- BBClist - maillist.psb.ugent.be

postdoctoral position at NKI, Amsterdam
by Sach Mukherjee 24 Oct '11

24 Oct '11

Dear all, A postdoctoral position is available in my group at the NKI to work on computational modelling of signalling networks in cancer. We are a dry lab focusing on statistical modelling, but as well as candidates with a quantitative background, I am also keen to hear from candidates with a more biological background, as the ability to work at the interface between statistical modelling and signalling biology is valuable in this area. Further information is available at: http://www.nki.nl/Research/Career/Vacancies/Default/Postdoc_2011_133.htm Please direct informal enquiries to s.mukherjee(a)nki.nl. Best regards, Sach Mukherjee -- Dr Sach Mukherjee Group Leader The Netherlands Cancer Institute, Amsterdam Associate Professor Department of Statistics, University of Warwick, U.K. Email: s.mukherjee(a)nki.nl Phone: +31 20 512 9053 Fax: +31 20 512 9070

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by Celia van Gelder 17 Oct '11

17 Oct '11

*NBIC PhD course Protein Structures: production, prowess, power, promises, and problems * _Date:_ 31 Oct- 4 Nov 2011 _Course coordinator_: Gert Vriend _Location:_ Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/ _ _ _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ *Target audience//* The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. *Course Description //* In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. *Course topics * Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after follwing the course: 1) Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? 2) This enzyme converts mannose. Can I make is specificity broader? 3) This enzyme doesn't function in my in vitro assay. Should I add some ions? 4) I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? 5) This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? More information about the course programme can be found on:/ /http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/./ / *NBIC PhD School//* This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. *More information//* For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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BITS Workshop: Comparative Genomics in Eukaryotes
by Joachim Jacob 12 Oct '11

12 Oct '11

Dear, BITS kindly invites you to their workshop about Comparative Genomics in Eukaryotes. *WHEN* 25 November 2011 *WHERE* Technologiepark Zwijnaarde, Gent, Belgium *POSTER* http://dl.dropbox.com/u/18352887/Compgen_BITS.pdf *More info and registration on* http://www.bits.vib.be/compgen You are kindly invited to this workshop! During a whole-day hands-on session, you will learn to perform the basic steps of gene family analysis to construct a gene family phylogenetic tree, detect species-specific duplicates, study orthologs and identify synteny. We will also look into comparative sequence analysis to study promoter sequences and identify conserved regulatory elements. More on http://www.bits.vib.be/compgen. /Please feel free to pass this invitation on to interested parties!/ Have a nice day! BITS http://www.bits.vib.be

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CAMDA'11 Announcement
by Yves Moreau 12 Oct '11

12 Oct '11

On behalf of Simon Lin, chair of CAMDA'11 > > ------------------- > CAMDA'11 - ISMB Satellite Meeting, Vienna, 15-16 July 2011 -- > > www.camda.info > > Programme announcement & Call for Posters > > Dear colleague! > > We enthusiastically invite you to attend this year's conference on > > Critical Assessment of Massive Data Analysis (CAMDA) . > > which will be held 15-16 July 2011 in Vienna, Austria (www.camda.info) > > > The early registration discount for CAMDA/ISMB ends 3 June – book now if you want to join us! This year's exciting line up of keynote speakers includes Terry Speed (WEHI), John Storey (Princeton) and Stefano Volinia (Ferrera). See the full two-day programme for details on papers and events... > > CAMDA still accepts poster submissions (abstracts will be published in the conference proceedings). > > > CAMDA was founded in 2000 to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, such as for high-dimensional gene expression profiling. It aims to establish state-of-the-art analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a scientific community-wide contest, with everybody analysing the same data sets. Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569). Accepted contributions are presented through talks and posters, and the results and methods of the different analyses are discussed and compared at the conference. > > As a special focus this year, we consider the integrated analysis of a particularly rich structured data set that includes gene and miRNA expression, DNA SNPs, copy number variation, and methylation for about 500 matched samples. With the fast ongoing development of novel genome-wide experimental techniques (such as next generation sequencing), an assessment of how we can gain better insight from an integration of heterogeneous large-scale data is particularly topical. > > CAMDA was founded by Simon Lin and Kimberly Johnson at Duke University (Nature 411, 885. Nature 424, 610). In 2006 CAMDA became a roving conference, with recent venues including Valencia and Chicago. This year, we will host CAMDA in Austria. For the first time, the conference is run as an official Satellite meeting of ISMB/ECCB, providing further opportunities for interaction with colleagues at the conference. > > We can still accept suitable posters for presentations of recent topical work in the dedicated poster session. Poster abstracts are published in the conference proceedings. > > Please also distribute this announcement to other colleagues who might be interested. > > We look forward to seeing you in Vienna! > > > David Kreil (Boku) > Joaquin Dopazo (CIPF) > Simon Lin (Northwestern) > (chairs) > > > Submission of poster abstracts: open (accepted in order of submission) > Early registration closes: 3 Jun 2011 > CAMDA 2011 Conference: 15-16 Jul 2011 > ISMB/ECCB 2011 Conference: 17-19 Jul 2011

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Bioinformatician vacancy
by Patrice Godard 06 Oct '11

06 Oct '11

Dear all, May I draw your attention to the following vacancy at DNAVision (see attachment). Thank you Best regards Patrice -- Patrice Godard, PhD Bioinformatics manager DNAVision SA 25 Av. Georges Lemaître B-6041 Gosselies, Belgium + 32 (0)71 34 78 90 / fax: + 32 (0)71 34 78 79 patricegodard(a)dnavision.com http://www.dnavision.com

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by Celia van Gelder 27 Sep '11

27 Sep '11

*NBIC PhD course Protein Structures: production, prowess, power, promises, and problems * _Date:_ 31 Oct- 4 Nov 2011 _Course coordinator_: Gert Vriend _Location:_ Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/ _ _ _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ *Target audience//* The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. *Course Description //* In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. *Course topics * Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after follwing the course: 1) Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? 2) This enzyme converts mannose. Can I make is specificity broader? 3) This enzyme doesn't function in my in vitro assay. Should I add some ions? 4) I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? 5) This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? More information about the course programme can be found on:/ /http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/./ / *NBIC PhD School//* This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. *More information//* For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl. ** -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Seminar invitation of Complete Genomics
by Joachim Jacob 09 Sep '11

09 Sep '11

*** SEMINAR INVITATION *** Complete Genomics, a whole human genome re-sequencing service provider, and BITS, the VIB Bioinformatics Training and Services Facility, are pleased to invite you to a complimentary event including presentations from leading researchers. Discover how large-scale, accurate and affordable whole human genome sequencing helps researchers advance their understanding of the impact of genetic changes on cancer and other diseases. *** When *** Monday, October 3, 2011 10:00 a.m. -- 5:15 p.m. *** Where *** University of Leuven, Gasthuisberg Campus Pentalfa Auditorium Teaching and Research Building, Herestraat 4, 3000 Leuven, Belgium *** Flyer *** Download on http://dl.dropbox.com/u/18352887/VIB-Agenda.pdf *** Registration*** - Lunch and refreshments will be served. - Space being limited, please register today for this complimentary event: http://info.completegenomicsinc.com/VIB-October-2011.html *** About *** Complete Genomics is the complete human genome sequencing company that has developed and commercialized an innovative DNA sequencing platform. The Complete Genomics Analysis Platform (CGA^(TM) Platform) combines Complete Genomics' proprietary human genome sequencing technology with its advanced informatics and data management software. Complete Genomics offersthis solution as an innovative, end-to-end, outsourced service, CGA Service, which provides customers with data that is immediately ready-to-use for genome-based research. ================================================================= Please feel free to pass along this email to other colleagues who may be interested in learning about accurate and affordable whole human genome sequencing provided as a turnkey service.

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DSM03260 (Associate) Scientist Bioinformatics
by Roubos, Hans 25 Aug '11

25 Aug '11

DSM03260 (Associate) Scientist Bioinformatics DSM is looking for professionals with a PhD degree in Bioinformatics, Metabolic engineering or Bioprocess modeling. Preferably, you have experience in metabolic pathway modeling / engineering with applications to microbial strain development or fermentation processes. Furthermore, you are a multidisciplinary team player, who takes initiative with good communication skills. Personal skills like problem analysis, judgment, creativity, leadership, adaptability characterize your identity. Behaviors like engaging people, drive for results, customer focus, improve, innovate and change are essential to make this job a success. Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:565123209@25082011-2FC6] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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DSM03232 Scientist Biostatistics
by Roubos, Hans 25 Aug '11

25 Aug '11

DSM03232 Scientist Biostatistics DSM is looking for professionals with a PhD degree in (Bio)Statistics or Chemometrics. Preferably, you have experience in statistical processing of biological relevant data from high throughput screening campaigns or metabolomics research. Furthermore, you are able to translate a biological question to a statistical approach and are well capable to communicate even complex statistical results to novices in statistics using visualization techniques. You are a multidisciplinary team player, who takes initiative with excellent communication skills. Behaviors like engaging people, drive for results, customer focus, improve, innovate and change are essential to make this job a success. Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:953443309@25082011-2FBF] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Vacature Biostatistician Pronota - Zwijnaarde
by Vicky Aerts 24 Aug '11

24 Aug '11

Biostatistician Pronota is looking for a biostatistician to join its team working on biomarker validation studies. The ideal candidate is highly motivated and enjoys a challenging environment. He will be involved in Pronota's key programs and have the opportunity to contribute to cutting-edge projects. Profile: * You are driven by data analysis and have pride in delivery. * You like to work in a structured and evolving environment within a dynamic team. * You are familiar with modern statistical methods. Responsibilities: * QC/QA of high-throughput proteomics data. * Analysis of clinical and protein expression data for biomarker validation studies. Qualifications: * Master or equivalent degree in statistics. * Working knowledge of R. * An experience in life sciences would be an asset, but is not essential. To apply Please send your CV and motivation (with a reference to the position applied for) to info(a)pronota.com<mailto:info@pronota.com> tel: +32 (0)9 241 11 64 fax: +32 (0)9 241 11 69 Website: www.pronota.com<http://www.pronota.com> Vicky Aerts ________________________________ Pronota nv Management Assistant Technologiepark 4 9052 Zwijnaarde - BELGIUM- T +32 9 241 11 47 F +32 9 241 11 69 www.pronota.com<http://www.pronota.com/> ________________________________ Confidential Notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)pronota.com<mailto:info@pronota.com>

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