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Scientific Contributions

DEFINITIVE PROGRAM including Posters (in PDF format: NGS2009-BOOK)

NEW! Some slides are available in the Abstracts page.

Invited Talks

INAUGURAL SPEECH: Sequencing the Cancer Genome
Richard K. Wilson
Washington University, MO, USA

Reverse Phenotyping: Towards an integrated (epi)genomic approach to complex phenotypes and common disease
Stephan Beck
UCL Cancer Institute, University College London, London WC1E 6BT, UK

Population Genomics in the Personal Genome Era
Carlos Bustamante
Dept of Biological Statistics and Computational Biology. Cornell University, (Ithaca) NY, USA

Discovering INDEL and Copy Number genomic variation from short reads
Michael Brudno
Dept of Computer Science. Pratt Bldg, Room 286C. 6 King's College Rd. University of Toronto. Toronto, ON M5S 3G4, Canada

Using short-read sequencing to dissect allele-specific expression
Andrew G. Clark
Department of Molecular Biology and Genetics. Cornell University, (Ithaca) NY, USA

Next generation sequencing in marine ecological genomics: tools and applications
Frank Oliver Glöckner
Max Planck Institute for Marine Microbiology, Microbial Genomics and Bioinformatics Group, Celsiusstrasse 1, 28359 Bremen, Germany, and Jacobs University Bremen.

Next-generation data analysis
Philip Green
Department of Genome Sciences. University of Washington, WA, USA

SNP discovery and analysis of selective sweeps using massive parallel short-read sequencing
Groenen, Martien AM(1), Megens H-J(1), Crooijmans RPMA(1), Amaral AJ(1), Ferretti L(2) and Schook LB(3)
1. Wageningen University, Animal Breeding and Genomics Centre, P.O. Box 338, 6700AH, Wageningen, The Netherlands. 2. Universitat Autonoma Barcelona - ICREA, 08193 Bellaterra, SPAIN. 3. University of Illinois, Institute for Genomic Biology, 382 ERML, 1201 W. Gregory Avenue, Urbana, IL 61801, USA.

The transcriptional complexity of the human genome: Insights from Next Generation Technologies
Roderic Guigó
Centre de Regulacio Genomica (2) Grup de Recerca en Informatica Biomedica (IMIM and UPF). Dr. Aiguader, 88. E-08003 Barcelona.

Plant genomics in the era of high-throughput sequencing: The case of the sugar beet
Heinz Himmelbauer(1,2), Juliane C. Dohm(1,2), Cornelia Lange(2), Ana P. Vivancos(1), Ester Castillo1, Maik Zehnsdorf(1,2), André Minoche(1,2), Thomas Kraft(3), Markus Wolf(4), Britta Schulz(5), Daniela Holtgräwe(6), Bernd Weisshaar(6)
1. Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain. 2. Max Planck Institute for Molecular Genetics, Berlin, Germany; Syngenta Seeds GmbH, Bad Salzuflen, Germany. 3. Strube Saatzucht, Söllingen, Germany; 4KWS Saat AG, Einbeck, Germany; 5University of Bielefeld, Bielefeld, Germany.

Maximum-Likelihood Estimation of Population-Genetic Parameters from High-Throughput Sequencing Data
Michael Lynch
Dept. of Biology, Indiana University. Bloomington, IN 47405

The 1000 Genomes Project.
Gil McVean
Department of Statistics. 1 South Parks Road. Oxford OX1 3TG. UK

Informatics tools for next-generation sequence analysis
Gabor T. Marth
Boston College Biology Department. Chestnut Hill, MA

Upcoming Challenges for Multiple Sequencing Alignment Methods
Cedric Notredame
Centre for Genomic Regulation. Barcelona. Spain.

Metagenomics versus Next Generation Sequencing Technologies
Douglas B. Rusch
J. Craig Venter Institute. 9704 Medical Center Drive. Rockville, MD 20850, USA

A systems biology view at transcription regulation networks
Henk Stunnenberg
Nijmegen Center for Molecular Life Sciences. Holland

Advanced data analysis in targeted resequencing projects
Bernd Timmermmann
MPI for Molecular Genetics Berlin, Germany

Understanding human genetic variation at the personal and population level through massively-parallel whole-genome sequencing
F. M. De La Vega(1), F. C. L. Hyland(1), S. McLaughlin(2), A.R. MacBride(3), E.F. Tsung(1), H. Peckham(2), C. Scafe(1), C. Lee(2), G. Costa(2), K. Bryc(4), A. Auton(4), C. D. Bustamante(4), M. G. Reese(3), and K. McKernan(2).
1. Applied Biosystems, Foster City, CA 94404. 2. Applied Biosystems, Beverly, MA 01915. 3. Omicia, Inc., Emerville, CA 92093. 4. Cornell University, Ithaca, NY, 14853, USA.

Selected Talks

Identification of EMS-Induced Mutations by Whole-Genome Sequencing
Blumenstiel, J. P. (1.2.); Gilliland, W. D. (2); Griffiths, J. A. (2); Hawley, R. S. (2,3); Noll, A. C. (2); Perera, A. G. (2); Staehling-Hampton, K. (2); Walton, K. N. (2)
1. Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045. 2. Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110. 3. Department of Physiology, Kansas University Medical Center, Kansas City, Kansas 66160

Peak selection coupled with de novo motif identification improves the accuracy of transcription factor binding site prediction in ChIP-Seq data analysis
Boeva, V. (1,2); Surdez,D. (2); Guillon, N. (2); Tirode, F. (2); Fejes, A.P. (3); Delattre, O. (2); Barillot, E. (1)
1. Lab. of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, INSERM Unit 900/Ecoles des Mines/Institut Curie, 11-13 rue Pierre et Marie Curie, 75005 Paris, FRANCE; 2. Lab. of Genetics and Biology of Cancers, INSERM Unit 830/Institut Curie, 26 rue dUlm, 75005 Paris, FRANCE; 3. Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6, USA.

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data
Corrada Bravo, H. and Irizarry, R. A.
Dept. of Biostatistics. Johns Hopkins Bloomberg School of Public Health. 615 N. Wolfe St. Baltimore, MD 21205-2179

Population genomics from individual and pool sequencing
Luca Ferretti(1), Sebastian E. Ramos-Onsins(1,2) and Miguel Pérez-Enciso(1,3)
1. Departamento de Ciencia Animal y de los Alimentos, Facultad de Veterinaria. Universidad Autónoma de Barcelona, Bellaterra, 08193, Spain. 2. Centre de Recerca en Agro-Genómica (CRAG), Bellaterra 08193, Spain. 3. Institut Catalá de Recrea i Estudis Avançats (ICREA), Barcelona 08010, Spain.

IntOGen: A novel framework for integration and data-mining of multidimensional oncogenomic data
Gunes Gundem (1), Christian Perez-Llamas (1), Alba Jené (1), Anna Kedzierska (2), Khademul Islam (1), Jordi Deu-Pons (1), Simon J. Furney (1) and Nuria Lopez-Bigas (1)
1. Research Unit on Biomedical Informatics. Experimental and Health Science Department. Universitat Pompeu Fabra. Barcelona Biomedical Research Park. Spain. 2. Bioinformatics and Genomics program. Centre for Genomic Regulation. Barcelona Biomedical Research Park. Spain.

Large-scale biodiversity analysis through next-generation sequencing
Hajibabaei, M.; Shokralla, S.; Singer GAC.,
Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada

Comparative Genomics of Tropical Evergreen Fagaceae
Kua CS (1) and Cannon CH (1,2)
1. Key Lab for Tropical Ecology, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, 666303 Menglun China. 2. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA

High-Resolution Genome-Wide Mapping of Hermes Transposon Insertion Sites in S. cerevisiae
Mularoni, L (1); Gangadharan, S. (2); Wheelan, S. (1); Craig, N (2)
1. Oncology Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. 2. Dept. of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA;

Quantification of Allele-specific Expression Patterns bt GS FLX 454 Technology
Naïra Naouar (1), Remco M. P. Van Poecke (2), Harrie Schneiders (2), Jifeng Tang (2), Antoine Janssen (2), Marcel Prins (2), Michiel J. T. van Eijk (2), Juliette de Meaux (3), Marnik Vuylsteke (1)
1. VIB Dept. of Plant Systems Biology Ghent University. 2. Keygene NV, Wageningen, The Netherlands. 3. Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany

Surfing on the surface: mutation detection in human genes coding for cell surface trans-membrane proteins
Parmigiani, RB. (1); Galante, PAF. (1); da Cunha, JPC. (1); Perez, RO. (2); Habr-Gama, A. (2); Gama-Rodrigues, J. (2); de Souza, SJ. (1); Camargo, AA. (1)
1. Ludwig Institute for Cancer Research, São Paulo Branch, 01323-903, SP, Brazil. 2. Hospital Alemão Oswaldo Cruz, 01323-903, SP, Brazil

High throughput sequencing analysis of linkage assay-identified candidate regions in familial breast cancer: methods, analysis pipeline and troubleshooting.
Juan Manuel Rosa-Rosa(1), FJ Gracia-Aznárez(1), Emily Hodges(2), Guillermo Pita(3), Michelle Rooks(2), Greg Hannon(2) and Javier Benitez(1,3).
1. Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. 2. Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, USA. 3. Genotyping Unit (CEGEN), Spanish National Cancer Research Centre, Madrid, Spain.

Whole Genome profiling: a new method for Sequence Based Whole Genome Physical Mapping
van Orsouw, NJ (1), van Oeveren, J (1), de Ruiter, M (1), van der Poel, H (1), Kelder, M. (1), Stormo, K (2), Bogden, R (2), van Eijk, MJT (1) Prins, M (1)
1. Keygene N.V., Agro Business Park 90, P.O. Box 216, 6700 AE Wageningen, The Netherlands. 2. Amplicon Express, 2345 NE Hopkins Ct., Pullman, WA 99163, USA

A pipeline for studying minor variants in complex genetic populations using long reads from high-throughput
sequencing technologies.
Ortega-Serrano, I. (1); Quer, J. (2,3); Rodriguez-Frias F. (3,4); Sánchez, A. (1,5)
1. Bioinformatics and Statistics Unit, Institut Recerca Hospital Vall d'Hebron, Barcelona, Spain. 2. Liver Unit, Internal Medicine, Hospital Vall d'Hebron, Barcelona, Spain. 3. CIBER enfermedades hepáticas y digestivas del Instituto de Salud Carlos III (CIBERehd), Madrid, Spain. 4. Biochemistry, Hospital Vall d'Hebron, Barcelona, Spain. 5. Dept. of Statistics, Universitat de Barcelona, Barcelona, Spain.

Combining Reduced Representation Libraries and Short-Read Sequencing for High-Throughput SNP Discovery in the Absence of Sequenced Genomes.
Satkoski, J. (1); Malhi, R. (2); Kanthaswamy, S. (3); Smith, D.G. (1,3)
1. Dept. of Anthropology, University of California, Davis, CA 95616, USA; 2. Dept. of Anthropology, University of Illinois, Urbana, IL 61801, USA; 3. California National Primate Research Center, University of California, Davis, CA 95616

Sequencing, sequencing and sequencing.
Bicheng Yang and Yun Wang
Beijing Genomics Institute-Shenzhen, Shenzhen, China..

Posters

The posters will have a maximum length of 190 cm and 95 cm width.

Finding selection footprints in the swine genome using massive parallel sequencing
Amaral AJ(1), Ferretti L.(2), Megens H-J(1), Crooijmans RPMA(1), Nie H(1), Ramos-Onsins S.E.(2), Perez-Enciso M(2), Schook L(3), Groenen MAM(1)
1. Wageningen University, Animal Breeding and Genomics Centre, P.O. Box 338, 6700AH, Wageningen, The Netherlands. 2. Universitat Autonoma Barcelona - ICREA, 08193 Bellaterra, SPAIN. 3. University of Illinois, Institute for Genomic Biology, 382 ERML, 1201 W. Gregory Avenue, Urbana, IL 61801, USA.

Novel tools and methods for exploring pyrosequencing data including quality assessment and simulation
Balzer, S. (1); Jonassen, I. (2); Malde, K. (1)
1. Institute of Marine Research, P. O. Box 1870 Nordnes, 5817 Bergen, Norway; 2. Department of Informatics and Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway

Towards the whole sequence of the melon genome
Benjak, A. (1); Gonzalez, V. (2); Mir, G. (1); Arús, P. (1); Aranda, M. (3); Álvarez-Tejado, M. (4); Droege, M. (5); Du, L. (6); Puigdomènech, P. (2); Garcia-Mas, J. (1)
1. IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB, Departament de Genètica Vegetal, Cabrils, Spain 2. IBMB Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB, Departament de Genètica Molecular, Barcelona, Spain 3. CEBAS-CSIC, Murcia, Spain 4. Roche Applied Science, Barcelona, Spain 5. Roche Applied Science, Penzberg, Germany 6. 454 Life Sciences, Branford, USA

Using 454 sequencing of ESTs for linkage analyses in a dioecious plant species
Bergero, R.; Suo, Q.; Charlesworth, D.
Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Kings Buildings, West Mains Road. Edinburgh, EH9 3JT, United Kingdom

StatSeq : Statistical challenges on the 1000 genome sequences in plants (EU COST Action TD0801)
Marco Bink (1), Thomas Schiex (2)
1. Biometris - Plant Research International b.v. P.O. Box 100, 6700AC, Wageningen. The Netherlands. 2 MIA INRA. Chemin de Borde Rouge, BP 52627, Castanet-Tolosan 31326 Cedex. France

Using a 'framework species' concept for ecological and evolutionary studies in comparative genomics
Cannon. CH (1,2) and Kua, CS (1)
1. Key Lab in Tropical Ecology, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, 666303 Menglun, China 2. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA

Pyrosequencing of non-model sentinel species for gene transcription profiling studies in environmental pollution monitoring
Díaz de Cerio, O; Fernández-Lanza, V; Cancio, I
Dept. of Zoology and Animal Cell Biology. School of Science and Technology. University of the Basque Country, E-48080 Bilbao.

Partial short-read resequencing of a highly inbred Iberian pig
A. Esteve(1), R. Kofler(2), A.P.Vivancos(2), H. Himmelbauer(2), MAM Groenen(3), JM. Folch(1), MC. Rodríguez(4), M. Pérez-Enciso(1,5)
1. Departament de Ciència dels Animals i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain. 2. Ultrasequencing Unit, Centre de Regulació Genòmica, 08003 Barcelona, Spain. 3. Wageningen University, Animal Breeding and Genomics Centre, 6700AH, Wageningen, The Netherlands. 4. Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain. 5. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain

High-throughput sequencing technologies applied to human gut microbiota research and genomics of pathogens
Gosalbes M.J. (1,2,3); Jiménez N. (2,3); D Auria G. (2,3); Durbán A. (2,3); Peris-Bondia F(1,2); Pérez-Cobas A.E. (3); Latorre A. (1,2,3); Moya A. (1,2,3).
1. Instittuo Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia. Polígono de la Coma s/n 46980 Paterna Valencia 2. CIBER Epidemiología y Salud Pública 3. Centro Superior de Investigación en Salud Pública. Avenida Cataluña,21, 46020 Valencia

Mutant HIV minority variants detected by ultradeep sequencing do not condition virological failure in patients starting ARV therapy including low genetic barrier drugs.
Hernández-Novoa B(1), Page C(1), Gutiérrez C(1), Manrique M(2), Pareja-Tobes E(2), Tobes R(2), Moreno S(1).
1. Hospital Ramón y Cajal, Madrid. 2. Era7 Information Technologies SLU, Granada. Spain

Genome-wide assessment of nucleotide diversity and signatures of selection in chicken using massive parallel sequencing
Megens, H.-J.(1); Zare Y. (1); Amaral A.J.(1); Crooijmans R.P.M.A. (1);Ferretti L. (2); Ramos-Onsins S.E. (2); Perez-Enciso M. (2);Groenen M.A.M. (1)
1. Wageningen University, Animal Breeding and Genomics Centre, P.O. Box 338, 6700AH, Wageningen, The Netherlands. 2. Universitat Autonoma Barcelona - ICREA, 08193 Bellaterra, SPAIN.

Cloud computing and NGS: massively parallel computing for massively parallel sequencing
Pareja-Tobes, E; Manrique, M; Pareja-Tobes, P; Pareja, E; Tobes, R;
Era7 Information Technologies SLU. BIC Granada Avda. de la Innovación 1. Armilla 18100 Granada SPAIN

Genome browser of genetic diversity in Drosophila
Ràmia, M; Casillas, S; Barrón, MG; Egea, R; Barbadilla, A
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain

Analysis of the gonadal transcriptome during sex determination, sex differentiation and gonadal maturation in the sea bass (Dicentrarchus labrax) and turbot (Scophthalmus maximus) by 454 sequencing and two specific oligo-based microarrays.
Ribas, L. (1); Crespo, B. (2); Díaz, N.(1); Gómez, A. (2); Pardo, B.G. (3); Reinhardt, R. (4); MacKenzie, S.(5); Martínez, P. (3); S. Zanuy, S. (2) and Piferrer, F. (1)
1. Institut de Ciències del Mar, CSIC. Passeig Marítim, 37-49, 08003 Barcelona, Spain. 2. Instituto de Acuicultura de Torre la Sal, CSIC. Ribera de Cabanes, 12595 Castelló, Spain. 3. Depto. de Genética, Facutad de Veterinaria, Campus de Lugo, 27002 Lugo, Spain. 4. Max Planck Institute for Molecular Genetics - Ihnestraße 63-73, 14195 Berlin, Germany. 5. Dept. Bio. Cel., Fisio. i Immunologia. Facultat de Ciències, 08193 Bellaterra, Spain.

Rhopalodia gibba and its spheroid body - sequencing endosymbiosis
Schönfeld, B I K
Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences. Massey University, Private Bag 11 222. Palmerston North 4442. New Zealand

Genome sequence of the recombinant protein production host Pichia pastoris
De Schutter K.(1,2,7); Lin Y.-C.(3,4,7); Tiels P.(1,5,7); Van Hecke A.(1,5); Glinka S.(6), Weber-Lehmann J.(6), Rouzé P.(3,4), Van de Peer Y.(3,4), Callewaert N.(1,5)
1. Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Ghent-Zwijnaarde, Belgium. 2. Department for Biomedical Molecular Biology, Ghent University, Ghent-Zwijnaarde, Belgium. 3. Department of Plant Systems Biology, VIB, Ghent-Zwijnaarde, Belgium. 4. Department of Plant Biotechnology and Genetics, Ghent University, Ghent, Belgium. 5. Unit for Molecular Glycobiology, L-ProBE, Department of Biochemistry and Microbiology, Ghent University, Ghent- Zwijnaarde, Belgium. 6. Eurofins MWG Operon, Ebersberg, Germany. 7. These authors contributed equally to this work.

Investigating molecular basis of response to selection in bank vole with next generation sequencing
Stuglik, M. (1); Babik, W. (1); Qi, W. (2); Kuenzli, M. (2); Gac, K. (1); Koteja, P. (1); Radwan, J. (1)
1. Institute of Environmental Sciences, Jagiellonian Universtiy, ul. Gronostajowa 7, 30-387 Krakow, POLAND; 2. Functional Genomics Center Zurich, Y32 H92, Winterthurerstr. 190, 8057 Zuerich, SWITZERLAND.

Selection of Cancer-Related Gene Exons for Targeted Resequencing with a Flexible and Fully Automated Microarray Platform
Summerer, D.(1); Schracke, N(1).; Wu, H.(2); Cheng, Y.(1); Haase, B.(1); Stähler, C.F.(1), Stähler, P.F.(1); Beier, M.(1)
1. febit biomed gmbh, Im Neuenheimer Feld 519, 69120 Heidelberg, Germany. 2. febit inc., 99 Hayden Ave, Suite 620, Lexington, MA 02421, USA

Including dominance effects in genomic selection
Toro, M.A. (1); Varona, L. (2)
1. Dpto. Producción Animal, ETS Ingenieros Agronomos, Universidad Politécnica de Madrid. 2. Dpto. Producción Animal, Facultad de Veterinaria, Universidad de Zaragoza

Using Next Generation Sequencing on ancient DNA - preamplified via a new Multiplex approach - to detect migration and population structure
M. Unterländer (1), S. Wilde (1), Ch. Schuh (2), C. Gerling (2), I. Popov (2), M. Woidich (2), Z. Samashev (3), E. Kaiser (2), W. Schier (2), H. Parzinger (4), J. Burger (1)
1. Institute of Anthropology, University of Mainz, Germany. 2. Institute of prehistoric Archaeology, FU Berlin, Germany. 3. Margulan Institute of Archaeology, Academy of Science Kazakhstan, Almaty. 4. Foundation of Prussian Cultural Heritage, Berlin, Germany