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Genome Informatics Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference GENOME INFORMATICS September 15–September 19, 2010 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Cold Spring Harbor Laboratory Institutional Repository Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference GENOME INFORMATICS September 15–September 19, 2010 Arranged by Inanc Birol, BC Cancer Agency, Canada Michele Clamp, BioTeam, Inc. James Kent, University of California, Santa Cruz, USA SCHEDULE AT A GLANCE Wednesday 15th September 2010 17.00-17.30 Registration – finger buffet dinner served from 17.30-19.30 19.30-20:50 Session 1: Epigenomics and Gene Regulation 20.50-21.10 Break 21.10-22.30 Session 1, continued Thursday 16th September 2010 07.30-09.00 Breakfast 09.00-10.20 Session 2: Population and Statistical Genomics 10.20-10:40 Morning Coffee 10:40-12:00 Session 2, continued 12.00-14.00 Lunch 14.00-15.20 Session 3: Environmental and Medical Genomics 15.20-15.40 Break 15.40-17.00 Session 3, continued 17.00-19.00 Poster Session I and Drinks Reception 19.00-21.00 Dinner Friday 17th September 2010 07.30-09.00 Breakfast 09.00-10.20 Session 4: Databases, Data Mining, Visualization and Curation 10.20-10.40 Morning Coffee 10.40-12.00 Session 4, continued 12.00-14.00 Lunch 14.00-16.00 Free afternoon 16.00-17.00 Keynote Speaker: Alex Bateman 17.00-19.00 Poster Session II and Drinks Reception 19.00-21.00 Dinner Saturday 18th September 2010 07.30-09.00 Breakfast 09.00-10.20 Session 5: Sequencing Pipelines and Assembly 10.20-10.40 Morning Coffee 10.40-12.00 Session 5, continued 12.00-14.00 Lunch 14.00-15.20 Session 6: Comparative and Evolutionary Genomics 15.20-15.40 Break 15.40-17.00 Session 6, continued 17.00-19.00 Pre Dinner Drinks 19.00-21.00 Conference Dinner Sunday 19th September 2010 07.30-09.00 Breakfast 09.00-10.20 Session 6: RNA Sequencing and Gene Prediction 10.20-10.40 Morning Coffee 10.40-12.00 Session 6, continued 12.00-14.00 Lunch 14.00 Return Transfers to Cambridge and LHR & STN Airports General Information Welcome to the Wellcome Trust Conference Centre and the Genome Informatics Conference. Conference Badges Please wear your name badge at all times to promote networking and to assist staff in identifying you. If you have advised us of any dietary requirements, you will find a small coloured dot on your badge. Please make yourself known to the catering team and they will assist you with your meal request. Scientific Session Protocol Photography, audio or video recording of the scientific sessions is not permitted. Internet Access Wireless internet access is available throughout the campus. Please inquire at reception for a Wireless Connection token. Presentations If you are an invited speaker or your abstract has been selected for an oral presentation, please provide an electronic copy of you talk to a member of the AV team who will be based in the auditorium. Poster Sessions Posters will be displayed throughout the conference. Please post your materials in the Cloisters on arrival. The abstract page number indicates to the assigned poster board number Social Events Thursday, 16 September – A drinks reception will take place in the Conference Centre Cloisters from 17.00 during poster session I. Friday, 17 September - A drinks reception will take place in the Conference Centre Cloisters from 17.00 during poster session II. Saturday, 18 September - Pre dinner drinks will take place in the Conference Centre Cloisters from 17.00. Conference Meals All meals will be served in the Hall Restaurant. Please refer to the conference programme in this book as times will vary based on the daily scientific presentations. All conference meals and social events are for registered delegates only. For Wellcome Trust Conference Centre Guests Check in If you are staying on site at the Wellcome Trust you may check into your room from 2.00pm. If you plan to arrive late at night you can check into your room as the conference centre reception is open 24 hours. Please note there will be no lunch or dinner facilities available outside of the conference timetable; however, there is a local public house (The Red Lion), serving both lunch and evening meals, located just 2 minute walk from the campus in the village of Hinxton. Breakfast Your breakfast will be served in the Hall restaurant from 07.30 – 09.00 every morning. Telephone If you are staying on-site and would like to use the telephone in your room, you will need to contact the Reception desk (Ext. 5000) to have your phone line activated - we will require your credit card number and expiry date to do so. Departures You must vacate your room by 10.00 on the day of your departure. Please ask at reception for assistance with luggage storage in the Conference Centre. Homerton College Guests Check in If you are staying at Homerton College in Cambridge, you are able to check into your room from 14.00 Breakfast Your breakfast will be served at the Homerton College from 07.30-08.15 You must vacate your room by 09.00 on the day of your departure. A luggage store is available in the Conference Centre please ask at the reception. Complimentary transfers have been arranged to and from the Conference Centre, please see below for times. Transfers Wednesday 15th September 2010 22.45 Conference Centre – Homerton College Thursday 16th September 2010 08.15 Homerton College – Conference Centre 21.30 Conference Centre – Homerton College Friday 17th September 2010 08.15 Homerton College – Conference Centre 21.30 Conference Centre – Homerton College Saturday 18th September 2010 08.15 Homerton College – Conference Centre 21.30 Conference Centre – Homerton College Sunday 19th September 2010 08.15 Homerton College – Conference Centre Return Ground Transportation Complimentary return transportation to Heathrow, Stansted Airport and the Cambridge Train Station and City Centre have been arranged for 14.00 on Sunday, 19 September. Please note: a sign-up sheet will be available at the registration desk. Places are limited so you are advised to book early. Taxis Please find a list of local taxi numbers should you require: Panther – 01223 715715 Mid Anglia - Tel: 01223 836000 Phil's Taxi Services - Tel: 01223 521918 A&M Carriages (Airport Specialist) - Tel: 01223 513703 Messages and Miscellaneous All messages will be posted on the registration desk in the Conference Centre Foyer. A number of toiletry and stationery items are available for purchase at the conference centre reception. Cards for our self-service laundry are also available. If you have any queries or comments, please do not hesitate to contact a member of staff who will be pleased to help you. Joint Cold Spring Harbor Laboratory/Wellcome Trust conferences at Hinxton are supported in part with funding courtesy of The Wellcome Trust. These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with consent of the author. Printed on 100% recycled paper. Front and Back Covers: Martin Krzywinski, British Columbia Cancer Agency, Vancouver, Canada. Sequences of genes mentioned in the list of abstracts of the conference, rendered as paths. For details, see http://mkweb.bcgsc.ca/genomeinfo2010. PROGRAM WEDNESDAY, September 15—7:30 PM SESSION 1 SEQUENCING PIPELINES AND ASSEMBLY Chairpersons: Z. Torok, Astrid Research, Debrecen, Hungary I. Birol, BC Cancer Agency, Vancouver, Canada Reference assembly in colour space Balazs Gór, Anett Balla, Edit Tukacs, Miklós Laczik, István Nagy, Zsolt Török. Presenter affiliation: Astrid Research Inc. , Debrecen, Hungary; University of Debrecen, Medical and Health Science Center, Debrecen, Hungary. 1 Columbus—Hybrid de novo and mapped assembly of short read transcriptomic or genomic data Daniel R. Zerbino, Wendy Lee, Chris Wilks, Mark Diekhans, Benedict J. Paten, Zachary J. Sanborn, Marcel H. Schulz, David Haussler. Presenter affiliation: University of California, Santa Cruz , Santa Cruz, California. 2 Efficient overlap-based assembly methods and applications to sequence variation detection Jared T. Simpson, Richard Durbin. Presenter affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom. 3 Sequencing and analyses of the hexaploid wheat chromosome 3B Frédéric Choulet, Etienne Paux, Philippe Leroy, Arnaud Couloux, Michael Alaux, Hadi Quesneville, Patrick Wincker, Catherine Feuillet. Presenter affiliation: INRA, Clermont-Ferrand, France. 4 A general method for assembling genomes from short reads David B. Jaffe, Iain A. MacCallum, Sante Gnerre, Filipe Ribeiro, Dariusz Przybylski, Bruce Walker, Joshua Burton, Ted Sharpe, Giles Hall, Carsten Russ, Chad Nusbaum. Presenter affiliation: Broad Institute, Cambridge, Massachusetts. 5 vii Capturing biological function in de novo assemblies of cereal genomes Shiran Pasternak, Jer-Ming Chia, Andrew Olson, Joshua Stein, Doreen Ware. Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. 6 WaveSeq—a novel algorithm for CNV detection from next- generation sequencing data Bojan Losic, Sujata Syam, Quang Trinh, Richard de Borja, Irina Kalatskaya, John McPherson, Lakshmi Muthuswamy. Presenter affiliation: Ontario Institute for Cancer Research, Toronto, Canada; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; University of Toronto, Toronto, Canada. 7 RNA-Seq in Ensembl Simon J. White, Bronwen Aken, John E. Collins, Susan Fairley, Thibaut Hourlier, Magali Ruffer, Steve Searle, Derek Stemple, Amy Tang, Jan-Hinnerk Vogel, Amonida Zadissa, Tim Hubbard. Presenter affiliation: Wellcome Trust Sanger Institute, Cambridge, United Kingdom. 8 THURSDAY, September 16—9:00 AM SESSION 2 POPULATION AND STATISTICAL GENOMICS Chairpersons: R. Durbin, Wellcome Trust Sanger Institute, Hinxton, UK E. Margulies, NHGRI, National Institutes of Health, Bethesda, Maryland, USA Efficient strategies for population genome sequencing Richard Durbin.
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