - GIGA - ULg
by Sandra Lopez - GIGA ULg 06 Sep '16

06 Sep '16

Dear all, The GIGA-Cardiovascular Sciences Research Unit, University of Liège, and the Department of Cardiology, University Hospital of Liège, Belgium, is searching for an experienced Full-Time Biostatistician to join their expanding team. The position is immediately available on site. Please find attached the job description. Sandra Lopez and Sandrina Evrard GIGA - Coordination Université de Liège Quartier Hôpital Avenue de l'Hôpital 11 - B34 B-4000 LIEGE Tél + 32 4 366 98 03 or 43 94 Fax + 32 4 366 41 98 www.giga.ulg.ac.be

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Benelearn 2016, final call for participation
by Yvan Saeys 05 Sep '16

05 Sep '16

FINAL CALL FOR PARTICIPATION: 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 is 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). PROGRAM: This anniversary edition of Benelearn is organised on two days, where the first day focuses on large scale data analysis. The program consists of 8 invited talks, 8 selected talks, 16 short talks and around 50 posters. In order to stimulate discussion among PhD students / postdocs and the invited speakers, we will have a meet-the-speaker session. Furthermore, the conference dinner and lunch breaks will provide ample opportunity for networking. Finally, a job board will be available for the participants where perhaps you will find your next job in industry or academia! The full program is available at the conference website:http://www.kuleuven-kulak.be/benelearn/. List of invited speakers: Jeff Ullman (Stanford University): A Complexity Theory for MapReduce Algorithms Isaac Triguero (UGent / University of Nottingham): Big Data Learning in Practice Hugo Ceulemans (Janssen R&D): Predicting the activity of chemical compounds across 1001 biological assays at industrial scale Kristian Kersting (TU Dortmund): To be announced Greg Tsoumakas (Aristotle University of Thessaloniki): Multi-Target prediction: Challenges and applications Emilia Barakova (Technische Universiteit Eindhoven): Learning robots for autism therapy Christian Blum (University of the Basque Country): Combining metaheuristics with ILP solvers: Construct, Merge, Solve & Adapt Luc De Raedt (KU Leuven): On the history and future of machine learning: a personal interpretation and perspective REGISTRATION: Registration can be done through the conference website:http://www.kuleuven-kulak.be/benelearn/. Registration is possible up to and including Sunday 4 September. -- ====================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine Inflammation Research Center, a VIB-UGent Department UGent Department of Internal Medicine, Respiratory Medicine (GE01) Technologiepark 927 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ======================================================================

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Open PHD Position Characterization and modeling of cellular migration at GIGA, University of Liege
by Raphael.Maree. 05 Sep '16

05 Sep '16

Dear colleagues, Please find below an open PhD position at the LBTD (GIGA, University of Liège) for an engineer/physicist. Best regards, Raphaël Marée. Transmis par Raphael.Maree. <Raphael.Maree(a)ULg.ac.be> ----------------------- Message d'origine ----------------------- From: silvia.blacher(a)ulg.ac.be To: Raphael.Maree(a)ulg.ac.be Date: Mon, 5 Sep 2016 09:38:42 +0200 (CEST) Subject: PHD Position ---- Salut Raphaël, Voici l'annonce. Merci pour ton aide Silvia Multidisciplinary PhD position for an engineer/physicist on the characterization and modeling of cellular migration The Laboratory of Tumor and Development Biology at the University of Liège, Belgium (Prof. Agnès Noël, Giga-Cancer) has an opening for a quantitatively-minded PhD candidate to work on the characterization of cellular patterns and on the modeling of cell migration. The laboratory focuses on the fundamental and therapeutic research about the manifold cellular processes involved in cancer development. This PhD project entails the development of 2D and 3D microscopy protocols as well as of specific image and data analysis for characterizing cellular patterns observed in biological in vivo and in vitro models. The modeling of the physicochemical aspects of the underlying phenomena will also be considered. The ideal candidate will have a Master in Physics or Engineering, with a taste for creative scientific programming. The candidate will be supervised by senior scientific staff with a background in physics and engineering (Dr. Silvia Blacher and Dr. Cedric Gommes), but she/he should also have the drive and social skills required to interacting daily with the experimental biologists in the lab. Although this is a four-year position, the successful completion of a PhD could lead to longer-term career prospects in a world-renown research group. The position starts in October 1st 2016. Interested candidates should send their résumé and application letter to Prof. Agnès Noël (agnes.noel(a)ulg.ac.be) no later than September 15th.

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[Gtpb] QPB16 - Quantitative Proteomics using Bioinformatics
by Pedro L. Fernandes 05 Sep '16

05 Sep '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course QPB16 - Quantitative Proteomics using Bioinformatics with Mikhail Savitski, Roman Zubarev and Bo Zhang Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/QPB16 for details. IMPORTANT DATES for this Course Deadline for applications: Sep 24th 2016 Course dates: Oct 17th - Oct 19th 2016 Course Description Recent years have seen rapid development in biological mass spectrometry and proteomics. In particular, the quantitative performance has taken a huge leap forward, both as a label-free (LF) approach and as multiplexed quantitative mass spectrometry. This development has enabled new technologies for unbiased characterization of drug molecules with protein targets, which is one of the major challenges in drug development. Here we will explain the basic principle of protein quantification by mass spectrometry. A pragmatic description of strengths and weaknesses of both label-free as well as the multiplexed methodology will be presented. A novel technology, thermal proteome profiling (TPP), will be explained that detects protein drug interactions in living cells. A practical session will take the students through the analysis and interpretation of quantitative mass spectrometry data stemming from the TPP experiment using an R package. In the LF part of the course, we will explain the basics of the identification software DeMix that performs deconvolution of the naturally multiplexed tandem mass spectra, thus significantly improving the identification aspects. An extension to quantification, DeMix Q, introduces the false discovery rate (FDR) for peptide identity transfer between the LC-MS runs, and greatly improves the quantification performance. Both DeMix and DeMix Q are realized based on Open MS package. The participants will learn how to use these programs and process their data. Target audience This course is intended for all scientists interested in mass spectrometry, proteomics and drug development. Pre-requisites Basic biological knowledge, especially with regard to proteins. Interest in biotechnology. General computer literacy, (e.g. editing plain text data files, familiarity with Excel, navigating using the command line) will be assumed. Best regards 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 Upcoming courses: PM16 - Precision Medicine, Sep 27 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17 AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] ANNOUNCEMENT: GTPB Bioinformatics Training course AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires
by Pedro L. Fernandes 05 Sep '16

05 Sep '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires With Simon Frost (U. Cambridge) are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/AAIRR16 for details. IMPORTANT DATES for this Course Deadline for applications: Oct 12th 2016 Course dates: Nov 2nd - Nov 4th 2016 Course Description This course will cover the analysis of B and T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data using bioinformatics workflows. Topics include germline allele assignment, identification of clones, and visualisation/analysis of clonal frequencies. The course will also cover emerging standards (VDJML, Change-O) in the analysis and reporting of Adaptive-immune Receptor Repertoire (AIRR) data. In addition to an introduction to software used, such as IgBLAST, pRESTO, Change-O, etc., the course will also provide an introduction to the use of Jupyter notebooks for conducting exploratory analyses and the Common Workflow Language to automate analyses. To get a flavour of the techniques and software that will be used in the course. IgBLAST pRESTO Change-O Discussion site: B-T.CR Best regards 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 Upcoming courses: PM16 - Precision Medicine, Sep 27 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17 AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] REMINDER: GTPB Bioinformatics Training course announcement/reminder - Precision Medicine - PM16
by Pedro L. Fernandes 05 Sep '16

05 Sep '16

Deadline for Applications - September 12th 2016 The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course PM16 - Precision Medicine with Fatima Al-Shahrour, Javier Perales and Elena Piñero are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/PM16 for details. Course Description The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Best regards 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 Upcoming courses: PM16 - Precision Medicine, Sep 27 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17 AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Announcement META-scan workshop: MRS and Systembiology 3-oct-2016 Utrecht NL - Registration deadline 19-sept-2016
by Jeneson, JAL (med) 02 Sep '16

02 Sep '16

Are you a Magnetic Resonance user? or a computational modeler? Then we have just the workshop for you! On Monday October 3rd 2016, we will bring together MR users, computational modelers and physicians to exchange methods and ideas on how these disciplines may be bundled to advance Systems Medicine efforts to combat complex human diseases such as cancer and metabolic disease including diabetes. This one-day workshop will feature a morning session with introductory lectures by experts from the field of Systems Medicine, followed by an afternoon session with break-out groups on specific organ/disease topics to stimulate discussion and future collaboration between in vivo MR experimentalists and computational modelers. A panel discussion followed by drinks will close the day. A more detailed program of the workshop can be found at the end of this email. Registration for this one-day workshop at UMC Utrecht is free. Just send an email that you will attend the workshop to: mrsandsystembiology(a)gmail.com<mailto:mrsandsystembiology@gmail.com> before Monday September 19th. Please specify your background (experimentalist versus modeler) as well as your preference for a particular break-out group in the afternoon session (choose from [1] cancer; [2] heart; [3] liver; [4] musculoskeletal). Please send out this invitation to your co-workers who might be interested to join! We look forward to seeing you in Utrecht on October 3rd! The organizers. - Jannie Wijnen, Jeanine Prompers and Jeroen Jeneson Program Workshop on Magnetic Resonance and Systems Medicine Monday October 3 2016 UMC Utrecht, Auditorium Q1 Program 9:30 - 10:00 Coffee and tea 10:00 - 10:05 Welcome and opening - Dennis Klomp Morning lectures: 10:05 - 10:30 "Complex Human Disease and Systems Medicine" - Hanneke van Laarhoven, MD/PhD, Clinical Oncology, AMC 10:30 - 11:15 "Systems Medicine - what is it? what does it bring to medical research and care?" - Barbara Bakker, PhD, Professor of Systems Medicine, Dept of Pediatrics, UMCG 11:15 - 12:00 "Systems Medicine and in vivo MRS - Examples from Cardiovascular Physiology and Medicine" - Dan Beard, PhD, Carl J. Wiggers Collegiate Professor of Cardiovascular Physiology and Professor of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA 12:00 - 12:25 "Systems Medicine and in vivo MRS: practice - in vivo MRS" - Ot Bakermans, Ir PhD, Postdoctoral Fellow, Dept of Radiology, AMC 12:25 - 12:30 Announcements afternoon program 12:30 - 13.30 Lunch Afternoon break-out sessions: 13:30 - 15:00 Oncology Moderated by Hanneke van Laarhoven and Natal van Riel (van Peperzeel room) Cardio Moderated by Tim Leiner and Dan Beard (Puylaart room) Musculoskeletal Moderated by Daniel Saris and Jeroen Jeneson (Klinkhamer room) Liver Moderated by Aart Nederveen and Barbara Bakker (Q01.305) 15:00 - 15:15 Coffee and tea 15:15 - 15:45 Wrap up of break-out sessions (van Peperzeel room) 15:45 Drinks ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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SECOND CALL - ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY
by Cuypers Bart 31 Aug '16

31 Aug '16

[cid:image008.png@01D1D2CF.7D3D07F0] SPECIAL BIOINFORMATICS EVENT ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY Friday, the 7th of October 2016 ULB-VUB La Plaine Campus, Brussels REGISTRATION (deadline 1st of October) Registration is free. Please register before the 1st of October with the following link : https://goo.gl/forms/qnJo31wynmyiiZ233 ABSTRACT CALL (deadline 16th of September) Twelve PhDs-Postdoc abstracts will be selected for oral presentations. Please send your abstract to this address ib2rgs(a)gmail.com<mailto:ib2rgs@gmail.com> For the Full program and abstract call information, please see the attached pdf Keynote speakers Prof. Richard REDON INSERM, Nantes, France Deciphering the genetic architecture of complex disorders: one experience on the Brugada syndrome 11.30 am – 12.30 pm Prof. Antonio RAUSELL IMAGINE, Paris, France Bioinformatics and functional genomics of human immune diseases: from genome analysis to single-cell transcriptomics 2 - 3 pm Prof. Jacques BECKMANN SWISS BIOINFORMATICS INSTITUTE, Lausanne, Switzerland Evidence-based precision medicine in the context of big data 5 - 6 pm On Behalf of RSG Belgium and IB2, Guillaume, Andrea and Bart

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