Accepted Posters

Category 'Q'- Population Genetics and Variation'

Poster Q01

3Dsim - 3D Structural Implication of Mutations

Jose Izarzugaza- CNIO - Spanish National Cancer Research Centre

Anja Baresic (University College London, Institute of Structural and Molecular Biology); Lisa McMillan (University College London, Institute of Structural and Molecular Biology); Corin Yeats (University College London, Institute of Structural and Molecular Biology); Andrew Clegg (University College London, Institute of Structural and Molecular Biology); Christine Orengo (University College London, Institute of Structural and Molecular Biology); Andrew Martin (University College London, Institute of Structural and Molecular Biology); Alfonso Valencia (CNIO - Spanish National Cancer Research Centre, Structural Biology and Biocomputing Programme);

Short Abstract: 3DSim is a web-application that facilitates the localization and visualization of single amino acid polymorphisms from SAAPdb by mapping them onto representative structures from the CATH database. The application provides a comprehensive overview of the distribution of neutral and pathogenic mutations in structural space.

Long Abstract: Click Here

Poster Q02

waviCGH v2.0: a web server for the analysis, integration and visualization of aCGH experiments

Angel Esteban- CNIO

Daniel Rico (CNIO, Structural biology and biocomputing ); Eduardo Andres (CNIO, Structural biology and biocomputing ); Oscar Rueda (CNIO, Structural biology and biocomputing ); Ramon Diaz (CNIO, Structural biology and biocomputing ); David Gonzalez (CNIO, Structural biology and biocomputing );

Short Abstract: waviCGH v2.0 is a versatile web server application for the analysis, visualization and integration of array-CGH (aCGH) data. The server is designed to bridge the gap between wet lab researchers doing aCGH and the methods for their numerical analysis.

Long Abstract: Click Here

Poster Q03

Sanity Check and Quality Control for Data Submitted to the European Genotype Archive (EGA)

Vasudev Kumanduri- EBI

Jonathan Hinton (EBI, Vertebrate Genomics); Ilkka Lappalainen (EBI, Vertebrate Genomics); Mario Caccamo (EBI, Vertebrate Genomics); Paul Flicek (EBI, Vertebrate Genomics);

Short Abstract: We have created a permanent archive for all types of personally identifiable genetic and phenotypic data. The service includes now a generic QC and sanity check pipelines for all submitted data that can also be customized for needs of data generating consortium or individual user. Our tools also allow direct comparison between different analysis methods.

Long Abstract: Click Here

Poster Q04

A Model of HIV-1 Coreceptor Tropism: Population Perspective

Gōkhan Ertaylan- University of Amsterdam

No additional authors

Short Abstract: The coreceptor tropism switch in Human Immunodeficiency Virus infection is associated with developing AIDS. We have developed a computational model for studying this phenomenon. Given the transmission with a CCR5 tropic virus, we evaluate the mutation rate carrying the virus quasispecies to an optimum fitness by changing coreceptor tropism.

Long Abstract: Click Here

Poster Q05

Complex hierarchical population subdivision in guppies from Trinidad and Venezuela revealed by high-density marker analyses

Eva-Maria Willing- Max Planck Institute for Devolpmental Biology

Margarete Hoffmann (Max Planck Institute for Devolpmental Biology, Molecular Biology); Detlef Weigel (Max Planck Institute for Devolpmental Biology, Molecular Biology); Christine Dreyer (Max Planck Institute for Devolpmental Biology, Molecular Biology);

Short Abstract: Guppies (Poecilia reticulata) are a long-standing model of ecological genetics, yet little is known about population subdivision at the whole-genome level. We analyzed divergence among populations applying different clustering approaches to genome wide SNP data. We found that population substructure agrees with geographic vicariance and hypothesized patterns of historical colonization.

Long Abstract: Click Here

Poster Q06

Genome-wide Association Analysis with Stochastic Block Lasso

Seyoung Kim- Carnegie Mellon University

Eric Xing (Carnegie Mellon University, Department of Machine Learning);

Short Abstract: We propose a new approach calleda stochastic block lasso for association mapping thatexploits prior knowledge on linkage disequilibrium structure in the genomesuch as recombination rate and distance between adjacent SNPs in orderto identify blocks of SNPs for association.

Long Abstract: Click Here

Poster Q07

Pathway analysis of genome-wide association studies

Karen Kapur- University of Lausanne

Sven Bergmann (University of Lausanne, Department of Medical Genetics);

Short Abstract: There has been much interest in extending analysis of genome-wide associationstudies to include epistatic effects between two genetic variants. Using a guidedsearch strategy to search within a restricted subset of SNP pairs, we apply anintegrative approach to combine information about protein interactions with epistasisgene-gene interactions.

Long Abstract: Click Here

Poster Q08

A closed-form asymptotic sampling formula for a two-locus model

Paul Jenkins- University of California, Berkeley

Yun Song (University of California, Berkeley, Electrical Engineering and Computer Science);

Short Abstract: We present the asymptotic behaviour of the sampling probability of genetic data in a two-locus, infinite alleles model, when recombination is large. The first two terms of an asymptotic expansion are given analytically. Extensive assessment of our formula finds close agreement with exact solutions for many configurations and parameter values.

Long Abstract: Click Here

Poster Q09

Method for inferring the frequencies of disease alleles in case-control studies

Leeyoung Park- Yonsei University

No additional authors

Short Abstract: A Bayesian approach is proposed for the inference of disease allele frequencies. This multi-parameter model focuses on the changed frequencies of marker alleles in cases compared to controls for Bayesian update. This approach implements Markov Chain Monte Carlo techniques for estimating the posterior probabilities of disease allele frequencies.

Long Abstract: Click Here

Poster Q10

MoDIL: Detecting INDEL Variation with Clone-end Sequencing

Seunghak Lee- University of Toronto

Fereydoun Hormozdiari (Simon Fraser University, School of Computing Science); Can Alkan (University of Washington and the Howard Hughes Medical Institute, Department of Genome Sciences); Michael Brudno (University of Toronto, Department of Computer Science, Banting and Best Dept. of Medical Research);

Short Abstract: We present a novel method for finding insertion/deletion polymorphisms from paired short reads. We model each genomic locus as a mixture of two haplotypes, and our method takes advantage of the high clone coverage to identify homozygous and heterozygous variation. Our experimental results demonstrates that MoDIL accurately identifies indels (>20bp).

Long Abstract: Click Here

Poster Q11

A new conditional sampling distribution for the coalescent with recombination

Joshua Paul- University of California, Berkeley

Yun Song (University of California, Berkeley, EECS Department);

Short Abstract: We describe a principled technique for approximating the conditional sampling distribution (CSD) for a general finite-sites, finite-alleles coalescent model with recombination, and provide evidence that it is more accurate than previously proposed methods. Additionally, we explore the effect of our new approximate CSD on importance sampling and PAC methods.

Long Abstract: Click Here

Poster Q13

Match probabilities in a finite, subdivided population

Anna-Sapfo Malaspinas- UC Berkeley

Yun Song (UC Berkeley, EECS and Statistics); Montgomery Slatkin (UC Berkeley, Integrative Biology);

Short Abstract: Recently a graphical framework was introduced to compute the probability that two individuals randomly chosen from a finite population have matching DNA profiles at several unlinked loci. Here, we extend that framework to include subdivided population structure and show that match probabilities depend strongly on migration rates.

Long Abstract: Click Here

Poster Q14

De novo transcriptome assembly from paired-end RNA-Seq data

Marcel Schulz- Max Planck Institute for Molecular Genetics

Daniel Zerbino (European Bioinformatics Institute, Protein and Nucleotide Database Group ); Ewan Birney (European Bioinformatics Institute, Protein and Nucleotide Database Group); Martin Vingron (Max Planck Institute for Molecular Genetics, Computational Molecular Biology);

Short Abstract: We consider the de novo transcriptome assembly problem from next-generation paired-end short read data. Extending the Velvet genome assembler we demonstrate how to assemble transcriptomes of different complexity.

Long Abstract: Click Here

Accepted Posters

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