February 2012 - BBClist - maillist.psb.ugent.be

(no subject)
by Nicolaes G (BIOCH) 10 Feb '12

10 Feb '12

Dear , I would like to post of job opening on the BCC list, the text is as follows: Structural Bioinformatician (M/F) - POSTDOC student position - 3 years Within the 3D structure-function group, part of the department of Biochemistry at the Cardiovascular Research Institute Maastricht (CARIM, Maastricht University), Main research Area I (Thrombosis and Haemostasis) there is a position for a Postdoc (m/f). The research group focuses on the implementation of structural bioinformatics techniques within the research infrastructure of the cardiovascular research that is currently being performed. Main topics of the group include protein modeling, molecular dynamics simulations, protein-protein docking, docking of small molecules (virtual ligand screening) and peptides onto relevant targets. The current project concerns the in silico drug design, using both small molecules and peptides and is performed under the supervision of Dr. Gerry Nicolaes in collaboration with other principal investigators. The group of Dr. Nicolaes has a main focus on the structure-function study of proteins, involved in thrombosis, bleeding, inflammation or atherosclerosis and provides an active input in other research areas within CARIM. Within our group we have a vacancy for an enthusiastic Postdoc (m/f). Suitable candidates should have a background in the biological, biochemical, pharmaceutical or medical sciences with a strong track record in structural bioinformatics and will be experienced in the use of molecular modeling packages, docking approaches and virtual ligand screening. The postdoc will be stationed at the Biochemistry department, which is composed of ~60 people, staff and students. Ability to speak, write and understand English fluently is a prerequisite and ability to speak Dutch will be considered an advantage. You will be responsible for the generation, processing, analysis and storage of data generated and drive the development of new approaches to the common research objectives. You are a team player, with good social skills working in collaboration with Dr. Nicolaes as well as with 3 PhD students. Our group has a close collaboration with the group of Dr. B. Villoutreix (INSERM U648, Paris, France) in the field of structural bioinformatics as well as with that of Prof. Vriend (CMBI, Nijmegen, the Netherlands). Salary will be according to standard Netherlands University Grades (depending on skills and experience); a moving allowance will be provided up to a maximum. An evaluation will be made after 1 year and upon positive outcome of the evaluation, the position may be extended for another 2 years. Maastricht is the most Bourgundic city in the Netherlands, being situated in a so-called Euregio with distances to Liège (French speaking part of Belgium) of 25 km and Aachen (Germany) of 35 km and good connections to the Thalys train. You may send a CV, with the names and addresses of two referees and a covering letter to Dr. G. Nicolaes, Department of Biochemistry, Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands. Tel: +31-43-3881688 For further information on the research topic contact Dr. G.A.F. Nicolaes G.Nicolaes(a)maastrichtuniversity.nl<mailto:G.Nicolaes@maastrichtuniversity.nl> http://www.carimmaastricht.nl/ www.unimaas.nl/3dstructure-function<http://www.unimaas.nl/3dstructure-function> For your convenience, I also included the text as a MS Word file, should you be needing that, Thanks for posting it! Regards, Gerry Nicolaes [cid:image001.jpg@01CCE7DB.D9C740F0] Gerry Nicolaes, PhD Senior Researcher Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.unimaas.nl/3dstructure-function [cid:image002.jpg@01CCE7DB.D9C740F0]Please consider your environmental responsibility before printing this e-mail.

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Job opening (postdoc): Epigenomic analyses within nation-wide functional genomics initiative (Leiden, The Netherlands)
by B.T.Heijmans＠lumc.nl 07 Feb '12

07 Feb '12

Epigenomic analyses within nation-wide functional genomics initiative Bioinformatician (postdoc), Leiden University Medical Center, The Netherlands Apply before February 27, 2012 at www.academictransfer.com/11762<http://www.academictransfer.com/11762> Job description As bioinformatician/postdoc you will analyze genome-wide DNA methylation profiles of 4000 individuals and link them to genetic, transcriptomic and phenotypic variation within a nation-wide functional genomics infrastructure to gain mechanistic insights into complex disease phenotypes. The project Recently, a high-profile €2M project was initiated to establish a nation-wide functional genomics infrastructure. The overall aim of the project is two-fold: (1) to gain insight in the mechanisms through which genetic variants identified in GWASs contribute to complex disease phenotypes and (2) to improve the classification of high-risk individuals by developing integrated genomic risk factors incorporating genetic, epigenomic and transcriptomic data. To this end, transcriptome (RNA-seq) and DNA methylome (Illumina 450k Chips and whole genome bisulfite sequencing) data will be generated in 4000 samples selected from in-depth characterized Dutch biobanks with GWAS and whole genome sequencing data. Hence, you will have the opportunity to work on a unique data set obtained with state-of-the-art technology and of unprecedented scale providing a platform for comprehensive and powerful analyses. As a bioinformatician/postdoc you will be responsible for the analyses in the epigenomics work package. This entails implementing a pipeline for the processing and analysis of 450k methylation data and creating genome-wide catalogs of genetic variation influencing DNA methylation (mQTLs) and DNA methylation influencing transcription. Moreover, your work will involve the execution of epigenome-wide association studies (EWASs) and the integration of 450k data with whole genome bisulfite sequencing data. The project is a collaborative effort and you will work with experts on functional genomics and biobank research in The Netherlands, including three other bioinformaticians/postdocs working on the other work packages. The project offers an excellent opportunity to develop an extended network and your successful role in project can be expected to result in good prospects for continuation of your career at a high level. Your research will be embedded within The Netherlands hub of the Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). For a background on the project, read the article in BBMRI-NL newsletter (see http://tinyurl.com/fungenomics, page 2). Requirements You hold a PhD (preferred) or Masters degree in bioinformatics or biostatistics with a focus on solving biological research questions. You have a strong background in the analysis and interpretation of high-dimensional data as evidenced by publications in peer-reviewed journals, you are an efficient programmer in various languages for the analysis of such data and you have shown to effectively collaborate with researchers from other disciplines. Experience with the analysis of Illumina 27k/450k methylation data, micro-array/RNA-seq data and/or high-throughput bisulfite sequencing data is recommended. Conditions of employment You will be employed on the basis of a 36-hour week for a period of two years. Your salary will, depending on experience, be maximum € 3,899 gross per month based on a full time position (scale 10 of the Collective Labour Agreement for University Hospitals). Contract type: Temporary, Appointment for two years. Additional information You can find the extended vacancy text on http://www.lumc.nl/home/0004/23583/80611011354221/1110280250005720?internal…. If you have any questions, or if you want more information about this position, please contact Dr. Bas Heijmans, principal investigator, telephone +31 (0)71 526 9785. Or by e-mail: bas.heijmans(a)lumc.nl.

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MLG Seminar : Structure, Unstructure and Alternative Splicing
by Tom Lenaerts 06 Feb '12

06 Feb '12

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ULB Machine Learning Group (MLG) S E M I N A R %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Apologies for cross-postings. Please send it to interested colleagues and students. Thanks! Title: "Structure, Unstructure and Alternative Splicing" by: Dr. Philip Kim, The Donnelly Centre for Cellular and Biomolecular Research Banting and Best Department of Medical Research Departments of Molecular Genetics and Computer Science University of Toronto http://www.kimlab.org http://www.thedonnellycentre.utoronto.ca When: 22 February 2012 at 16:00 (until 17:30) Where: Building NO, Sale Solvay (5th floor in the rotule) Université Libre de Bruxelles Boulevard du Triomphe 1050 Bruxelles Campus access : http://mlg.ulb.ac.be/access Abstract: Many protein interactions, in particular those in signaling networks, are mediated by peptide recognition domains. These recognize short, linear amino acid stretches on the surface of their cognate partners with high specificity. Residues in these stretches are usually assumed to contribute independently to binding, which has led to a simplified understanding of protein interactions. Conversely, in large binding peptide data sets different residue positions display highly significant correlations for many domains in three distinct families (PDZ, SH3 and WW). These correlation patterns reveal a widespread occurrence of multiple binding specificities and give novel structural insights into protein interactions. For example, a new binding mode of PDZ domains can be predicted and structurally rationalized for DLG1 PDZ1. While protein structure is very important for peptide binding domains, the regions they bind are usually unstructured (intrinsically disordered). These regions are widespread, especially in proteomes of higher eukaryotes, and have been associated with a plethora of different cellular functions. Aside from general importance for signaling networks, they are also important for such diverse processes as protein folding or DNA binding. Leveraging knowledge from systems biology can help to structure the phenomenon. Strikingly, disorder can be partitioned into three biologically distinct phenomena: regions where disorder is conserved but with quickly evolving amino acid sequences (flexible disorder), regions of conserved disorder with also highly conserved amino acid sequence (constrained disorder) and, lastly, non-conserved disorder. I will also introduce new efforts to map protein interactions affected by alternative splicing. Speaker:Dr. Philip Kim is Associate professor at University of Toronto (The Donnelly Centre for Cellular and Biomolecular Research) where he has set up a research group investigating protein interaction and genetic variation His group has pioneered some integrative approaches combining structural and systems knowledge (see Kim et al. Science 2006), as well as methodologies from genetics and network biology (see Kim et al. PNAS 2007), in an active attempt to bring genetic and protein biophysical research closer together. He has also played an import role in the understanding of specificities of the modular domains typically found in proteins. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MLG http://mlg.ulb.ac.be/ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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BeneLearn and PMLS 2012: Call for Abstracts and Full Papers
by Willem Waegeman 05 Feb '12

05 Feb '12

(Apologies for multiple postings) BENELEARN 2012 -- PMLS 2012 The 21st annual Machine Learning Conference of Belgium and The Netherlands Workshop Predictive Modeling for the Life Sciences www.benelearn2012.ugent.be <http://www.benelearn2012.ugent.be> May 24th and 25th, 2012 Ghent University, Belgium Call for Abstracts and Full Papers 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 21st edition of the annual Belgian-Dutch Conference on Machine Learning (BeneLearn) will be organized in Ghent, in conjunction with a workshop on Predictive Modeling in Life Sciences (PMLS). This year we have chosen for a two-day program to showcase the use of predictive modeling in the life sciences. This is in part motivated by the increasing focus on applicability of scientific research. The joint event takes place on the 24th and 25th of May 2012 at the Faculty of Bioscience Engineering of Ghent University. It is organized by the research unit Knowledge-based Systems (KERMIT). Scope We invite the submission of abstracts or full papers on all aspects of machine learning and related disciplines, including, but not limited to Kernel Methods Bayesian Learning Case-based Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Hybrid Learning Systems Graphical Models Inductive Logic Programming Knowledge Discovery in Databases Online Learning Web/Link Mining Learning in Multi-Agent Systems Learning in Dynamic Domains / Data Streams Multi-Strategy Learning Neural Networks Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Multi-task and Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Prediction / Learning from Multi-Label Data Learning for Language and Speech Image, Video, Audio and Text Analysis Applications of Machine Learning Learning and Ubiquitous Computing In addition to theoretical and applied work in machine learning in general, we warmly welcome applications for the PMLS workshop, in areas such as: Bioinformatics Medicine / Biomedical Engineering Systems Biology / Microbiology Chemometrics / Computational Drug Discovery Ecology / Environmental Sciences Agriculture and Soil Management Food Sciences Geographical Information Systems Weather and Climate Forecasting Submission One can submit full papers up to 6 pages or one-page abstracts. Full papers need to report original, unpublished work and they are meant for researchers that prefer to obtain an official publication via BeneLearn, including feedback from the program committee. Abstracts can also concern work in progress and past published work, if the precise references to the original publication are mentioned. This way we aim to provide the same broad overview as in previous years, and make it attractive and easy to attend by both senior as well as junior researchers, from both academia and industry. To attract as many people as possible, registration fees will be low and three international speakers are invited for a keynote talk. We consider a single submission procedure for the main conference and its satellite workshop. The program committee will make a selection for oral presentations among abstracts and full papers to ensure a program that has academic quality but is also interesting and inspiring for the attendees. The remainder of the submissions will be presented during a poster session and poster spotlight presentations. Abstracts and papers should be submitted electronically, no later than Friday March 2nd, 2012. Notification of acceptance is on Friday April 6th. Please follow the guidelines that are mentioned on our website: http://www.benelearn2012.ugent.be/submission.php During submission authors will be able to indicate their preference for an oral or a poster presentation. Submissions that concern an application in the life sciences will be considered for PMLS, all other submissions will be considered for the main conference day. Organizing Committee Bernard De Baets, Michaël Rademaker, Willem Waegeman (UGent) Bernard Manderick (VUB)

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NGS course
by Martie Verschuren 03 Feb '12

03 Feb '12

Dear reader, We organise an international shortcourse on next generation sequencing in Breda in March. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in BReda Best regards Martie C.M. Verschuren Avans university of applied science p.o. box 90116 4800 RA Breda The Netherlands --------------------------------------------------------------------------- Op deze e-mail zijn de volgende voorwaarden van toepassing: The following conditions apply to this e-mail: http://emaildisclaimer.avans.nl ---------------------------------------------------------------------------

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NSBM Spring Meeting April 25th CALL FOR ABSTRACTS
by Barbara van Kampen 02 Feb '12

02 Feb '12

NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Spring Meeting April 25th 2012 in conjunction with the Netherlands Bioinformatics Conference 2012 Venue: Congrescentrum De Werelt, Lunteren CALL FOR ABSTRACTS The NSBM cordially invites you to visit its spring meeting, which is being held in conjunction with the Netherlands Bioinformatics Conference 2012. During the parallel session, the floor will be given to PhD students and post-docs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC 2012 activities and visit key note lectures by Gerard Kleywegt of the European Bioinformatics Institute, Cambridge and by Dorus Gadella, of the Centre for Advanced Microscopy (CAM) at the University of Amsterdam. Abstract Format Abstracts should be limited to a maximum of 10 lines, with 12-pt font and single-spaced text, giving a short description of the research done. Please include a title in bold. The name(s) and affiliation(s) of the author(s) should follow the title. The opportunity will be given to present a poster, though this is not mandatory. If you wish to present a poster, please indicate so. Abstract Submission All abstracts, also for those who already registered for the NBIC meeting, should be submitted electronically in MSWord via e-mail attachment to g.nicolaes(a)maastrichtuniversity.nl The deadline for receipt of all abstracts is April 15th 2012. Selected candidates will be notified no later than April 18th 2012. Presentations will be 20 min, including a 5 min discussion. Starting PhD students are particularly encouraged to present their research. For questions regarding the abstract or meeting please contact Gerry Nicolaes, +31-(0)43 3881688, g.nicolaes(a)maastrichtuniversity.nl Registration Registration can be performed through the NBIC site at: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/registr… The 1-day conference fee amounts €62,50 for NBIC members and € 75,- for non-NBIC members and includes participation to the conference and poster sessions on April 25th, lunch, coffee/tea during breaks, internet access. Should a lack of funding be a hurdle for visiting the NSBM Spring Meeting, please contact prof. Gert Vriend at vriend(a)cmbi.ru.nl so that an arrangement can be made. Topics for presentations may include, but are not limited to: • Computational Biology and Bioinformatics • Computer-aided drug design • Drug design and drug discovery • Grid computing • Homology modelling • Molecular and supramolecular dynamics • Molecular modeling and simulation • Mutational analysis • Protein crystallography • Protein NMR • Protein structure analysis • Protein structure prediction • Protein-protein interactions • Protein-small molecules interaction • Protein software design • Proteomics • Structural bioinformatics • Structure-function analysis • Text mining & information extraction • Virtual screening Links http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/program… -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

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