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19.10 at the hotel foyer: meet for dinner!

19.10 at the hotel foyer: meet for dinner!. Huber Group. 26 February 2009. Goals. Develop mathematical and statistical methods for the design and analysis of biologically and technologically novel experiments in order to understand and engineer

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19.10 at the hotel foyer: meet for dinner!

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  1. 19.10 at the hotel foyer: meet for dinner!

  2. Huber Group 26 February 2009

  3. Goals Develop mathematical and statistical methods for the design and analysis of biologically and technologically novel experiments in order to understand and engineer how variations in the genome create variations in phenotypes

  4. Collaboration model Typically, projects involve one-on-one collaborations with experimentalists and include Experiment design, quality control, "normalisation" Statistical analysis Biological interpretation Comparison with other datasets Identification and design of follow up experiments Required skills Solid maths Statistics Programming Speed and efficiency Communication Perfection Perfectionism

  5. Highlights 2004-2009 Pervasive transcription, non-coding & antisense RNA, bidirectional promoters PNAS 2006, Bioinformatics 2006, BMC Biol. 2007, Nature 2009 High-resolution mapping of recombination events - by genotyping with tiling arrays Nature 2008 RNAi-screen data analysis Genome Biology 2006 Microarray preprocessing and quality assessment Proteomics 2005, BMC Bioinf 2007, NAR 2008, NAR 2009, Bioinformatics 2009 Bioconductor Two books: 2005, 2008

  6. Ongoing projects Genome-wide RNAi screens and genetic interaction networks (with M. Boutros, DKFZ Heidelberg) Mapping a genome scale network of synthetic genetic interactions Automated imaging and phenotyping by image analysis and machine learning Systems Biology - Genetics (with L. Steinmetz, Gene Expression) Mapping a genome-wide network of genotype-phenotype relationships using a library of 12000 reciprocal hemizygous strainsSolexa sequencing, statistical data analysis

  7. Bioconductor Good scientific software is like good research: it is… • Reproducible. • Openly accessible. • Built upon past work. • A building block for future work. Bioconductor • An open source and open development software project for the analysis of biomedical and genomic data. • Initiated in 2001 by Robert Gentleman, FHCRC, Seattle. • ~10 core developers, ~100 contributors, ~180 packages, thousands of users.

  8. Proposed Project

  9. imaging of embryonic development at subcellular resolution histone 2B labelled by fusing with eGFP cell tracking in the entire zebrafish embryo during the first 24h, from 16 to 16000 cells 2048 x 2048 x 400 (~1.6x109) voxels at ~1000 time points

  10. show movies

  11. Computational challenges • Cell tracking for organogenesis, "dynamic anatomy" • Characterizing natural variation (between individuals, within individual over time) and channeling, robustness • Detect mutation or drug treatment phenotypes • Each individual embryo dataset is ~4 Terabytes (2x1012 numbers)

  12. Heidelberg • My group is going to the Gene Expression Programme in Heidelberg • This position will be based at EMBL Heidelberg

  13. Raeka Aiyar Simon Anders Elin Axelsson Richard Bourgon Lígia Brás Alessandro Brozzi Tineke Casneuf Rémy Clement Kristen Feher Bernd Fischer Florian Hahne Thomas Horn Audrey Kauffmann Paul McGettigan Daniel Murrell Gregoire Pau Matt Ritchie Ramona Schmid Oleg Sklyar Michael Smith Jörn Tödling Zhenyu Xu David Jitao Zhang Collaborations Robert Gentleman (FHCRC) Lars Steinmetz (EMBL-HD) Michael Boutros (DKFZ) Alvis Brazma Ewan Birney Jan Ellenberg (EMBL-HD) Thank you Group 2004-2009

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