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    Archived pages: 141 . Archive date: 2012-07.

  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: .. Who and where.. Address.. Office.. Staff.. Students.. Bioinformatics and Medicine.. About.. Current.. Research.. Publications.. Collaborations.. Spin-offs.. Groups.. Comparative genomics.. Systems biology.. Bacterial genomics.. Computational drug discovery.. Protein Structure Bioinformatics.. Education.. Courses for students.. Courses for researchers.. Courses for teachers.. Webtutorials.. Mastertrack.. Information for.. Employees.. Guests.. Applicants.. Teachers.. Researchers.. HighSchool.. Services.. Bioinformatics services.. Cheminformatics services.. Jobs.. Tools.. Intranet.. Introduction.. Software.. ICDD2012.. CMBI.. Welcome to the Centre for Molecular and Biomolecular Informatics, the CMBI.. We do research and education, and provide services in bioinformatics and cheminformatics.. The five  ...   Bacterial genomics.. De Vlieg: Computational drug design.. Vriend: Protein Structure Bioinformatics.. Education: The CMBI is committed to a series of educational projects, ranging from high school to postgraduate courses and from a MSc-programme in Bioinformatics to international workshops.. Services: We maintain computational facilities, databases, and software packages in bioinformatics and cheminformatics.. The cheminformatics services are directly available at CMBI, many of the bioinformatics services are offered via the (inter-)national service platforms (NBIC, EBI, etc).. The CMBI hosts the central office of.. NBIC.. , the Netherlands Bioinformatics Centre.. Webmaster..

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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Mail address.. CMBI 260.. NCMLS, Radboud University Nijmegen Medical Centre.. PO Box 9101.. 6500 HB Nijmegen.. Visiting address.. Geert Grooteplein Zuid 26-28.. 6525 GA Nijmegen.. route 260.. Contact.. Tel: +31 (0)24 36 19390 (CMBI office; room 010).. Fax: +31 (0)24 36 19395.. Directions.. Please visit Information for Guests.. and.. Map of the Campus..

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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Visiting Address:.. CMBI, Radboud University Nijmegen-Medical Centre, NCMLS,.. Geert Grooteplein 26-28, route 260, Room 0.. 02.. Phone: +31 (0)24 36 19390.. Barbara van Kampen.. , assistant manager.. (Out of office on Wednesday).. Ellen Bos.. , secretary.. (Tue, Thu, Fri)..

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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Note: Telephone numbers stated are for internal use only.. External calls should be preceded by +31 24 36.. Name.. Group.. E-mail.. Room.. Phone.. Wynand Alkema.. 0.. 09.. 19826.. Coos Baakman.. 12.. 19763.. Lennart Backus.. 08.. 19827.. Jumamurat Bayjanov.. Tim te Beek.. 13.. 19759.. Jos Boekhorst.. Support.. 19390.. John van Dam.. 11.. 19774.. Jurgen Doreleijers.. 18.. 19674.. Bas E.. Dutilh.. 10.. 19797.. Wilco Fleuren.. Christof Francke.. 24.. 19389.. Celia van Gelder..  ...   22.. 19543.. Victor de Jager.. Shivakumar Keerthikumar.. Philip Kensche.. 17.. 19693.. Jules Kerssemakers.. Elmar Krieger.. -.. Robin van der Lee.. Xiaowen Lu.. Wout Megchelenbrink.. Systems Biology.. Fredrick Maati Mobegi.. Richard Notebaart.. Martin Oti.. Lex Overmars.. Bernadette Renckens.. 21.. 19559.. Tina Ritschel.. Sergio Rossell.. Gijs Schaftenaar.. Roland Siezen.. Radek Szklarczyk.. Wilmar Teunissen.. 16.. 19758.. Tilman Todt.. Hanka Venselaar.. Jacob de Vlieg.. Gert Vriend.. 27.. 19521.. Michiel Wels.. Kuntal Worah.. External.. Aldert Zomer..

    Original link path: /who-and-where/staff/
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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Karen Berntsen.. Tom Ederveen.. Jonas Falck.. Jakob Goldmann.. Bo Hanssen.. 14.. 19760.. Susanne Hermans.. Sander van Horen.. Sander Jans.. Joey Kampman.. Rob van der Kant.. Daniel Rademaker.. Marlou Snelleman.. Erik Stens.. Ying Zeng..

    Original link path: /who-and-where/students/
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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Bioinformatics will have a series of important roles in the medicinal sciences.. Biology and medicine are living in a time of rapidly increasing involvement of knowledge about processes at the molecular level, and bioinformatics can help cope with this rapid increase of required skills.. An important function for bioinformatics is explaining things at the molecular level.. To do so, enzymes from pathogens or mutated native enzymes can be modelled by homology.. These models can be used to explain the effects determined by molecular biology.. P63 mutations.. The human genome will be known and properly annotated in a few years.. At that moment we know nearly all targets for medicins.. Getting the same information for a parasite will enable us to make better medicins against infections with less side effects.. After all, such a medicin should block a process that is crucial for the parasite, but it should of course not block the equivalent process in the host.. Parasite and active site.. Many research projects are aiming at the discovery of information about molecules or molecular interactions.. Bioinformatics can help here.. Correlated mutation analysis (CMA) is a technique to find co-variation in pairs of sequences.. Bioinformaticists originally thought that CMA could be used to solve the protein folding problem, but it became clear that co-variation is a much better indicator for functional dependencies and inter-molecular contacts.. It is more important for the medicinal sciences, however, to get an overview of entire process and not just about one or a few steps.. Putting the pieces of the big jigsaw puzzle together, to get an overview of networks of interconnected steps is a typical task for bioinformatics.. Networks and regulation.. Information about a molecule, or even a complicated network of interactions between proteins, is just the beginning.. We want to understand the entire interplay of networks, and all forms of communication inside cells, between cells, between organs, and between organisms.. Bioinformatics is the ideal tool to integrate data at all levels from molecule to man.. The G protein-coupled receptors (GPCRs) are our first attempt at integrating heterogenous  ...   about expression levels.. In real life things are a bit more complicated, but from a bioinformatics point of view this is the minimal required knowledge.. Bioinformatics can help with the selection of probes to put on the chip, with the extraction of data from the chip, but most interestingly, a lot of bioinformatics will be needed.. An array spotter.. Bioinformatics and medicine will meet mainly in two ways.. First, collaborations on the research topics listed above will bring researchers together.. Not only can bioinformatics be used to explain experimental results, but when used properly, bioinformatics can also generate ideas for new experiments to answer old questions, or stronger even, bioinformatics can raise new questions.. Second, bioinformatics will have to become part of the curriculum of all medical students.. Slogans like Computers will take over in all corners of the world , or, Without good computer skills you won t make it in the future , are surely overdone, but it is clear that a minimal amount of computer knowledge is an essential ingredient of the study of every student in the faculty of medical sciences.. And what better way to generate this computer savvyness with a course that teaches the student skills he or she will use regularly throughout the career? Bioinformatics will provide just that: education of essential skills (searching and finding information using the WWW, using biomedical databases, etc.. ).. The faculty of medical sciences.. It is not an exaggeration to state that the CMBI plays a leading role in the Dutch bioinformatics field, and probably also in Europe.. This opens up beautiful opportunities for students and scientists.. In Nijmegen a student can get in contact with this science of the future called bioinformatics, but it is also possible to become a well-trained bioinformatician, ready for the challenges that come with the better jobs.. Experimental scientists in Nijmegen have better opportunities than at other universities in the Netherlands to discuss their research with bioinformaticians, and to collaborate with them.. This potentially gives our experimental scientists a significant step ahead that comes for free..

    Original link path: /who-and-where/bioinformatics-and-medicine/
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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: About the.. CMBI.. The.. C.. entre for.. M.. olecular and.. B.. iomolecular.. I.. nformatics is the Dutch national centre for computational molecular sciences.. The institute pursues a rigorous research program with topics ranging from computational small-molecule chemistry to bioinformatics.. All research is related to molecular aspects of life sciences, often with a focus on the relation health - disease.. The institute s facilities, databases and software packages are available to external scientists.. is strongly committed to a series of educational projects, ranging from high school to postgraduate courses and from local university student courses to international workshops.. Presently the.. staff.. are involved in the following activities:.. bioinformatics research.. computational small-molecule research.. organising courses and tutorials to support scientists for scientists in many fields.. maintaining WWW-based servers to give scientists in the Netherlands rapid access to commonly used bioinformatics and small-molecule databases and information systems.. facilitating data- or expertise-intensive research by allowing scientists to visit us and work in the.. for a while.. Information leaflets provide more detailed information about the centre  ...   Gert Vriend: macromolecular structure analysis.. The service activities of the institute focus on the availability of databases and information systems for small molecules and biomolecules, and the software needed to make the best use of them.. Many services are provided free of charge, but a user-license is needed to access services for which the institute needs to pay a fee.. is involved in many collaborations, most notably in the.. IMM.. and in the life-sciences initiative with.. NCMLS.. The institute is involved in many types of biomedical research.. Indeed, medicinal bioinformatics is such an important topic that it deserves a.. special introductory page about bioinformatics and medicine.. Altogether, the institute provides a lively environment for molecular computational scientists.. The availability of a large number of experts in the many sub-disciplines of molecular computation make the.. the ideal environment for students, AIOs and young scientists to learn about bioinformatics, drug design, and many forms of computational chemistry.. offers different oppurtunties for.. students.. , to follow courses, and job openings for.. applicants.. on different levels..

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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Seminars.. Reservations.. Cleaning.. CMBI Intra.. Cleaning schedule.. INTRAnet.. for CMBI only.. - Beer Committee: Gert..

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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: The CMBI performs research in cheminformatics and in the molecular aspects of bioinformatics.. This research is performed by the following groups:.. Huynen.. Computational genomics.. Whole genome comparisons.. The sequencing of complete genomes raises the question: how do we show that a genome is more than the sum of its genes?, or, how do the proteins encoded in these genomes interact with each other to produce cells and phenotypes? The core research focus of the Huynen group is to predict such functional interactions between proteins as there exist e.. g.. in metabolic pathways, signalling pathways or protein complexes.. Siezen.. Food bacteria.. Microorganisms such as yeasts, fungi and bacteria are used extensively in the preparation of foodstuffs.. The carefully controlled use of food-grade bacteria plays an important role in starter cultures (mainly lactic acid bacteria) and in the production of specific  ...   well-established scientific discipline in pharmaceutical research, critical in the development of new treatments.. It has created many opportunities to speed up and rationalise the multidisciplinary drug discovery process, and provide novel approaches to the design of drugs otherwise not possible.. Vriend.. Protein structure analysis and prediction.. Data mining.. Proteins are the core of life, they do all the work, and they give you feelings, contact with the outside world, etc.. Proteins, therefore, are the most important molecules on earth.. We want to understand life; why are we what we are, why do we do what we do, how come you can think what you think? Therefore we must understand proteins and all our work is amimed at just that: understanding proteins.. We want to use this understanding to improve the world around us in a careful and responsible manner..

    Original link path: /research/
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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: Publications 2011.. Publications 2010.. Publications 2009.. publications 2008.. publications 2007.. publications 2006.. publications 2005.. publications 2004.. publications 2003.. publications 2002.. publications 2001.. publications 2000.. publications archive.. Most recent publications.. :.. Older publications can be viewed by publication date selected from the left menu.. Ngu LH, Nijtmans LG, Distelmaier F, Venselaar H, van Emst-de Vries SE, van den Brand MA, Stoltenborg BJ, Wintjes LT, Willems PH, van den Heuvel LP, Smeitink JA, Rodenburg RJ.. A catalytic defect in mitochondrial respiratory chain complex I due to a mutation in NDUFS2 in a patient with Leigh syndrome.. Biochim Biophys Acta.. , Feb;1822(2):168-175.. ,.. 2012.. Details.. Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R,  ...   Microbiol.. , Feb;78(4):1123-1131.. Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA.. Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome.. J Bacteriol.. , Jan;194(1):195-196.. Lusher SJ, Raaijmakers HC, Vu Pham D, Kazemier B, Bosch R, McGuire R, Azevedo R, Dechering K, Oubrie A, van Duin M, de Vlieg J.. X-ray structures of the progesterone receptor ligand-binding domain in its agonist state reveal differing mechanisms for the mixed profiles of 11β-substituted steroids.. J Biol Chem.. , Apr 25.. [Epub ahead of print],.. Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, Kops GJ.. The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase.. Dev Cell.. , Jun 12;22(6):1321-1329..

    Original link path: /research/publications/
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  • Title: Centre for Molecular and Biomolecular Informatics
    Descriptive info: CMBI has a lot of national and international cooperations with research institutes in academia and industry.. Protein Structure Validation is a cooperation with.. Protein Biophysics.. ;.. Comparative Genomics is cooperating with.. Bacterial Genomics is collaborating with.. ,.. TI Food and Nutrition.. NIZO food research.. and the.. Kluyver Centre for Genomics of Industrial Fermentation..

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  • Archived pages: 141