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[Gtpb] Clarification about the CSDM training course
by Pedro Fernandes 14 Nov '13

14 Nov '13

Dear All It may be useful to provide further explanations about the content of the upcoming CSDM13 - Chromosome structure determination using modelling and Hi-C data - training course. I spoke with several people that questioned me about its usefulness in evolution studies, for example. The following text is an attempt to correct this. IMPORTANT DATES for this Course Deadline for applications: November 20th 2013 Notification of acceptance within 72 hours of application (working days count) Course date: November 27th to November 29th 2013 Thank you Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt CSDM13 training Course Chromosome structure determination using modelling and Hi-C data In the analysis of patterns and processes occurred during the evolution of our genome, the detection of evolutionary forces acting in protein coding genes has already proved its relevance in the context of human health and disease [1]⁠. The tools generally used in this field are based in the concepts and methods of evolutionary genomics, phylogenetic analysis, and bioinformatics on the complete genomes of different mammalian species [2]⁠. The main outcome from this kind of analysis is the classification of specific features of our genomes into categories, according to the impact of these differences on changes to evolution. In the context of epigenetics, the relation with disease has been extensively studied, at the level of DNA methylation, histone modification and even chromatin remodeling [3]⁠. Under this last category some work has been done, more specifically on chromatin structure, that is able to highlight structural variations directly linked to human disease [4,5]⁠. Overall it is now widely accepted that the complete elucidation of chromatin three-dimensional structure is the next frontier in epigenetic studies; and some of its possible applications to human health are promising, as markers for gene expression state [6]⁠, in the understanding of the cancer process 7⁠, in the maintenance of cellular memories or in the modulation of phenotypes [8]⁠. However, in the context of epigenetics the relation between selective pressure and the potential impact of observing epigenetic variation, although it has been reported [9,10⁠], has not yet been modeled or measured. The chromatin interaction map, that somehow summarizes the epigenetic state of a given genomic region [11]⁠, stands as a outstanding candidate to study how evolution may shape our epigenomic landscape, and, at present, potentially the only candidate to offer significant clues about the real role of the non-genic 95% of our genomes. The CSDM13 course content In this course we aim to share our experience in analyzing and inferring the structure of chromatin (how it folds in three-dimensions) [1215]⁠. Using available Hi-C data,course participants will be asked to find topologically associating domains10⁠, infer evolutionary conservation (or cell specificity), calculate the physical distances between a gene and its promoter, infer chromatin accessibility of specific regions, etc. Some computational skills are recommended for this course. However, the tools presented in this course are designed to be used by non computer-scientists. We will provide a basic introduction to the linux operating system and the Python programming language, aiming at quickly creating a working environment where every participant is guaranteed to engage. With this, we will minimize the danger of leaving anyone behind because of healthy differences in background literacy about computing. 1. Thomas, P. D. & Kejariwal, A. Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. Proc. Natl. Acad. Sci. U. S. A. 101, 15398 (2004). 2. Sánchez, R. et al. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 39, W4704 (2011). 3. Portela, A. & Esteller, M. Epigenetic modifications and human disease. Nat. Biotechnol. 28, 105768 (2010). 4. Vavouri, T. & Lehner, B. Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. PLoS Genet. 7, e1002036 (2011). 5. Engreitz, J. M., Agarwala, V. & Mirny, L. a. Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. PLoS One 7, e44196 (2012). 6. Crutchley, J. L., Wang, X. Q. D., Ferraiuolo, M. a & Dostie, J. Chromatin conformation signatures: ideal human disease biomarkers? Biomark. Med. 4, 61129 (2010). 7. Göndör, A. Nuclear architecture and chromatin structure on the path to cancer. Semin. Cancer Biol. 23, 634 (2013). 8. Göndör, A. Dynamic chromatin loops bridge health and disease in the nuclear landscape. Semin. Cancer Biol. 23, 908 (2013). 9. Nagase, H. & Ghosh, S. Epigenetics: differential DNA methylation in mammalian somatic tissues. FEBS J. 275, 161723 (2008). 10. Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 37680 (2012). 11. Tanay, A. & Cavalli, G. Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization. Curr. Opin. Genet. Dev. 23, 197203 (2013). 12. Dekker, J., Marti-Renom, M. a & Mirny, L. a. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390403 (2013). 13. Baù, D. et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat. Struct. Mol. Biol. 18, 10714 (2011). 14. Umbarger, M. a et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell 44, 25264 (2011). 15. Baù, D. & Marti-Renom, M. a. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res. 19, 2535 (2011).

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[Gtpb] Bioinformatics Training Course CSDM13 - Reminder
by Pedro Fernandes 11 Nov '13

11 Nov '13

Course Announcement (Reminder) Applications are open for: CSDM13 "Chromosome structure determination using modeling and Hi-C data" with Davide Baù and François Serra (CNAG and CRG, Barcelona) IMPORTANT DATES for this Course Deadline for applications: November 20th 2013 Notification of acceptance within 72 hours of application Course date: November 27th to November 29th 2013 More details at the course website http://gtpb.igc.gulbenkian.pt/bicourses/CSDM13/ *Course description* The sequence of a genome alone does not carry enough information to fully understand how genomic processes are carried out in the cell nucleus; to achieve this, the knowledge of the three-dimensional (3D) architecture of a genome is necessary. Advances in genomic technologies and the development of new analytical methods, such as 3C-based methods, have allowed getting insights at unprecedented resolution into how the genome is organized. Recently, it has been shown that chromatin is organized in Topologically Associating Domains (TADs), large interaction domains that appear to be conserved among different cell types. In this course, participants will learn to use TADBit, a software for the analysis and 3D modeling of Topologically Associated Domains (TADs) and genomes. TADBit is based on a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. Participants can bring-in specific biological questions and/or their on data to work on during the course. *Target Audience* The course is oriented to experimental researchers with minimal computational skills, at the graduate and post-graduate levels. It is also suitable for bioinformatics developers at all levels. We anticipate that this course is attended by people with several types of interests in genome organization. It is likely that they may also aim at getting involved in generating Hi-C data for chromosome structure determination and that they want to model its 3D representation, but that does not need to be the case for all the participants: they may, for example, just want to explore publicly available data. -- -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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AlCoB 2014: 2nd call for papers
by GRLMC 09 Nov '13

09 Nov '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 1st INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY AlCoB 2014 Tarragona, Spain July 1-3, 2014 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/alcob2014/ ********************************************************************* AIMS: AlCoB aims at promoting and displaying excellent research using string and graph algorithms and combinatorial optimization to deal with problems in biological sequence analysis, genome rearrangement, evolutionary trees, and structure prediction. The conference will address several of the current challenges in computational biology by investigating algorithms aimed at: 1) assembling sequence reads into a complete genome, 2) identifying gene structures in the genome, 3) recognizing regulatory motifs, 4) aligning nucleotides and comparing genomes, 5) reconstructing regulatory networks of genes, and 6) inferring the evolutionary phylogeny of species. Particular focus will be put on methodology and significant room will be reserved to young scholars at the beginning of their career. VENUE: AlCoB 2014 will take place in Tarragona, located 90 kms. to the south of Barcelona. The venue will be the Catalunya Campus. SCOPE: Topics of either theoretical or applied interest include, but are not limited to: Exact sequence analysis Approximate sequence analysis Pairwise sequence alignment Multiple sequence alignment Sequence assembly Genome rearrangement Regulatory motif finding Phylogeny reconstruction Phylogeny comparison Structure prediction Compressive genomics Proteomics: molecular pathways, interaction networks ... Transcriptomics: splicing variants, isoform inference and quantification, differential analysis Next-generation sequencing: population genomics, metagenomics, metatranscriptomics ... Microbiome analysis Systems biology STRUCTURE: AlCoB 2014 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: Michael Galperin (National Center for Biotechnology Information, Bethesda), Comparative Genomics Approaches to Identifying Functionally Related Genes Uwe Ohler (Max-Delbrück Centre for Molecular Medicine, Berlin), Decoding Non-coding Regulatory Regions in DNA and RNA (tutorial) Jason Papin (University of Virginia, Charlottesville), Network Analysis of Microbial Pathogens PROGRAMME COMMITTEE: Tatsuya Akutsu (Kyoto, JP) Amihood Amir (Ramat-Gan, IL) Alberto Apostolico (Atlanta, US) Joel Bader (Baltimore, US) Pierre Baldi (Irvine, US) Serafim Batzoglou (Stanford, US) Bonnie Berger (Cambridge, US) Francis Y.L. Chin (Hong Kong, HK) Benny Chor (Tel Aviv, IL) Keith A. Crandall (Washington, US) Bhaskar DasGupta (Chicago, US) Joaquín Dopazo (Valencia, ES) Liliana Florea (Baltimore, US) Olivier Gascuel (Montpellier, FR) David Gilbert (Uxbridge, UK) Gaston H. Gonnet (Zurich, CH) Roderic Guigó (Barcelona, ES) Dan Gusfield (Davis, US) Vasant Honavar (University College, US) Sorin Istrail (Providence, US) Tao Jiang (Riverside, US) Inge Jonassen (Bergen, NO) Anders Krogh (Copenhagen, DK) Giovanni Manzini (Alessandria, IT) Carlos Martín-Vide (Tarragona, ES, chair) Satoru Miyano (Tokyo, JP) Burkhard Morgenstern (Göttingen, DE) Shinichi Morishita (Tokyo, JP) Cédric Notredame (Barcelona, ES) Graziano Pesole (Bari, IT) Mark Ragan (Brisbane, AU) Timothy Ravasi (Thuwal, SA) Allen G. Rodrigo (Durham, US) Steven Salzberg (Baltimore, US) David Sankoff (Ottawa, CA) Thomas Schiex (Toulouse, FR) João C. Setubal (São Paulo, BR) Steven Skiena (Stony Brook, US) Peter F. Stadler (Leipzig, DE) Wing-Kin Sung (Singapore, SG) Alfonso Valencia (Madrid, ES) Jacques van Helden (Marseille, FR) Arndt von Haeseler (Vienna, AT) Lusheng Wang (Hong Kong, HK) Limsoon Wong (Singapore, SG) Xiaohui Xie (Irvine, US) Dong Xu (Columbia, US) Zohar Yakhini (Santa Clara, US) Alex Zelikovsky (Atlanta, US) Michael Q. Zhang (Dallas, US) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) SUBMISSIONS: Authors are invited to submit non-anonymized papers in English presenting original and unpublished research. Papers should not exceed 12 single-spaced pages (including eventual appendices) and should be formatted according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=alcob2014 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS/LNBI series will be available by the time of the conference. A special issue of a major journal will be later published containing peer-reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from September 21, 2013 to July 1, 2014. The registration form can be found at: http://grammars.grlmc.com/alcob2014/Registration.php DEADLINES: Paper submission: February 4, 2014 (23:59 CET) Notification of paper acceptance or rejection: March 15, 2014 Final version of the paper for the LNCS/LNBI proceedings: March 22, 2014 Early registration: March 29, 2014 Late registration: June 17, 2014 Starting of the conference: July 1, 2014 End of the conference: July 3, 2014 Submission to the post-conference journal special issue: October 3, 2014 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: AlCoB 2014 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559543 Fax: +34 977 558386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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Mini symposium: "Bridging the gap between two omics worlds: transcriptomics and proteomics" - first announcement
by Gerben Menschaert 08 Nov '13

08 Nov '13

Dear colleagues, You are cordially invited to attend the free mini symposium on “Bridging the gap between two omics worlds: transcriptomics and proteomics", which will take place on November 29th, at Ghent University, Rommelaere Institute - Auditorium 1.39, A. Baertsoenkaai 3, 9000 GENT. Three (inter)national speakers will discuss, each from a different perspective, how the transcriptomics and proteomics worlds can be brought together: (1) Integration of high-throughput RNA sequencing and mass spectrometry (MS)-based proteomics in the cancer research, (2) Integration of the new ribosome profiling technique (sequencing of ribosome protected mRNA) and MS-based proteomics and (3) ways to boost the MS identification rate, based on machine learning, necessary due to the increased (RNA-seq derived) sequence search space. For more details about the program, I refer to the attachment. Please, feel free to spread this announcement in your department or to forward it to anyone who you think may be interested. Registration is free, but required. Registration is possible until Monday, November 25th. To do so, send an E-mail message to Gerben.Menschaert(a)Ugent.be. Should you have any questions, please feel free to ask. Sincerely, Gerben Menschaert dr. ir. Gerben Menschaert Post-doctoral fellow FWO Lab of Bioinformatics and Computational Genomics FBE - Ghent University Coupure Links 653 9000 Ghent, Belgium MAIL Gerben.Menschaert(a)Ugent.be PHONE +32 9 264 99 22 SKYPE gerben.menschaert

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open postdoc position exascale computing and software applications for next generation sequencing
by Tim Van den Bulcke 08 Nov '13

08 Nov '13

Dear all, we are looking for a motivated and independent *postdoctoral researcher*for the prestigious *Exascience Life project* (www.exascience.com) in collaboration with Janssen Pharmaceuticals, Intel, IMEC and Flemish universities. Please find the full description of this position below or at http://www.biomina.be/careers/postdoc-exascience-2013. Kind regards, Tim Van den Bulcke. ------- *Postdoctoral researcher computer science/bioinformatics: exascale computing and software applications for next generation sequencing* We are looking for a motivated and independent postdoctoral researcher for the prestigious *Exascience Life project* in collaboration with Janssen Pharmaceuticals, Intel, IMEC and Flemish universities. The exponential cost decline for DNA sequencing is revolutionizing biology and medicine. To take full advantage of these new technologies and to integrate these technologies in clinical workflows, important computational challenges need to be solved to reduce the analysis times and to make optimal use of novel computer architectures for exascale computing. Secondly, to demonstrate the results on both current and future computer architectures, novel prototype software applications need to be developed. In this 2-year project, you will: - Develop computationally optimized RNA and DNA sequencing analysis pipelines - Develop more efficient data representations for the analytical steps - Develop novel prototype software applications for NGS analysis - Integrate your research within the consortium and take full advantage of novel technologies and computer architectures for exascale computing *Profile *The ideal candidate holds a PhD degree in computer science and/or bioinformatics. Excellent programming and bioinformatics data analysis skills are essential, experience with next generation sequencing is highly recommended. Experience with design and optimization of algorithms and analytical pipelines are core assets. As part of a large Exascience team, good communication skills are important. The candidate will collaborate closely with researchers across the whole consortium. Qualified and ambitious candidates can have the opportunity to work semi-independently, write project grants and mentor PhD students. As this project has recently started and given the short and intense two-year project period, a full commitment is essential and the preferred start date is as soon as possible. We offer a competitive package and a challenging dynamic environment as part of the Exascience Lab, a world-class collaboration with IMEC ( www.imec.be) Janssen Pharmaceuticals (en.janssenpharmaceutica.be) and Intel (www.intel.com) You will work part-time embedded at IMEC in the Exascience Lab and part-time at the University of Antwerp within the ADReM research group (adrem.ua.ac.be). As part of the biomina consortium ( www.biomina.be) at the University of Antwerp, you will have the opportunity to collaborate with a large group of bioinformatics researchers at Antwerp University and Antwerp University Hospital. To apply, send your curriculum vitae, publication list, motivation letter and two references to prof. Tim Van den Bulcke. *Contract duration:* 2 years *Contact person:* prof. Tim Van den Bulcke (tim.vandenbulcke(a)uantwerpen.be) *Relevant links:* www.exascience.com, www.biomina.be, adrem.ua.ac.be<file:///P:/Documenten2/administratie/UA/adrem.ua.ac.be>, www.imec.be, en.janssenpharmaceutica.be<file:///P:/Documenten2/administratie/UA/en.janssenpharmaceutica.be>, www.intel.com. _________________________________________________ prof. dr. ir. Tim Van den Bulcke research coordinator biomedical informatics *biomina *- biomedical informatics research group *UZA - Universitair Ziekenhuis Antwerpen* Wilrijkstraat 10 2650 Edegem *ADReM* - Advanced Database Research and Modelling *University Antwerp* Middelheimlaan 1 2020 Antwerp T +32 (0)3 821 52 85 F +32 (0)3 821 44 30 E tim.van.den.bulcke(a)uza.be W www.biomina.be, www.uza.be, www.adrem.ua.ac.be _________________________________________________

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three Bioinformatics vacancies in Maastricht
by Egon Willighagen 08 Nov '13

08 Nov '13

Hi all, there are three open vacancies in our group, two PhD positions, and one post-doc position (for up to 3 years): These two are within the context of a EU FP7 project, eNanoMapper, for setting up a data platform using ontologies, ISATab, and more, to support data analysis and bioinformatics studies in the area of the European NanoSafety Cluster, both with a strong focus on systems nanotoxicology: https://www.academictransfer.com/20445/ https://www.academictransfer.com/20444/ The second PhD positions is about the development of approaches to make genetic variation accessible in pathway representations for instance by connecting WikiPathways to the resources mentioned above and using that information to answer biological questions and develop the analytical tools to do so, including pathway and network approaches: https://www.academictransfer.com/20596/ With kind regards, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286

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Fwd: Postdoc search: Postdoctoral computer scientist – Algorithms for high-performance genomic data fusion
by mimi deprez 08 Nov '13

08 Nov '13

Postdoctoral computer scientist – Algorithms for high-performance genomic data fusion Do you know how to tackle large data sets? Do you know how to leverage high-performance computing for machine learning in computational biology? We are looking for a motivated postdoctoral researcher who can help us to scale up machine learning algorithms for data fusion of genomic data. How to mine multiple heterogeneous sources of genomic data in an integrated fashion is still an open problem. Researchers need to analyse and integrate sequences and their variants, expression data, protein-protein interactions, functional annotations, biomedical literature, and so on – all at the same time. Genomic data fusion (Moreau and Tranchevent, 2012; Aerts et al., 2006) offers a range of approaches to tackle this challenge. Among such methods, the University of Leuven has been a pioneer in 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). The goal of the project is to develop simple, efficient, and scalable kernel methods for genomic data fusion using low-rank approximation, random projections, or ensemble methods and implement them in a large-scale parallel execution environment. We offer a competitive package and a fun, dynamic environment as part of the Exascience Lab, a world-class collaboration with Intel (intel.eu), Janssen Pharmaceuticals (janssenpharmaceuticalsinc.com) and IMEC (imec.be). 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 efficient algorithms for machine learning and scale-up of such algorithms to large genomic data sets via high-performance, cloud, or grid computing are core assets. Programming and data analysis experience is essential. Willingness to interact with genomics experts is mandatory. Good communication skills are important for this role. The candidate will collaborate closely with researchers across the consortium and contribute to the reporting of the project. Qualified candidates will be offered the opportunity to work semi-independently under the supervision of a senior investigator, mentor PhD students, and contribute to the acquisition of new funding. A two-year commitment is expected from the candidate. Preferred start date as soon as possible. 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. How to apply Please send in PDF before November 30, 2013: 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 Ms. 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/

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BBC 2013 early registration deadline extended
by BBC2013 06 Nov '13

06 Nov '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Early registration deadline (extended): November 13, 2013 Dear Colleagues, We extended the early registration deadline to BBC 2013 to November 13, 2013! Note that this is also the deadline for taking advantage of the discounted rates for single and double rooms at the NH Hotels in Brussels. If you have already registered, you also have received in the confirmation email the form to fill in and to send to the hotel before November 13, 2013. Note also that a provisional program of the conference is now available on the conference web-site: http://bbc2013.ibsquare.be/content/program . The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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[Gtpb] Reminder: Bioinformatics training course announcement CSDM13
by Pedro Fernandes 05 Nov '13

05 Nov '13

Course Announcement (Reminder) Applications are open for: CSDM13 "Chromosome structure determination using modeling and Hi-C data" with Davide Baù and François Serra (CNAG and CRG, Barcelona) IMPORTANT DATES for this Course Deadline for applications: November 20th 2013 Notification of acceptance within 72 hours of application Course date: November 27th to November 29th 2013 More details at the course website http://gtpb.igc.gulbenkian.pt/bicourses/CSDM13/ *Course description* The sequence of a genome alone does not carry enough information to fully understand how genomic processes are carried out in the cell nucleus; to achieve this, the knowledge of the three-dimensional (3D) architecture of a genome is necessary. Advances in genomic technologies and the development of new analytical methods, such as 3C-based methods, have allowed getting insights at unprecedented resolution into how the genome is organized. Recently, it has been shown that chromatin is organized in Topologically Associating Domains (TADs), large interaction domains that appear to be conserved among different cell types. In this course, participants will learn to use TADBit, a software for the analysis and 3D modeling of Topologically Associated Domains (TADs) and genomes. TADBit is based on a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. Participants can bring-in specific biological questions and/or their on data to work on during the course. *Target Audience* The course is oriented to experimental researchers with minimal computational skills, at the graduate and post-graduate levels. It is also suitable for bioinformatics developers at all levels. We anticipate that this course is attended by people with several types of interests in genome organization. It is likely that they may also aim at getting involved in generating Hi-C data for chromosome structure determination and that they want to model its 3D representation, but that does not need to be the case for all the participants: they may, for example, just want to explore publicly available data. Pedro Fernandes GTPB Organiser PS. You may be interested in a recent review on the subject of this course, "Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data" Job Dekker, Marc A. Marti-Renom & Leonid A. Mirny Nature Reviews Genetics, 14, 390403 (2013) doi:10.1038/nrg3454 http://sgt.cnag.cat/services/BBibTeX/pdfs/20130509_DekkerMarti-RenomMirny_N… -- -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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TPNC 2013: call for participation
by GRLMC - URV 04 Nov '13

04 Nov '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ----------------------------------------------------------------------------------------------------------- 2nd INTERNATIONAL CONFERENCE ON THE THEORY AND PRACTICE OF NATURAL COMPUTING TPNC 2013 Cáceres, Spain December 3-5, 2013 http://grammars.grlmc.com/tpnc2013/ ---------------------------------------------------------------------------------------------------------- PROGRAMME Tuesday, December 3 09:00 - 09:50 Registration 09:50 - 10:00 Opening 10:00 - 10:50 Eugen Czeizler, Pekka Orponen: Yield optimization strategies for (DNA) staged Tile Assembly Systems Vinay Kumar Gautam, Pauline C. Haddow, Martin Kuiper: Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles 10:50 - 11:20 Coffee Break 11:20 - 13:00 Mirosław Kordos, Andrzej Rusiecki: Improving MLP Neural Network Performance by Noise Reduction Omar K. Shoukry, Magda B. Fayek: Evolutionary Scheduling for Mobile Content Pre-fetching Marius Nagy, Naya Nagy: General Quantum Encryption Scheme based on Quantum Memory Marius Nagy, Naya Nagy: Quantum Secret Communication without an Encryption Key 13:00 - 14:45 Lunch 14:45 - 15:35 Oliver Rice, Robert Smith, Rickard Nyman: GPU Multi-Objective Genetic Algorithm: Asynchronously Parallel Distributed NSGA-II Anne Jeannin-Girardon, Pascal Ballet, Vincent Rodin: An Efficient Biomechanical Cell Model to Simulate Large Multi-cellular Tissue Morphogenesis: Application to Cell Sorting Simulation on GPU 15:35 - 15:50 Break 15:50 - 16:40 Joel Lehman, Risto Miikkulainen: Boosting Interactive Evolution using Human Computation Markets – Invited Tutorial I Wednesday, December 4 09:00 - 10:40 Rim Hentech, Ilyes Jenhani, Zied Elouedi: Learning from Uncertain Data Using Possibilistic Artificial Immune Recognition Systems Massimiliano D’Angelo, Berend Weel, Agoston E. Eiben: Online Gait Learning for Modular Robots with Arbitrary Shapes and Sizes José M. Lanza-Gutiérrez, Juan A. Gómez-Pulido, Miguel Ángel Vega-Rodríguez: A Trajectory Algorithm to Solve the Relay Node Placement Problem in Wireless Sensor Networks Rafael Nogueras, Carlos Cotta, Carlos M. Fernandes, Juan Luis Jiménez Laredo, Juan Julián Merelo, Agostinho C. Rosa: An Analysis of a Selecto-Lamarckian Model of Multimemetic Algorithms with Dynamic Self-Organized Topology 10:40 - 11:10 Coffee Break 11:10 - 12:00 Poster session I Orlando Duran: A Hybrid Solution to the Multi-Echelon Inventory Problem of Repairable Spare Parts Using Discrete Swarm Intelligence and a Local Search Procedure Jesús Torrecilla-Pinero, Fernando Torrecilla-Pinero, Juan A. Gómez-Pulido, Carlos Urueña-Fernández: A Novel Way to Optimize Cantilever Walls by Means of Natural Computing and Multiobjective Optimization Hector Zenil: Complexity and Algorithmic Probability of Animal Behaviour from Cognition to Communication Ron Cottam, Willy Ranson, Roger Vounckx: A Framework for Computing like Nature Cristina Martínez-Ramírez, Alberto Besana: Models for the Distribution of Letters in Random Generated Words Raúl Domínguez, Tim Köhler, Christian Rauch, Elmar Berghöfer, Frank Kirchner: Autonomous Robot Long Distance Traversing by a Robust Nature-Inspired Behaviour Control Model Using Sensor Feedback Expectations 12:00 - 12:15 Break 12:15 - 13:05 Joel Lehman, Risto Miikkulainen: Boosting Interactive Evolution using Human Computation Markets – Invited Tutorial II 13:05 - 14:50 Lunch 14:50 - 15:50 Poster session II Kazunari Ozasa, Jeesoo Lee, Simon Song, Masahiko Hara, Mizuo Maeda: Introduction of Artificial Pheromone Effects on Euglena Cells Toward Ant Colony Optimization Experiments Kristīne Cīpola, Rūsiņš Freivalds: Examples of Advantages for Ultrametric Automata Mikhail Peretyat’kin: Combinatorial Computation in First-Order Predicate Logic as a Formal Prototype of Natural Computing Alidra Abdelghani, Mohamed Tahar Kimour: Biology Inspired Decision Making for Self-Healing Realtime Systems Kristīne Cīpola, Kārlis Ceziņš, Rūsiņš Freivalds, Viesturs Vēzis: Producing Learning Tools to Teach Quantum and Ultrametric Automata Antonio J. Tallón-Ballesteros, José C. Riquelme, César Hervás-Martínez, Roberto Ruiz: Enhancing the Performance of a Feature Selection Method Based Jointly on Feature Ranking and Feature Subset Selection in the Context of a Neural Network Classifier Ángela Villota, Jesús Aranda: Towards a General Approach to Model Biological Systems from Membrane Systems into a Concurrent Constraint Calculus 15:55 Visit to the City Thursday, December 5 09:00 – 09:50 Xin Yao: Evolutionary Algorithm Portfolios for Numerical Optimisation - Invited Talk 09:50 - 10:05 Break 10:05 - 11:20 Yara Khaluf, Mauro Birattari, Franz Rammig: Probabilistic Analysis of Long-term Swarm Performance under Spatial Interferences Víctor Berrocal-Plaza, Miguel Ángel Vega-Rodríguez, Juan M. Sánchez-Pérez: A New Version of the Multiobjective Artificial Bee Colony Algorithm for Optimizing the Location Areas Planning in a Realistic Network Takuya Nishida, Takaaki Mizuki, Hideaki Sone: Securely Computing the Three-Input Majority Function with Eight Cards 11:20 - 11:50 Coffee Break 11:50 - 13:05 Yahya O. Mohamed Elhadj, Mansour Alghamdi, Mohamed Alkanhal: Approach for Recognizing Allophonic Sounds of the Classical Arabic Based on Quran Recitations Antonio Martí Campoy, Francisco Rodríguez-Ballester, Rafael Ors Carot: Using Dynamic, Full Cache Locking and Genetic Algorithms for Cache Size Minimization in Multitasking, Preemptive, Real-time Systems Lingling Jin, Ian McQuillan: Computational Modelling of the Interruptional Activities between Transposable Elements 13:05 Closing

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