- BBClist - maillist.psb.ugent.be

ALLBIO training workshop - Analysing thousands of bacterial genomes
by Jacques van Helden 28 May '14

28 May '14

================================================================ ALLBIO training workshop Analysing thousands of bacterial genomes: gene annotation, metabolism, regulation ================================================================ ALLBIO training workshop – Marseille, June 23-25, 2014 Practical info -------------- Registration, schedule, details: http://www.allbioinformatics.eu/doku.php?id=public:valid-ulb Organizer: Jacques van Helden <Jacques.van-Helden(a)univ-amu.fr> Dates: June 23-25, 2014 Location: Site de Luminy, Aix-Marseille Université (AMU), Marseille, France Expected participants: 20 Cost: 0€ Registration: before June 11, 2014 Motivation ---------- Sequencing technologies allow microbiologists to sequence, for a moderate cost, not only the genome of their favourite species, but a few dozens of related species, a collection of strains, and even to characterize inter-individual variations. The Ensembl Genomes resource contains over 10,000 completely sequenced genomes. The availability of such data requires new bioinformatics resources suited for annotating, querying and analysing multitudes of sequenced bacterial genomes in parallel. This training workshop will show how to combine several specialized bioinformatics resources to extract information about bacterial genes and their annotations (Ensembl Genomes), metabolism (MICROSCOPE), and regulation (RSAT). The course will be oriented towards comparative genomics, and give a perspective about advances that can be expected from the massive reduction of sequencing costs resulting from Next Generation Sequencing. The course will mainly be based on user-friendly Web interfaces. It will also include a basic introduction about the programmatic access to bioinformatics resources, showing by simple and well-documented examples how to automatize the collection of data, and extract information from multiple data sets. Target audience --------------- This course is addressed to microbiologists confronted to the need to use bioinformatics resources to analyse multiple genomes. Prerequisites ------------- The course does not require any computing skills. A basic knowledge of the Linux environment is welcome, but not required. Computer environment -------------------- The training room is equipped with Linux computers, but participants are welcome to bring their own laptop if they wish to work in their familiar environment. Contents -------- This training course will include - Short talks illustrating the functionalities offered by bioinformatics resources suited for the analysis of multiple bacterial genomes. - Practicals based on concrete study cases; * collecting multiple genomes from bacteria; * comparing annotations between different species; * extracting metabolic information for selected genomes; * metabolic projection: coverage of reference pathways by enzymes found in a genome; * phylogenetic profiling: detecting genes co-occurrences across genomes; * phylogenetic footprints: detection of conserved cis-regulatory elements. - Practicals on programmatic use of the tools: * extracting data for multiple genomes; * combining data from diverse sources. Teachers -------- Dan Staines European Bioinformatics Institute (EBI), UK Ensembl Genomes http://ensemblgenomes.org/ François LeFevre, Eugeni Belda, Claudine Médigue Genoscope (CEA), France MICROSCOPE http://www.genoscope.cns.fr/agc/microscope/ Jacques van Helden, Denis Puthier Aix-Marseille Université (AMU), France Regulatory Sequence Analysis Tools (RSAT) http://www.rsat.eu/ Funding ------- This training workshop is funded by the ALLBIO project (http://www.allbioinformatics.eu/) whose goal is to establish the link between bioinformatics and biologist communities who express uncovered needs for other fields than human genomics (microbial, plant, livestock). =================================================================

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International Chemical Discovery & Design Course, 16-27 June 2014, Nijmegen, NL
by Celia.vanGelder＠radboudumc.nl 27 May '14

27 May '14

International Chemical Discovery & Design Course, 16-27 June 2014, Nijmegen. We would like to draw your attention to the 10th annual International Chemical Discovery & Design Course (course website<http://www2.cmbi.ru.nl/groups/computational-discovery-and-design/icdd2014/>) which will be held from 16-27 June 2014 at the Radboud University Nijmegen. This course covers the recent advances in discovery informatics, with a focus on the application to real life problems. The course, combining practicals and lectures, will introduce and discuss different scientific concepts as well as providing an opportunity to gain practical experience using industry standard software. You can expect lectures and practicals on the following topics: * Introduction to Computational Discovery & Design * Comparative Protein Modelling * Sequence Retrieval, Analysis and Alignment Techniques * Computational Medicinal Chemistry; Molecular Descriptors & Library Design * The Application of Computational Drug Design to Real Life Problems * Molecular Docking and Virtual Screening * Advanced 3D Database Searches and Scaffold Hopping * QSAR and COMFA methods * Structure Based Drug Design Techniques Confirmed speakers: For the third time we were able to invite keynote speakers from the Netherlands and abroad. As experts in their field of research they will summarize the core message of the course in their presentations * Gerard JP van Westen, EBI, Hinxton, UK. ChEMBL: A large-scale open access bioactivity database for drug discovery and medicinal chemistry The course is targeted to MSc students, PhD students and post-docs. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Registration via email to Barbara van Kampen<mailto:barbara.vankampen@radboudumc.nl>. Please, provide information about your background and your motivation to participate in the course. The course is free. You should however pay for travelling and lodging expenses yourself. Best regards Tina Ritschel (CDD/CMBI/UMC Nijmegen) Celia van Gelder (CMBI/RUN & Netherlands Bioinformatics Centre) 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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SMBM 2014 - 6th International Symposium on Semantic Mining in Biomedicine
by José Luis Oliveira 23 May '14

23 May '14

** Call for Papers ** ** Apologies if you received multiple copies of this CFP. Please kindly forward to those who may be interested. ** Sixth International Symposium on Semantic Mining in Biomedicine (SMBM 2014) http://www.smbm.org October 6th and 7th, University of Aveiro, Portugal SMBM 2014 aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers active in biomedical ontology design and engineering, and the Semantic Web. The combined research helps to promote full integration of data and factual content from large text collections, biological databases, ontological and terminological resources, and from the Web. We are inviting papers from a full range of topics (see below), emphasizing in particular work on methods deployed in a production-like research environment, user-facing applications of text mining technology, the integration of text with domain resources such as content from reference databases (e.g., UniProt, EntrezGene, OMIM) and semantic resources such as GO, UMLS etc. We also welcome contributions from across the biomedical domains, including genomics, translational medicine, clinical practice, and public health. Topics of interest include (but are not limited to): • Development and use of biomedical semantic resources • Terminology and ontology development for biomedical information systems including terminology evolution • Integration of text and data mining in the biomedical domain • (Semantic) Web mining of biomedical information • Text mining, information extraction, and information retrieval for the biomedical domain • Evaluation techniques and standards for text mining solutions • Annotation schemes for biomedical corpora • Text mining for resource building, e.g. ontologies, and resource enrichment, e.g., biomedical databases • Representation and discovery of biomedical domain knowledge • Image/caption processing in relation to content extraction • Domain-specific reasoning processes, e.g., to infer non-explicit information, validation (trust-worthiness, believability, safety) of extracted information • Integration of text mining in biological database curation workflows All accepted papers will be published in the conference proceedings that will be available online. We invite three categories of papers: full research papers, short papers and system papers. Research papers will be given an oral presentation, short papers a poster presentation, and systems papers will be presented in systems demonstration sessions. System papers should describe an implemented system related to a topic of interest that the authors will demonstrate live during the symposium. The final modality of presentation will be decided by the organizing committee. Authors of selected papers will be invited to submit an extended version for publication in a special issue of the Journal of Biomedical Semantics (JBMS), an open-access journal published by BioMed Central (BMC). Submissions should follow the ACL instructions for authors, with a maximal limit of 8 pages. The recommended length for system papers and poster submissions is four (4) pages. Manuscripts will be submitted electronically as PDF files. Reviewing will be double-blind, and submissions should therefore NOT contain author names or other obviously identifying information. Important Dates • Full paper submission deadline: June 20th 2014 • Poster and system demonstration paper submission deadline: July 4th 2014 • Notification of acceptance for full papers: July 21st 2014 • Notification of poster and system demonstration papers: July 28th 2014 • Symposium dates: October 6-7th 2014 -- José Luis Oliveira on behalf of the SMBM 2014 program committee

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3rd RSG Belgium seminar
by Jurgen CLAESEN 20 May '14

20 May '14

Dear all, We are very pleased to announce the third RSG Belgium seminar. It will take place in *Antwerp* on Wednesday, the 28th of May 2014 from 14h to 17h. Program: 14h - 14h15 Welcome 14h15 - 15h Prof. dr. Kris Laukens (UA) - From supermarkets to living organisms: mining a world full of patterns. 15h - 15h30 Nolen Joy Perualila (UH) - Rationalizing connectivity map gene expression readouts via target prediction 15h30 - 15h45 BREAK 15h45 - 16h15 Bart Cuypers (UA) - DNA structure surrounding the transcription regulating Base J in *Leishmania*. 16h10-16h45 Martin Otava (UH) - Prediction of gene expression in humans using rat in vivo gene expression 16h45 - ... Reception and get together Place: Room G.016 Middelheim Campus building G Middelheimlaan 1, Antwerp For more information about RSG Belgium, please have a look at the following link: http://www.iscbsc.org/rsg/rsg-belgium Please diffuse this call to anyone who might also be interested in joining. Hope to see you there! Best Regards, RSG Belgium committee

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Postdoctoral computer scientist – vacancy at KU Leuven -
by mimi deprez 19 May '14

19 May '14

Dear Colleagues, We have currently one postdoctoral computer scientist vacancy at the department of ESAT/ STADIUS SymbioSys Center for Computational Systems Biology at KU Leuven. Please feel free to apply or forward this message to colleagues and groups who might be interested. Sincerely, Mimi Deprez on behalf of prof. dr. ir. Yves Moreau ========= Postdoctoral computer scientist – Kernel methods and network analysis for data fusion in chemobioinformatics University of Leuven ESAT-STADIUS SymBioSys Center for Computational Systems Biology In the framework of a collaboration with Janssen Pharmaceuticals, we are looking for a talented postdoctoral researcher to develop kernel methods that link drug targets, disease phenotypes, and pharmaceutical compounds. Leveraging large-scale public and in-house data sets, you will develop kernel methods and/or network-based methods to predict potential links between targets, diseases, or candidate drugs. This research builds upon the expertise of Janssen Pharma and previous work of our team on genomic data fusion. The research will be also carried out with a team of the University of Linz, Austria (Prof. Sepp Hochreiter) specialized in kernel learning and chemoinformatics. Genomic data fusion (Moreau and Tranchevent, 2012; Aerts et al., 2006) offers a range of approaches to tackle the challenge described above. Among such methods, the University of Leuven has pioneered the use of kernel methods to integrate heterogeneous omics data (De Bie et al., 2007; Yu et al., 2009). The key advantage of kernel methods for mining heterogeneous data is that when multiple data sets are available, they all lead to kernel similarity matrices independently of the original type of data. Those kernels can then be efficiently integrated using Multiple Kernel Learning (De Bie et al., 2007; Yu et al., 2009). Similarly, our team has developed network analysis methods using kernel diffusion to identify potential targets of a drug. The goal of the project is to refine and generalize these methods to the complex and large-scale data sets available at a major pharmaceutical company. The STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics at KU Leuven is an academic research center, with a research focus on mathematical engineering, where mathematical tools from numerical linear and multi-linear algebra, statistics and optimization are used for applications of dynamical systems and control, signal processing, data modeling and analytics. The project is embedded within the SymBioSys Center for Computational Systems Biology, a universitywide center aiming at linking genomic variation to disease, and within the Exascience Life Lab, a major collaboration on scaling up genomic data analysis methods at exaflop scale. The University of Leuven is one of Europe’s leading research universities, with English as the working language for research. Leuven lies just east of Brussels, at the heart of Europe. PROFILE The ideal candidate holds a PhD degree in computer science or computational biology. Experience with machine learning, in particular kernel methods, is a core asset. Ability to develop powerful machine learning algorithms and scale them up to large data sets is essential. Capacity to plan and deliver on time, as well as strong communication skills, are important to manage a successful collaboration with our pharmaceutical and academic partners. A two-year commitment is expected from the candidate. Preferred start date is July 2014. RELEVANT PUBLICATIONS Moreau Y, Tranchevent LC. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet. 2012 Jul 3;13(8):523-36. Yu S, Falck T, Daemen A, Tranchevent LC, Suykens JA, De Moor B, Moreau Y. L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics. 2010 Jun 8;11:309. De Bie T, Tranchevent LC, van Oeffelen LM, Moreau Y. Kernel-based data fusion for gene prioritization. Bioinformatics. 2007 Jul 1;23(13):i125-32. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006 May;24(5):537-44. Laenen G, Thorrez L, Börnigen D, Moreau Y. Finding the targets of a drug by integration of gene expression data with a protein interaction network. Mol Biosyst. 2013 Jul;9(7):1676-85. HOW TO APPLY (Publication date of the vacancy: May 15, 2014) Please send in PDF at your earliest convenience: 1. CV including education, research experience, and bibliography 2. Three references (with phone and email) 3. A statement of purpose describing why you are qualified for the position and what your contribution could be to Mrs. Mimi Deprez (mimi.deprez(a)esat.kuleuven.be) cc Prof. Yves Moreau (yves.moreau(a)esat.kuleuven.be) and Ms. Ida Tassens (ida.tassens(a)esat.kuleuven.be) Pre-application inquiries can be sent to Yves.Moreau(a)esat.kuleuven.be. URL: http://www.kuleuven.be/bioinformatics Mimi Deprez Project Coordinator KU Leuven - University of Leuven Dept. Elektrotechniek-ESAT-STADIUS (STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics) iMinds Department Medical Information Technologies t:+ 32 (0) 16 32 85 55 m: + 32 476 72 68 59 Kasteelpark Arenberg 10, bus 2446 B-3001 Leuven http://www.esat.kuleuven.be http://www.kuleuven.be/iMinds/ > > ============

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Registration open! - NBIC/BioSB course Comparative Genomics, 2-6 June 2014
by Celia.vanGelder＠radboudumc.nl 18 May '14

18 May '14

NBIC/BioSB Course Comparative Genomics: from evolution to function (2nd edition) - Registration open! Date: June 2 - June 6, 2014 Location: VU University, Amsterdam, the Netherlands Course coordinators: Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (NBIC/BioSB, education(a)biosb.nl<mailto:education@biosb.nl>) Course website: http://biosb.nl/comparative-genomics-2014/ Registration: http://biosb.nl/education/enrollment-comparative-genomics/ More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes. The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of more sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements. Target audience The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species. Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. Programme Monday June 2: Distant homology and protein domains (lecturer Jaap Heringa) Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction Tuesday June 3: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam) Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization Wednesday June 4: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel) Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission Thursday June 5: Genome duplications (lecturer Berend Snel) Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart Friday June 6: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen) Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands 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. 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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CFP: WCB'14, The 10th Workshop on Constraint-Based Methods for Bioinformatics
by Nicos Angelopoulos 15 May '14

15 May '14

------------------------------------------------------------ CALL FOR PAPERS ------------------------------------------------------------ WCB 2014 10th Workshop on Constraint-Based Methods for Bioinformatics http://cp2014.a4cp.org/workshops/bioinfo14 Co-located with 20th International Conference on Principles and Practice of Constraint Programming September 8 2014, Lyon, France ------------------------------------------------------------ Technical Description --------------------- During the last years, Biology has become a source of challenging problems for the entire field of Computer Science in general, and for the areas of computational logic and constraint programming in particular. Successful approaches to these problems are likely to have significant applications in several fields of research, such as medicine, agriculture, industry, etc. Several successful applications of the Logic and Constraint Programming paradigms in Bioinformatics have been carried out in the last years, in the area of phylogenetic tree reconstruction, in haplotype inference, in proteins structure prediction, in RNA secondary structure prediction, and in system biology, just to cite a few. The workshop aims at exchanging ideas between researchers and collecting, if possible, new problems to be faced in the next future by our community. Workshop Format --------------- WCB'14 is the 10-th of a series of consecutive Workshops on Constraint-Based Methods for Bioinformatics. Previous editions of WCB were co-located with various important international conferences, as reported below: - WCB'05: co-located with ICLP-CP 2005 in Sitges - WCB'06: co-located with CP 2006 in Nantes - WCB'07: co-located with ICLP 2007 in Porto - WCB'08: co-located with CPAIOR 2008 in Paris - WCB'09: co-located with CP 2009 in Lisbon - WCB'10: co-located with FLOC 2010 in Edinburgh - WCB'11: co-located with CP 2011 in Perugia - WCB'12: co-located with ICLP 2012 in Budapest - WCB'13: co-located with CP 2013 in Uppsala Details about last-year WCB'13 can be found at http://cp2013.a4cp.org/workshops/wcb Paper Submission ---------------- The topic of interest are all those concerning bioinformatics and constraints and related (SAT/ASP/Logic Programming/ILP) techniques, such as: - RNA prediction and motif search - protein structure and functional prediction - genetic linkage analysis and haplotype inference - pedigree reconstruction and diagnosis - genomic selection design - gene regulatory network inference and analysis - biochemical network simulation and visualization - solvers for problems in biology - metabolic pathway analysis - DNA sequence assembly - contig scaffolding - multiple sequence alignment - machine learning and big data - ontologies - constraint databases - logical interfaces to relational databases - web services - databases integration and federation - RDF graphs and tools Submitted papers can be: - Full papers describing new research results - Extended Abstracts concerning original (unpublished) results. - Abstracts describing ongoing work. - System descriptions (with demos at the workshop). - Summaries of already accepted or recently published papers/results. - Well-motivated proposals of bioinformatics problems for constraint based methods. Submitted papers should be 3-15 pages long in the LNCS format. Submissions are managed through EasyChair https://www.easychair.org/conferences/?conf=wcb14 Important dates --------------- - Paper Submission Dealine June 30 - Notification to Authors July 28 - Final Version August 18 - Workshop Date September 8 Invited Speaker --------------- - Graham Kemp, Chalmers University, Sweden Workshop Organizers ------------------- - Nicos Angelopoulos, Imperial College, London, UK - Simon de Givry, MIAT INRA, Toulouse, France Program Committee ----------------- - Pedro Barahona, Universidade Nova de Lisboa, Portugal - Alexander Bockmayr, Freie Universitat Berlin, Germany - Mats Carlsson, SICS AB, Uppsala, Sweden - Agostino Dovier, Universita degli Studi di Udine, Italy - Francois Fages, INRIA Paris-Rocquencourt, France - Arun Konagurthu, Monash University, Australia - David Lesaint, University of Angers, France - Ines Lynce, INESC-ID, Lisbon, Portugal - Nigel Martin, Birkbeck College, UK - Chris Mungall, Lawrence Berkeley National Laboratory, CA, USA - Alessandro Dal Palu, Universita degli Studi di Parma, Italy - Enrico Pontelli, New Mexico State University, USA - Sylvain Soliman, INRIA France - Sebastian Will, University Leipzig, Germany - Matthias Zytnicki, MIAT INRA, Toulouse, France

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REMINDER: The 4th VIB International PhD Symposium - VIBes in Bioscience 2014
by Şule Yılmaz 15 May '14

15 May '14

Dear Pre-docs, We are happy to remind you about the event “VIBes in Biosciences 2014”, a symposium which aims to bring together Ph.D. candidates from different areas of life sciences. This symposium is organized to stimulate networking, listen to renowned speakers, including a Nobel laureate, and transfer skills through workshops.** As you probably already know from our previous e-mail, the symposium will take place *from* *17 to 19 September 2014* in the Horta venue in *Antwerp, Belgium.* For the practical info on speakers visit our website: www.vibes2014.org <http://www.vibes2014.org> The *Registration *is now open!*PhD students can benefit from a reduced early-bird registration fee for two more weeks only (until 1 June)!* The final registration deadline is 31 July. You simply cannot miss the scientific event of the year! You can register here: http://vibes2014.org/registration.html. Check out our YT movies: https://www.youtube.com/watch?v=1LicxBaOXQ0 https://www.youtube.com/watch?v=mI43rwJUC6A&feature=youtu.be! With kind regards, The VIBes 2014 Organizing Committee Liesbeth Aerts, Özden Akay , Alice Borghi , Michaela Conrad, Sylvester Holt, Nevena Hristozova, Michal Janiak, Michiel Krols, Marie Lork, Laura Meloni, Esther Meersman, Raffaele Mori, Ehsan Sabaghian, Karolina Slowicka, Giel Tanghe, Kevin Titeca, Niels Vandamme , Lana Vandersarren, Tessa Vermeire, Elke Ydens and Şule Yılmaz -- Şule Yılmaz Junior researcher, Ph.D. student Computational Omics and Systems Biology Group Department of Medical Protein Research Universiteit Gent - VIB A. Baertsoenkaai 3 B9000 Gent Belgium Tel: +32-92649359 Fax: +32-92649484

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From NGS to mutation to structural interpretation - Course 3-4 June Nijmegen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 15 May '14

15 May '14

The effects of a mutation on protein structure and function >From NGS to mutation to structural interpretation Date: June 3-4, 2014 Location: CMBI, UMC Radboud, Nijmegen, the Netherlands Course teachers: Gert Vriend (CMBI), Hanka Venselaar (CMBI) Course website & registration: http://swift.cmbi.ru.nl/gv/NGS . More information: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> Course description Much research in NGS human DNA diagnostics labs is aimed at determining mutations causal for disease states. Many journals these days do no longer publish such studies unless accompanied from at least a computational prediction of what the mutation does to the protein in terms of its structure and function. This two day course aims at generating a level of understanding of the relation between protein structures, amino acids, and function. After the course the participants will be able to understand the output of compute servers that predict the structural and functional effects of mutations in proteins with known structure (or for which the structure can be predicted with homology modelling). The users will also be able to perform elementary visual inspections of protein structures with and without mutations using the YASARA software (that is free and runs on all computers). During the course we will work with the YASARA visualizer and the HOPE mutation effect prediction software (http://www.cmbi.ru.nl/hope/ ). The educational material and the seminars will be sufficiently general, though, to be applicable to other computational tools too. Target audience The course is meant for novices in the protein structure field. As prior knowledge we expect that people have some minimal knowledge about amino acids, have an idea about how to operate BLAST, and can use a browser. Course programme The course website, including the full course programme, can be found at : http://swift.cmbi.ru.nl/gv/NGS Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands 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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Bioinformatician position (Thomson-Reuters)
by Patrice Godard 14 May '14

14 May '14

Hi Thomson-Reuters is looking for a Bioinformatian in Europe. Here is the description of the position: http://jobs.thomsonreuters.com/job/London-Research-Scientist-2C-Bioinformat… Could you forward this job offer please? Many thanks Kind regards Patrice Godard

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