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

call for abstracts 'Regulatory Genomics Special Interest Group – RegGenSIG'
by Michiel Van Bel 23 Apr '12

23 Apr '12

Dear All, Note that the deadline for abstract submission of the 'Regulatory Genomics Special Interest Group – RegGenSIG' satellite meeting of ISMB is fastly approaching (April 27 for oral presentations and May 18 for poster presentations). RegGenSIG 2012 will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research, and a joint panel discussion with the Alternative Splicing SIG. RegGenSIG will bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following ·inference of gene regulatory networks, ·utilization of information pertaining to epigenetics, chromatin structure, and histone modifications, ·determination of the roles of regulatory RNAs, ·prediction of transcriptional regulation from RNA-seq data and ChIP-seq data, ·pattern discovery in sequences, and ·sequence based modeling of gene expression. If you would still consider submitting an abstract please consult http://www.iscb.org/ismb2012-program/ismb2012-satellitemeetings#regulatory Looking forward seeing you at ISMB 2012 Best Regards, Finn Drabløs, Norwegian Univ. of Science and Technology, Norway Kathleen Marchal, Univ Ghent/K.U. Leuven, Belgium Isidore Rigoutsos, Thomas Jefferson University, USA Saurabh Sinha, University of Illinois, USA Lonnie R. Welch, Ohio University, USA

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Seventh Summer School on Advanced Statistics and Data Mining (Madrid, June 25th - July 6th, 2012)
by Rubén Armañanzas 12 Apr '12

12 Apr '12

Dear colleagues, The Technical University of Madrid (UPM) will once more organize the summer school on 'Advanced Statistics and Data Mining' in Madrid between June 25th and July 6th. This year's programme comprises 12 courses divided into 2 weeks. Attendees may register in each course independently. Early registration is now *OPEN*. Extended information on course programmes, price, venue, accommodation and transport is available at the school's website: http://www.dia.fi.upm.es/ASDM Best regards, -- The coordinators of the school. *List of courses and brief description* Week 1 (June 25th - June 29th, 2012) Course 1: Bayesian networks (15 h) Basics of Bayesian networks. Inference in Bayesian networks. Learning Bayesian networks from data. Course 2: Statistical inference (15 h) Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrap methods. Introduction to Robust Statistics. Course 3: Supervised pattern recognition (15 h) Introduction. Assessing the performance of supervised classification algorithms. Preprocessing. Classification techniques. Combining multiple classifiers. Comparing supervised classification algorithms. Course 4: Multivariate data analysis (15 h) Introduction. Data Examination. Principal component analysis (PCA). Factor Analysis. Multidimensional Scaling (MDS). Correspondence analysis. Multivariate Analysis of Variance (MANOVA). Canonical correlation. Course 5: Neural networks (15 h) Introduction. Perceptrons. Training algorithms. Accelerating convergence. Useful tricks for MLPs. Deep networks. Course 6: Feature Subset Selection (15 h) Introduction. Filter approaches. Wrapper methods. Embedded methods. Drawbacks and future strands. Practical session. Week 2 (July 2nd - July 6th, 2012) Course 7: Time series analysis (15 h) Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 8: Hidden Markov Models (15 h) Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semicontinuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs. Course 9: Hot topics in intelligent data analysis (15 h) Multi-label and multi-dimensional classification. Advanced Bayesian classifiers. Advanced Clustering. Partially supervised classification with uncertain class labels. Directional statistics. Spatial point processes. Course 10: Unsupervised pattern recognition (15 h) Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. Course 11: Support vector machines and kernel methods (15 h) Introduction. SVM models. SVM learning algorithms. Other kernel methods: Kernel PCA, Kernel FDA, Kernel K-means. Practical work. Course 12: Regression (15 h) Introduction. Simple Linear Regression Model. Measures of model adequacy. Multiple Linear Regression. Regression Diagnostics and model violations. Polynomial regression. Variable selection. Indicator variables as regressors. Logistic regression. Nonlinear Regression.

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FW: PhD Position in Molecular Ecology
by Tim De Meyer 11 Apr '12

11 Apr '12

to forward to potential candidates (a bioinformatics background is desirable) Prof. Godelieve Gheysen Ghent University Department Molecular Biotechnology Coupure links 653 9000 Ghent Belgium tel 32 9 264 5888 fax 32 9 264 6219 ----- Original Message ----- From: cristina.tamo(a)ips.unibe.ch Sent: Tuesday, April 10, 2012 3:52 PM Subject: PhD Position in Molecular Ecology Dear colleague, Please find attached an advertisement for a PhD Student position at our institute. I would very much appreciate if you could bring it to the attention of interested candidates from your laboratory. Thank you very much for your help. Cris Kuhlemeier Professor of Plant Sciences Institute of Plant Sciences Altenbergrain 21 CH-3013 Bern Switzerland phone +41 31 631 49 13 fax +41 31 631 49 42 <mailto:cris.kuhlemeier@ips.unibe.ch> cris.kuhlemeier(a)ips.unibe.ch <http://www.botany.unibe.ch/> http://www.botany.unibe.ch/ _____ Geen virus gevonden in dit bericht. Gecontroleerd door AVG - www.avg.com Versie: 2012.0.1913 / Virusdatabase: 2411/4926 - datum van uitgifte: 04/10/12

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postdoc job vacancy at KU Leuven - ESAT-SCD-SISTA-BIOI group : Candidate gene prioritization by genomic data fusion
by Michiel Van Bel 10 Apr '12

10 Apr '12

> Candidate gene prioritization by genomic data fusion > > > > Promotor: <http://www.kuleuven.be/wieiswie/en/person/00012794>Yves Moreau > > Description: The Bioinformatics Lab at the University of Leuven is searching for an exceptional postdoctoral fellow who will work under the supervision of Prof. Yves Moreau to develop a novel platform for candidate gene prioritization by genomic data fusion. The lab has developed Endeavour for the prioritization of candidate diseases genes using heterogeneous genomic data (Aerts et al., 2006). This platform is now broadly established within the human genetics community as an effective tool to support disease gene discovery (Thienpont et al., 2010). We have also extended our original methodology using network analysis (Lage et al., 2007) and kernel methods (De Bie et al., 2007; Yu et al., 2010). The goal of the postdoctoral fellow will be to develop a platform for gene prioritization that implements such strategies and is broadly usable by wet-bench biologists (web interface) and bioinformaticians (API or web service). > > The candidate will hold a PhD in bioinformatics with an excellent publication record. The ideal candidate will have a strong record in software engineering of bioinformatics methods, analysis of molecular networks, and practical applications of kernel methods. Excellent Java and web application development skills are essential. The candidate should have extensive practical knowledge of kernel methods, including software libraries (for example, Shogun). Knowledge of multiple kernel learning and feature selection methods is a plus, as well as the capacity to develop novel kernel algorithms. Knowledge of molecular network analysis and bag-of-word text-mining methods are additional assets. > > The postdoctoral fellow will be embedded in the SymBioSys Center for Computational Systems Biology, which is a consortium of computational scientists and molecular biologists at the University of Leuven that focuses on how individual genomic variation leads to disease through cascading effects across biological networks (in constitutional disorders and leukemias). We develop innovative computational strategies for next-gen sequencing and biological network analysis, with demonstrated contributions to actual biological breakthroughs. Eagerness to collaborate with biologists and geneticists on gene discovery projects is crucial. Ability to contribute to coaching PhD students and acquiring external funding is another plus. > > We offer a competitive package and a fun, dynamic environment with a top-notch consortium of young leading scientists in bioinformatics, human genetics, and cancer. Our consortium offers a rare level of interdisciplinarity, from machine learning algorithms to fundamental advances in molecular biology to direct access to the clinic. The University of Leuven is one of Europe’s leading research universities, with English as the working language for research. Leuven is one of Europe’s most beautiful university towns, just outside Brussels, at the heart of Europe. > > Related publications by the lab > oAerts S et al. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006. > oThienpont B et al. Haploinsufficiency of TAB2 causes congenital heart defects in humans. Am J Hum Genet. 2010. > oLage K et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol. 2007. > oDe Bie T et al. Kernel-based data fusion for gene prioritization. Bioinformatics. 2007. > oYu S et al. L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics. 2010. > > > Key words: bioinformatics, candidate gene prioritization, genomic data fusion, network analysis, kernel methods, software engineering, Endeavour > > Start date: 2012-09-1 > Application date: 2012-06-26 > Publication date: 2012-03-26 > > Financing: SymBioSys > > Link: <http://www.esat.kuleuven.be/scd/>http://www.esat.kuleuven.be/scd/ > > Research group: Department of Electrical Engineering (ESAT) > > Remarks: Please send in PDF: > (1) a CV including education (with Grade Point Average, class rank, honors, etc.), research experience, and bibliography, > (2) a one-page research statement, and > (3) three references (with phone and email) to Prof. Yves Moreau, c/o Ms. Mimi Deprez – <mailto:mimi.deprez@esat.kuleuven.be>mimi.deprez(a)esat.kuleuven.be. Preferred start date is September 2012. The candidate will commit to a three-year postdoc period. > > Apply to <http://phd.kuleuven.be/set/postdoc/voorstellen_departement?departement=5000…>Click here to apply to this project

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