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Mathematical and Statistical Aspects of Molecular Biology
21st Annual MASAMB Workshop, Biocenter Vienna, 11/12 April 2011

Programme and Talk Abstracts (pdf)   Poster Abstracts (pdf)   Participants


11:00 - 13.45 Registration

12:45 - 13.45 Lunch

13:45 - 14:00 Welcome and Introduction

SESSION 1 Population Genetics (NGS, SNPs and Structural Variation)
CHAIR: Joachim Hermisson

14:00 - 14:20 Peter Arndt, "Bayesian SNP polarisation"

14:20 - 14:40 Andreas Futschik, "Optimal pooling strategies for SNP detection using next generation sequencing"

14:40 - 15:00 Luca Ferretti, Sebastian Ramos-Onsins and Miguel Perez-Enciso "Population genomics from next generation sequencing data"

15:00 - 15:20 Ines Hellmann, Olaf Thalmann, Anne Fischer and Linda Vigilant "Effects of sex-biased evolution on patterns of diversity in apes"

15:20 - 15:40 Botond Sipos, Tim Massingham and Nick Goldman "Sequencing of repetitive genomic DNA aided by mutagenesis - a simulation study"

15:40 - 16:00 Lorenz Wernisch, Klaudia Walter and Matt Hurles "Hierarchical Bayesian classifier for inferring genomic deletions"


SESSION 2 Evolutionary Genomics and Sequence Analysis
CHAIR: Jonathan Bollback

16:30 - 16:50 Richard Goldstein, Asif Tamuri and Mario Dos Reis "Characterising selection coefficients using from site- and time-dependent substitution models"

16:50 - 17:10 James Allen, and Simon Whelan "Quantifying the effect of evolution and genomic alignment on de novo RNA gene prediction"

17:10 - 17:30 Anne Kupczok, and Jonathan Bollback "Modeling the Evolutionary Dynamics of CRISPR spacers"


20:00 - open end Conference Dinner at MARX Restauration



SESSION 3 Gene expression and RNA-Seq
CHAIR: Christian Schlötterer

09:00 - 09:20 Peter Glaus, Antti Honkela and Magnus Rattray "Estimating differential expression of transcripts with RNA-seq by using Bayesian Inference"

09:20 - 09:40 Shengyu Ni, "Gene expression comparison between RNA-seq and microarrays based on ranked genes list"

09:40 - 10:00 Simon Anders, Alejandro Reyes and Wolfgang Huber "Studying alternative isoform regulation with RNA-Seq"

10:00 - 10:20 Alex Lewin, and Ernest Turro "MMSEQ: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads"


SESSION 4 Genomics and Parameter Selection
CHAIR: Andreas Futschik

11:00 - 11:20 Verena Zuber, and Korbinian Strimmer "Improving biomarker discovery by taking account of correlation: the CAT-CAR approach"

11:20 - 11:40 Florian Frommlet, Felix Ruhaltinger and Bogdan Malgorzata "Bayes optimal selection rules under sparsity with applications in GWAS"

11:40 - 11:50 Vote / Announcement of next MASAMB meeting

SHORT BREAK (group photograph, no coffee)

SESSION 5 Systems Biology I
CHAIR: Magnus Rattray

12:00 - 12:20 Elisenda Feliu, and Carsten Wiuf "Enzyme sharing as a cause of multistationarity in signaling systems"

12:20 - 12:40 Thomas Thorne, and Michael Stumpf "Sequential Monte Carlo samplers for biological network inference"

12:40 - 13:00 James Hensman, Magnus Rattray and Neil Lawrence "Functional nonparametric clustering of irregularly sampled gene expression time series"


SESSION 6 Systems Biology II
CHAIR: David Kreil

14:00 - 14:20 Emma Cooke, Richard S Savage, Paul D W Kirk and David L Wild "Bayesian Hierarchical Clustering for Microarray Time Series Data with Replicates and Outlier Measurements"

14:20 - 14:40 Maxime Garcia, Olivier Stahl, Pascal Finetti, Daniel Birnbaum, François Bertucci and Ghislain Bidaut "Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration"

14:40 -15:00 Julia Lasserre, Alexander Zien, Klaus-Robert Müller and Martin Vingron "ProARTS: towards unfolding the structure of the sequence around human transcription start sites"

15:00 - 15:20 Alexey Stukalov, and Jacques Colinge "Bayesian Inference of Protein Complexes from Mass Spectrometry Data"

15:20 - 15:40 Heather Harrington, Gian Michele Ratto and Michael Stumpf "Spatio-temporal models of Erk1 and Erk2 in vivo"

15:40 - 16:00 Antti Honkela, Neil Lawrence and Magnus Rattray "Hierarchical Gaussian Process Models of Gene Expression and Transcriptional Regulation"