November 2013 - BBClist - maillist.psb.ugent.be

BBC 2013 abstract submission through EasyChair
by BBC2013 01 Apr '14

01 Apr '14

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 1, 2013 Dear Colleagues, The 8th edition of the BeNeLux Bioinformatics Conference will take place in Brussels on the 9th and 10th of December 2013. 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) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 . Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . 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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Postdoc position Raes lab - genome-microbiome associations
by jeroen raes 29 Nov '13

29 Nov '13

Dear all - I have a vacancy for a postdoctoral position in our lab for someone with a strong background in clinical genetics/genomics data analysis who is keen to explore the wonderful world of the human microbiome! Please also forward to any potentially interested candidates you might know. cheers, jeroen -- Prof. Jeroen Raes, PhD Bioinformatics and (eco-)systems biology lab *NEW* Department of Microbiology and Immunology, KU Leuven (from jan 2014 onwards) VIB Department of Structural Biology, Brussels Department of Microbiology, VUB jeroen.raes(a)med.kuleuven.be Phone: +32 (0)2 629 13 41 http://www.raeslab.org -- Prof. Jeroen Raes, PhD Bioinformatics and (eco-)systems biology lab Department of Microbiology and Immunology, KU Leuven VIB Department of Structural Biology, Brussels Department of Microbiology, VUB jeroen.raes(a)med.kuleuven.be Phone: +32 (0)2 629 13 41 http://www.raeslab.org

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Fwd: Open position for Postdoc bioinformatics – High-performance genomic data fusion
by mimi deprez 28 Nov '13

28 Nov '13

Dear team: On behalf of prof. Moreau , we are looking for a enthousiastic and motivated postdoctoral researcher for the prestigious ExaScience Life Pharma IWT O&O project (www.exascience.com) in collaboration with Janssen Pharmaceuticals, Intel, IMEC and Flemish universities. Please find the detailed description of the position below . Sincerely, Mimi ------- Postdoc bioinformatics – High-performance genomic data fusion For the Bioinformatics research group of Yves Moreau at ESAT – STADIUS Centre for Dynamical Systems, Signal Processing and Data Analytics (KU Leuven), we are looking for a postdoctoral researcher to scale up machine learning algorithms for data fusion of genomic data Computational biology is entering the big data era. Genomic data and relatives are indeed archetypes of the big data paradigm: Volume, Velocity and Variety. 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. This integrated mining is essential for correct interpretation of the mass of Next Gen Sequencing data currently produced, with its importance diffusing from biomedical research into drug discovery pipelines and clinical trials. Mining multiple heterogeneous sources of genomic data in an integrated fashion, is still an open problem. It therefore is a key research question for the ExaScience Lab, a world-class collaboration with Intel (intel.eu), Janssen Pharmaceuticals (janssenpharmaceuticalsinc.com) and Imec (imec.be) on the next generation of high-performance computing for biomedical challenges. 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 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. 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. STADIUS offers recognized expertise in diverse application fields such as industrial automation, audio and speech communication, digital communications, biomedical signal and data processing, and bio-informatics Profile The ideal candidate holds a PhD degree in computer science or computational biology. Exceptional PhD candidates can also be considered. 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 15 December 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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[Gtpb] REMINDER: Bioinformatics training course announcement IB13S
by Pedro Fernandes 28 Nov '13

28 Nov '13

DEADLINE approaching: DECEMBER 1st 2013 Course Announcement Applications are open for: IB13S "Introductory Bioinformatics" with David P.Judge, Cambridge University, Cambridge UK Phil Cunningham, Kings College London, London UK and Pedro Fernandes, Inst Gulbenkian de Ciência, Oeiras PT IMPORTANT DATES for this Course Deadline for applications: December 1st 2013 Course date: December 9th - 12th 2013 http://gtpb.igc.gulbenkian.pt/bicourses/IB13S/ As usual, we run this course twice a year due to its popularity. The course is named "Introductory" because of the low level of pre-requisites. It does provide a set of skills that allow participants handle sequence data and survive in the world of biological information using computational tools. Former attendees have stated that the content of our IB course enabled them to go a lot further, by figuring out what Bioinformatics really offers and how its results can influence their attitude towards research. The website at http://gtpb.igc.gulbenkian.pt/bicourses/IB13S offers both a standard and a detailed description of the course content. Pedro Fernandes GTPB Organiser -- -- 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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SSTiC 2014: 1st announcement
by GRLMC 23 Nov '13

23 Nov '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 2014 TARRAGONA INTERNATIONAL SUMMER SCHOOL ON TRENDS IN COMPUTING SSTiC 2014 Tarragona, Spain July 7-11, 2014 Organized by Rovira i Virgili University http://grammars.grlmc.com/sstic2014/ ********************************************************************* AIM: SSTiC 2014 is the second edition in a series started in 2013. For the previous event, see http://grammars.grlmc.com/SSTiC2013/ SSTiC 2014 will be a research training event mainly addressed to PhD students and PhD holders in the first steps of their academic career. It intends to update them about the most recent developments in the diverse branches of computer science and its neighbouring areas. To that purpose, renowned scholars will lecture and will be available for interaction with the audience. SSTiC 2014 will cover the whole spectrum of computer science through 5 keynote lectures and 30 six-hour courses dealing with the hottest topics in the field. The organizers share the idea that outstanding speakers will really attract high-quality students. ADDRESSED TO: Graduate students from around the world. There are no formal pre-requisites in terms of the academic degree the attendee must hold. However, since there will be several levels in the courses, reference may be made to specific knowledge background in the description of some of them. SSTiC 2014 is also appropriate for more senior people who want to keep themselves updated on developments in their own field or in other branches of computer science. They will surely find it fruitful to listen and discuss with scholars who are main references in computing nowadays. REGIME: In addition to keynotes, 3 parallel sessions will be held during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: SSTiC 2014 will take place in Tarragona, located 90 kms. to the south of Barcelona. The venue will be: Campus Catalunya Universitat Rovira i Virgili Av. Catalunya, 35 43002 Tarragona KEYNOTE SPEAKERS: Larry S. Davis (U Maryland, College Park), A Historical Perspective of Computer Vision Models for Object Recognition and Scene Analysis George Karypis (U Minnesota, Twin Cities), Recommender Systems Past, Present, & Future Ronald R. Yager (Iona C, New Rochelle), tba ... more will come ... COURSES AND PROFESSORS: Divyakant Agrawal (U California, Santa Barbara), [intermediate] Scalable Data Management in Enterprise and Cloud Computing Infrastructures Rajkumar Buyya (U Melbourne), [intermediate] Cloud Computing Kwang-Ting (Tim) Cheng (U California, Santa Barbara), [introductory/intermediate] Smartphones: Hardware Platform, Software Development, and Emerging Apps Richard M. Fujimoto (Georgia Tech, Atlanta), [introductory] Parallel and Distributed Simulation Mark Guzdial (Georgia Tech, Atlanta), [introductory] Computing Education Research: What We Know about Learning and Teaching Computer Science George Karypis (U Minnesota, Twin Cities), [intermediate] Programming Models/Frameworks for Parallel & Distributed Computing Arie E. Kaufman (U Stony Brook), [advanced] Visualization Sudhakar M. Reddy (U Iowa, Iowa City), [introductory] Test and Design for Test of Digital Logic Circuits Robert Sargent (Syracuse U), [introductory] Validation of Models Mubarak Shah (U Central Florida, Orlando), [intermediate] Visual Crowd Analysis Steffen Staab (U Koblenz), [intermediate] Programming the Semantic Web Mike Thelwall (U Wolverhampton), [introductory] Sentiment Strength Detection for Twitter and the Social Web Nitin Vaidya (U Illinois, Urbana-Champaign), [introductory/intermediate] Distributed Consensus: Theory and Applications Philip Wadler (U Edinburgh), [intermediate] Topics in Lambda Calculus and Life ... more will come ... ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) REGISTRATION: It has to be done at http://grammars.grlmc.com/sstic2014/registration.php The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course. Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed when the capacity of the venue will be complete. It is very convenient to register prior to the event. FEES: As far as possible, participants are expected to attend for the whole (or most of the) week (full-time). Fees are a flat rate allowing one to attend all courses. They vary depending on the registration deadline. If seats will still be available, shortly prior to the event attending only a few days (part-time) may be permitted, with the appropriate adjustment of the fees. ACCOMMODATION: Information about accommodation will be available on the website of the School in due time. CERTIFICATE: Participants will be delivered a certificate of attendance. QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: SSTiC 2014 Lilica Voicu Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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Final announcement: Mini symposium "Bridging the gap between two omics worlds: transcriptomics and proteomics"
by Gerben Menschaert 21 Nov '13

21 Nov '13

Dear colleagues, There are still seats available for 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 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 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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[Gtpb] Bioinformatics training course announcement IB13S
by Pedro Fernandes 18 Nov '13

18 Nov '13

Course Announcement Applications are open for: IB13S "Introductory Bioinformatics" with David P.Judge, Cambridge University, Cambridge UK Phil Cunningham, Kings College London, London UK and Pedro Fernandes, Inst Gulbenkian de Ciência, Oeiras PT IMPORTANT DATES for this Course Deadline for applications: December 1st 2013 Course date: December 9th - 12th 2013 http://gtpb.igc.gulbenkian.pt/bicourses/IB13S/ As usual, we run this course twice a year due to its popularity. The course is named "Introductory" because of the low level of pre-requisites. It does provide a set of skills that allow participants handle sequence data and survive in the world of biological information using computational tools. Former attendees have stated that the content of our IB course enabled them to go a lot further, by figuring out what Bioinformatics really offers and how its results can influence their attitude towards research. The website at http://gtpb.igc.gulbenkian.pt/bicourses/IB13S offers both a standard and a detailed description of the course content. Pedro Fernandes GTPB Organiser -- -- 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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Fwd: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI
by Jacques van Helden 15 Nov '13

15 Nov '13

Begin forwarded message: From: Nicholas Luscombe <nick(a)valleyofpigs.org> Subject: FINAL CALL: Faculty positions in Bioinformatics/Computational Biology in the Crick at LRI Date: 15 November 2013 11:33:23 CET To: Nicholas Luscombe <Nicholas.Luscombe(a)cancer.org.uk> Cc: Paul Nurse <paul.nurse(a)royalsociety.org>, Jim Smith <director(a)nimr.mrc.ac.uk>, Richard Treisman <richard.treisman(a)cancer.org.uk> Dear Colleagues, Thank you for your help in circulating information about the Bioinformatics/Computational Biology position at the Crick@LRI. We’ve had a lot of interest and we’re hoping that many will result in applications! I would like to remind you that the deadline is 22 November 2013; I should be grateful if you would continue to spread the word. With many thanks for your support, Nick Luscombe Website: http://tinyurl.com/ohgnxw8 Application deadline: 22 November 2013 Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk --- Faculty positions for Bioinformatics and Computational Biology Francis Crick Institute group leaders at the CRUK London Research Institute An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The Francis Crick Institute http://www.crick.ac.uk The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies. The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-the-art data centre. The London Research Institute http://www.london-research-institute.org.uk The London Research Institute (LRI) is the largest Cancer Research UK research institute, with 40 research groups focusing on fundamental cancer biology. The Institute is based in well-equipped laboratories at Lincoln's Inn Fields in central London, and at Clare Hall in Hertfordshire. Computational Biology in Cancer http://tinyurl.com/ohgnxw8 An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis. The LRI recruitment process for 2013 will carried out jointly with the Crick Institute. We shall appoint outstanding scientists seeking to establish independent and innovative research programmes focussed on: Newly appointed group leaders will receive core funding for research personnel, travel and consumables, and access to the Institute's comprehensive computational core facilities, backed by competitive employment terms. The new group leaders will move to the Crick laboratories in 2015. Website: http://tinyurl.com/ohgnxw8 Application deadline: 22 November 2013 Informal enquiries may be made by e-mail to nicholas.luscombe(a)cancer.org.uk --- Check out our new website: www.luscombelab.org Nicholas M LUSCOMBE, Professor of Computational Biology University College London (joint appointment) UCL Genetics Institute, Dept of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute (joint appointment) 44 Lincoln's Inn Fields, London WC2A 3LY, UK Okinawa Institute of Science & Technology (adjunct faculty) 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan

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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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