February 2015 - BBClist - maillist.psb.ugent.be

N2N seminar Thursday, February 19 at 11 am: ': 'Learning Bayesian Networks with Biomedical Applications' By Prof. de Campos
by Katrijn Vannerum 12 Feb '15

12 Feb '15

Dear All, Prof. Cassio P. de Campos will give a seminar on Thursday, February 19 at 11 am: 'Learning Bayesian Networks with Biomedical Applications'. (See abstract below) Please contact me if you would like to have a meeting with Prof. Cassio P. de Campos in the afternoon. The lunch meeting (12-14h) is open to PhD students registered at the Doctoral Schools. With kind regards, Katrijn Vannerum PhD Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image003.png@01D046AB.FE0F4570] [cid:image004.png@01D046AB.FE0F4570] "Learning Bayesian Networks with Biomedical Applications" Professor Cassio de Campos Queens's University Belfast, School of Electronics, Electrical Engineering and Computer Science, Belfast, Ireland February 19, 2015 (11:00) Lunch meeting for Doctoral Schools students 12:00-14:00 Jozef Schell seminar room, Technologiepark 927 - 9052 Zwijnaarde http://www.nucleotides2networks.be/node/232 http://www.nucleotides2networks.be/events Abstract This talk presents an overview of Bayesian networks and methods for learning them. It discusses on recent methods and theoretical results to speed up computations and to improve accuracy. Applications arising in real-data biomedical problems are described, where it is argued that Bayesian networks can provide meaningful and interpretable results. In particular, we discuss on unsupervised clustering of copy number data, as well as data imputation with application in survival analysis of diffuse large B cell and marginal zone lymphoma patients.

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Course 'Life Sciences and biomedical technology' with session on 'Introduction into bio-informatics and computational biology' at Ghent University
by Katrijn Vannerum 10 Feb '15

10 Feb '15

Click here<http://www.ivpv.ugent.be/opleidingen/aanbod/life2015/index.htm> if you are not able to read the content of this e-mail [cid:part2.08030104.06080605@ugent.be] [cid:image001.jpg@01D0454A.CB66C1F0] More information <http://www.ivpv.ugent.be/opleidingen/aanbod/life2015/index.htm> Post-academic course Life Sciences and biomedical technology "Life sciences" is a broad field encompassing different disciplines and expertise, involving biologists, geneticists, biomedical scientists, medical doctors as well as bio- and biomedical engineers and computer scientists. The aim of this course is to provide to the student, in an accessible and comprehensive way, the essentials of life sciences. * Session 1: Architecture and structure of cells 25 March 2015 * Session 2: Energetic and metabolic aspects of cells 1 April 2015 * Session 3: Hereditary information - on DNA and genes 22 April 2015 * Session 4: From cell to tissues - techniques for analysis 29 April 2015 * Session 5: Gene technology and molecular diagnostics 6 May 2015 * Session 6: Oncology 13 May 2015 * Session 7: Medical imaging 20 May 2015 * Session 8: Introduction into bio-informatics and computational biology 27 May 2015 * Session 9: Immunology 3 June 2015 2015 * Session 10: Microbiology and the microbiome 17 June 2015 © 2015 Instituut voor Permanente Vorming (IVPV) - UGent Let us know if You don't want to receive these e-mails<mailto:els.vanlierde@ugent.be?subject=stopEmaillife> anymore. An Balcaen Coördinator Instituut voor Permanente Vorming - Universiteit Gent Technologiepark 904, 9052 Zwijnaarde 09 264 55 92 an.balcaen(a)ugent.be<mailto:an.balcaen@ugent.be> www.ivpv.ugent.be<http://www.ivpv.ugent.be>

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Registration open: NBIC/BioSB Course Pattern Recognition (4th edition), 23-27 March 2015, Amsterdam
by Celia.vanGelder＠radboudumc.nl 10 Feb '15

10 Feb '15

NBIC/BioSB Course Pattern Recognition (4th edition) Date: 23-27 March, 2015 Location: Amsterdam Course Coordinator: Perry Moerland (AMC) Website: http://biosb.nl/education/course-portfolio/pattern-recognition/ Registration: http://biosb.nl/education/enrollment-pattern-recognition-course-4th-edition/ On March 23-27, 2015, NIBC/BioSB organises the fourth edition of the PhD Course Pattern Recognition in Amsterdam. The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. Preparation material on statistics and linear algebra will be distributed before the course, to be studied by students missing the required background. This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre 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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Announcement mini-symposium 19 February at VU University Amsterdam: Data Crunching for Medicinal Chemistry and Life Sciences
by Barbara.vanKampen＠radboudumc.nl 10 Feb '15

10 Feb '15

Dear all, You are cordially invited to join us for a mini-symposium on Thursday 19th February from 11:00 hours at VU University Amsterdam. For catering, your registration is required but participation is free. Please register here before 17 February: http://www.formdesk.com/vuamsterdam/data_crunch_mini_symp The detailed agenda is given below. Best regards, Medicinal Chemistry VU University Amsterdam --- Data Crunching for Medicinal Chemistry and Life Sciences Mini-symposium on Thursday 19th February in lecture theater WN-F123, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands 11:00 Chair: Iwan de Esch (Division Medicinal Chemistry, VU University Amsterdam) 11:05 Translating biological and chemical data into structure-based protein-ligand interaction prediction Chris de Graaf (Division Medicinal Chemistry, VU University Amsterdam) 11:30 Competitive inhibitors of receptor tyrosine kinases: Rational design, synthesis and in vivo evaluation Didier Rognan (CNRS/Universite de Strasbourg, FR) 12:00 High End StaR-Based GPCR Ligand Design Andrea Bortolato (Heptares Therapeutics, UK) 12:30 Lunch & Networking 13:15 Data-driven medicinal chemistry in the era of big data Scott Lusher (Netherlands eScience Center) 13:45 Explaining Disease Using Big Data: How Valid Is Your Pathway? Jaap Heringa (Centre for Integrative Bioinformatics, VU University Amsterdam) 14:15 Closing remarks --- At 15.45 Albert Kooistra (Medicinal Chemistry, VU University Amsterdam) will defend his PhD thesis entitled "In silico Medicinal Chemistry. Investigating GPCRs: key regulators of signal transduction and cell function", in the Aula of VU University Amsterdam. [cid:06f41657-a295-4e4b-be0a-c53a0cd26ab8@umcn.nl] 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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[Gtpb] Courses Apr-Sep 2015 announced
by Pedro Fernandes 09 Feb '15

09 Feb '15

Dear GTPB audience, Please have a look at the course titles for the April to September 2015 period http://gtpb.igc.gulbenkian.pt Individual course announcements will follow, when they open for applications. Best wishes P. Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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MIC'15 Deadline Extension
by El-ghazali Talbi 07 Feb '15

07 Feb '15

************************************************* 11th Metaheuristics International Conference MIC'2015 7-10 June, 2015 Agadir, Morocco http://www.lifl.fr/MIC2015 ************************************************* Scope of the Conference ======================== The Metaheuristics International Conference (MIC) series was established in 1995 and this is its 11th edition. MIC is the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, MIC'2015 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. MIC'2015 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. MIC'2015 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. Relevant Research Areas ======================== MIC'2015 solicits contributions dealing with any aspect of metaheuristics. Typical, but not exclusive, topics of interest are: + Metaheuristic techniques such as tabu search, simulated annealing, iterated local search, variable neighborhood search, memory-based optimization, dynamic local search, evolutionary algorithms, memetic algorithms, ant colony optimization, variable neighborhood search, particle swarm optimization, scatter search, path relinking, etc. + Techniques that enhance the usability and increase the potential of metaheuristic algorithms such as reactive search mechanisms for self-tuning, offline metaheuristic algorithm configuration techniques, algorithm portfolios, parallelization of metaheuristic algorithms, etc. + Empirical and theoretical research in metaheuristics including large-scale experimental analyses, algorithm comparisons, new experimental methodologies, engineering methodologies for metaheuristic algorithms, search space analysis, theoretical insights into properties of metaheuristic algorithms, etc. + High-impact applications of metaheuristics in fields such as bioinformatics, electrical and mechanical engineering, telecommunications, sustainability, business, scheduling and timetabling. Particularly welcome are innovative applications of metaheuristic algorithms that have a potential of pushing research frontiers. + Contributions on the combination of metaheuristic techniques with those from other areas, such as integer programming, constraint programming, machine learning, etc. + Challenging applications areas such as continuous, mixed discrete-continuous, multi-objective, stochastic, or dynamic problems. Important Dates ================ Extended deadline Feb 28, 2015 Notification of acceptance March 20, 2015 Camera ready copy April 10, 2015 Early registration April 10, 2015 Conference June 7-10, 2015 Submission Details =================== We will accept submissions in three different formats. S1) Original research contributions for publication in the conference proceedings of a maximum of 10 pages S2) Extended abstracts of work-in-progress and position papers on an important research aspect of a maximum of 3 pages S3) High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication Accepted contributions of categories S1 and S2 will be published in the MIC'2015 conference proceedings. Accepted contributions of category S3 will be orally presented at the conference, but not be included into the conference proceedings. The submission server is available at http://www.lifl.fr/MIC2015 Proceedings and publication ============================ Edited book in Springer indexed by ISI Web of Science Conference Proceedings, DBLP, Ulrichs, SCOPUS, MathSciNet, Current Mathematical Publications, Mathematical Reviews, Zentralblatt Math: MetaPress and Springerlink. special issue of the International Journal of Metaheuristics special issue of the Concurrency and Computation: Practice and Experience Conference Location ==================== The conference will be held in Agadir, Morocco. Agadir is the top tourist destination in Marocco in the border of the ocean. Further Information ==================== Up-to-date information will be published on the web site http://www.lifl.fr/MIC2015. For information about local arrangements, registration forms, etc., please refer to the above-mentioned web site or contact the organizers. MIC'2015 Conference Committee ============================== Conference Chair - El-ghazali Talbi, University of Lille, CNRS, INRIA, France Steering committee - Fred Glover, University of Colorado and OptTek Systems, USA - Celso Ribeiro, Universidade Federal Fluminense, Brazil - Éric Taillard, University of Applied Sciences of Western Switzerland, Switzerland - Stefan Voß, University of Hamburg, Germany Organization committee chairs - L. Jourdan (Univ. Lille, CNRS, INRIA) - M-E. Marmion (Univ. Lille, CNRS, INRIA) - R. Ellaia (EMI, Rabat, Morocco, Local chair) Session/Proceedings chair - F. Yalaoui (UTT, France) Tutorial chair - A. Nakib (UPEC, France) Publicity chair - G. Danoy (Univ. Luxembourg) - H. Masri (University of Bahrain, Bahrain) - S. Nesmachnow (Universidad de la República, Uruguay) -- Prof. E-G. Talbi Univ. Lille, CNRS, INRIA MIC'2015 7-10 June 2015, Agadir, Morocco http://www.lifl.fr/MIC2015

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2 open PhD positions in bioinformatics (Van de Peer lab)
by Lieven Sterck 05 Feb '15

05 Feb '15

In the frame of a Marie Curie EU project, we currently have two PhD student positions open in the bioinformatics group of Prof Van de Peer. More information can be found in the advert below and on the website mentioned therein. Feel free to spread this to any potentially interested candidates. best regards, lieven Now offering 15 PhD positions in Algal Research and Biotechnology Do you hold a MSc degree or are you expecting to complete one before July 15 th , 2015? If you want to undertake further doctoral research and training as part of an international and highly inter-disciplinary team, combining a unique and ambitious theoretical, field, hands-on training and research, then ALFF is the programme for you. ALFF: The ALgal microbiome - Friends or Foes Algal aquaculture is developing exponentially worldwide, with multiple applications in the food, chemical and pharmaceutical industries. Current research in algal biotechnology mostly focuses on metabolite discovery, aquaculture yield improvement and engineering bottle-necks. However, agronomical experience shows that controlling the interaction of land crops with mutualistic or pathogenic microbes is critical to successful production. Likewise, controlling the microbial flora associated with algae (the 'algal microbiome') is emerging as the biggest biological challenge for their increased usage. Bacteria can control the morphogenesis of algae, while others are indispensable to algal survival. Pathogens are causing devastating diseases, the impact of which worsens with the intensification of aquaculture practices. ALFF aims to achieve a scientific step-change in our understanding of algal-microbial interactions, whilst also leading to the development of superior mass algal cultivation and biocontrol strategies. Scientific excellence, creativity, entrepreneurship and innovation ALFF is funded under the prestigious EU Marie Sklodowska-Curie Initial Training Networks (ITN) programme and is specifically designed to train students in research and algal biotechnology. We offer highly interdisciplinary and international training for 15 PhD students throughout the EU, with a highly competitive salary and close contacts with the industry, government agencies and leading laboratories. In addition to conducting research, students will be enrolled on an extensive programme of short courses, conferences and secondments at other institutions. ALFF also encompasses an ambitious outreach and public engagement programme, in collaboration with highly renowned institutions such as the Flanders Marine Institute and the United Nations University. Desired skills and experience To apply for the Algal Microbiome: Friends or Foes (ALFF) Programme you should normally have a good MSc degree or an equivalent qualification, or be expected to complete a MSc degree by mid-July 2015, or have a background in one of the fields of environmental and life sciences. Depending on the project(s) you decide to apply for, an appropriate background could include marine biology, marine science, aquatic biology, micro-biology, phycology, biology, chemistry, environmental sciences or information technology. At the time of recruitment, you must not have resided or carried out your main activity (work, studies, etc.) in the country of your host organisation for more than 12 months in the 3 years immediately prior to the reference date. The selection process will take into consideration the whole range of experience of applicants. Career breaks, evidence of non-formal qualifications and evidence of previous international mobility will be regarded favourably. For more details on the PhD projects being advertised, please go to: http://www.sams.ac.uk/Algal-doctorate-EU-Marie-Curie/algal-microbiome-frien… Closing date for applications: Sunday, March 1 st 2015.

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Mathematical and Computational Evolutionary Biology Conference 2015
by Guy Baele 03 Feb '15

03 Feb '15

-- UPDATED ANNOUNCEMENT -- MCEB - Mathematical and Computational Evolutionary Biology 21-25 June 2015 - Porquerolles Island and Conservation area, South of France. Webpage: http://www.lirmm.fr/mceb2015/ Pre-registration deadline: February 28th Notification to applicants: March 15th Final list of attendees: April 15th Scope: Mathematical and computational tools and concepts form an essential basis for modern evolutionary studies. The goal of the MCEB conference (at its 7th edition) is to bring together scientists with diverse backgrounds to present recent advances and discuss open problems in the field of mathematical and computational evolutionary biology. The theme of this year's edition will be new data, new questions, new methods. New generation sequencing techniques have multiplied not just the amount, but also the types of genetic data produced, giving rise to new questions, and new methodologies to answer them. These methodologies are often cross-disciplinary, with applications to diverse research topics. General concepts, models, methods and algorithms will be presented and discussed, as during the previous conference editions. Where and when: Porquerolles Island, near HyËres, in the South of France, 21-25 June 2015. (http://en.wikipedia.org/wiki/Porquerolles) Cost: Conference fees including accommodation for four nights, meals, coffee breaks, etc., will be between 300§ and 630§, all inclusive, varying depending on the room. PhD students and postdocs will benefit of cheap rooms. Keynote speakers: David Bryant - http://www.maths.otago.ac.nz/~dbryant/ University of Otago, NZ Recovering phylogeny and demographics from SNPs: prospects and limitations Jukka Corander - http://www.helsinki.fi/bsg/ Bayesian Statistics Group, University of Helsinki, FI ABC meets machine learning - fitting intractable models to genome data Asger Hobolth - http://www.cs.au.dk/~asger/index.html Bioinformatics Research Center (BiRC), Aarhus University, DK Modelling DNA sequence evolution within and between species Philippe Lemey https://rega.kuleuven.be/cev/ecv/lab-members/PhilippeLemey.html Rega Institute, Clinical and Epidemiological Virology, BE Data integrating in viral evolutionary inference: from spatial dynamics to trait evolution Bernard Moret - http://lcbb.epfl.ch/ Laboratory for Computational Biology and Bioinformatics, EPFL, CH Phylogenetic Transfer of Knowledge Ludovic Orlando - http://geogenetics.ku.dk/research_groups/palaeomix_group/ Center for GeoGenetics, Natural History Museum of Denmark, DK Ancient DNA: from very old molecules to genomes and epigenomes Molly Przeworski - http://przeworski.c2b2.columbia.edu/ Columbia University, New york, USA A population-genetic approach to the study of mutation and recombination in humans Katherine St. John - http://comet.lehman.cuny.edu/stjohn City University of New York, USA For more information, visit the website at: http://www.lirmm.fr/mceb2015/ Please forward this announcement.

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post-doc position in Tours (France)
by Xavier De Bolle 03 Feb '15

03 Feb '15

Dear Sir/Madam, I would be great if you could distribute this post-doc announcement around you. Best wishes, Xavier De Bolle Prof. Xavier De Bolle (PhD) Our website : http://www.urbm.be/home-xa.html Teaching : http://www.unamur.be/en/teaching/masters/biochemistry/bacteriology Unité de Recherche en Biologie des Microorganismes (URBM) Université de Namur (UNamur) Rue de Bruxelles 61 e-mail: xavier.debolle(a)unamur.be B-5000 Namur telephone: 32 - (0)81 - 72 44 38 BELGIUM fax: 32 - (0)81 - 72 42 97 Please consider the environment before printing this e-mail This message is confidential. It may also be privileged or otherwise protected by work product immunity or other legal rules. If you have received it by mistake please let us know by reply and then delete it from your system; you should not copy the message or disclose its contents to anyone.

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