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

Announcement, Utrecht Bioinformatics Center Annual Symposium: Keith Baggerly
by Breukelen, B. van (Bas) 13 Sep '16

13 Sep '16

On Monday October 3rd 13:00 till 18:00 there will be the Utrecht Bioinformatics Center Annual Symposium Don't miss this event and register today. This symposium is free of charge. Location: Zaalverhuur 7, Boothstraat 7, 3512 BT Utrecht<http://ubc.us12.list-manage1.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> Register at: ubc2016.eventbrite.com<http://ubc2016.eventbrite.com> Keynote speaker, Keith Baggerly research interests involve the analysis of high-throughput biological data, and centers on themes of experimental design and reproducible research. He is best known as a practitioner of "forensic bioinformatics", where raw data and reported results are used to reconstruct what the methods must have been. He has been the leading investigator exposing the flaws and shortcomings of research performed by Anil Potti at Duke university. In the end, this has led to the retraction of four high-profile publications from Duke and shutdown of three clinical trials using these results. Prof. Baggerly is a strong advocate of sharing all data and code and having appropriate data manageme! nt plans t o ensure that research results are reusable and reproducible. The title of his talk is: When is Reproducibility an Ethical Issue? Genomics, Personalized Medicine, and Human Error Moreover we will have three more great talks by: * Bernd Helms<http://ubc.us12.list-manage1.com/track/click?u=02d188b181bc253cd9b1e5c1b&id…> (Veterinary Medicine, Utrecht University), “Lipidomic analysis reveals dynamic fluxes in lipid storage organelles of liver cells” * Lodewyk Wessels<http://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id=…> (Dutch Cancer Institute), Molecular networks and therapy response. * Rob de Boer<http://ubc.us12.list-manage.com/track/click?u=02d188b181bc253cd9b1e5c1b&id=…> (Theoretical Biology and Bioinformatics, Utrecht University), Simple models and complicated bioinformatics to study diverse T cell repertoires. Programme: * 13:00 - 13:15 Registration and coffee * 13:15 - 13:30 Welcome by Prof Berend Snel, chair of the UBC: UBC progress report * 13:30 - 15:00 Talks by, Bernd Helms, Lodewyk Wessels and Rob de Boer * 15:00 - 15:30 Coffee / Tea * 15:30 - 16:15 Keynote speaker: Keith Baggerly (MD Anderson Cancer Center, The University of Texas) * 16:15 - 18:00 Reception with drinks and snacks We hope you to see you at the symposium, And with kind regards, The Utrecht Bioinformatics Center

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Job offer - engineer, Ph.D. student or Post Doc in bioinformatics (Laboratory of cancer epigenetics)
by mbizet 13 Sep '16

13 Sep '16

Dear all, The laboratory of cancer Epigenetics (head: Pr. F. Fuks) is searching for a bioinformatician to join their team. See descriptions below (and in attachment). Job description: ---------------- A position is available for highly motivated bioinformatician that wishes to join the Laboratory of Cancer Epigenetics headed by Prof. François Fuks (ULB-Cancer Research Center, Brussels). The candidates will use and adapt bioinformatics tools in order to analyze transcriptomic and epigenomic changes (e.g. DNA methylation, histone and RNA modifications) that arise in cancers. Particularly the analysis of a novel epigenetic modification, which our lab recently investigated, using next generation sequencing data, will also be one of his/her task (Delatte et al., Science 2016). The candidates will experiment the analysis of many different types of very up-to-date high throughput technologies (Infinium, ChIP-Seq, RNA-Seq and the very recent RIP-Seq technology) coming from a wide range of biological data (cancer cell lines, embryonic stem cells, patients tissues, …). 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 candidates will join other experienced bioinformaticians working on transcriptomics and epigenomics, and in particular he/she will work closely with the group of Dr. Matthieu Defrance at the “Interuniversity Institute of Bioinformatics in Brussels“ (http://ibsquare.be) Profile/Starting date: ---------------------- Three profiles can apply: * A candidate that 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) can postulate as bioinformatician engineer. * A candidate that 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) can also postulate as Ph.D. student. The main subject of the thesis will be defined with the candidate. * A candidate that hold Ph.D. in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics and programming (e.g. R, python) can postulate for a Post Doc position. Experience with sequence data, genome-wide data sets (e.g. ChIP-Seq, RNA-Seq ...) or massive datasets analysis will be assets for both positions. The applicants should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. 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. Both positions are funded for 2 years, with possible extension. 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 for PhD applicant) 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: ---------------------- - Delatte et al. Science 2016 - Boumahdi et al. Nature 2014 - Deplus et al. Cell Rep. 2014 - Dedeurwaerder*, Defrance* 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*, Defrance* et al. Epigenomics 2011 - Fuks F. Nature 2010 - Villa et al. Cancer Cell 2007 - Viré et al. Nature 2006 --- Bizet Martin Laboratory of Cancer Epigenetics

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[Gtpb] NEW Deadline: GTPB Bioinformatics Training course announcement/reminder - Precision Medicine - PM16
by Pedro L. Fernandes 13 Sep '16

13 Sep '16

NEW Deadline for Applications - September 19th 2016 Honoring the requests from people that happened to be away in August. A few seats are still available. 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. IMPORTANT DATES for this Course Deadline for applications: Sept 19th 2016 Course dates: Sept 27th - Sept 30th 2016 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 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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FW: Program sympoisum and workshop MRS and Systembiology
by Jeneson, JAL (med) 12 Sep '16

12 Sep '16

Dear colleges, We have finalized the program for the symposium and workshop about combining Systems biology and in vivo Magnetic Resonance, that will hopefully result in new ideas and collaborations! Please find the program below and attached a poster for advertisement. We kindly ask you to distribute the poster in your institutes and notify your co-workers about this event. Thank you in advance! Workshop "in vivo Magnetic Resonance and Systems Medicine, UMC Utrecht, October 3rd 2016 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, Professor of Medical 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 Medicine" Dan Beard, PhD, Carl J. Wiggers Collegiate Professor of Cardiovascular Physiology 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 12:30 - 13.30 Lunch 13:30 - 15:00 Afternoon break-out sessions: Oncology | Cardiovascular | Musculoskeletal | Liver 15:00 - 15:15 Coffee and tea 15:15 - 15:45 Wrap up of break-out sessions 15:45 Drinks Registration to the workshop is free. Just send an email to: mrsandsystembiology(a)gmail.com<mailto:mrsandsystembiology@gmail.com> before Monday September 19th. Please indicate your preferred afternoon breakout session. The organizers. - Jannie Wijnen, Jeanine Prompers and Jeroen Jeneson Jannie Wijnen, PhD [Beschrijving: cid:EEA90C32-0871-49FB-AB50-67779C278527@ds.umcutrecht.nl] Assistant Professor| Radiology University Medical Centre Utrecht | Room number Q 02 4311 | Internal Post E 01.132| Postbus 85500| 3508 GA UTRECHT T +31 (0)88 75 51353 | F +31 (0)30-2581098 | www.umcutrecht.nl<http://www.umcutrecht.nl/> ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. ________________________________ 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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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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