AMATA 2008: Speakers
RNA-Based Gene Regulation in Eukaryotic Development We are exploring the thesis that the genetic programming of higher organisms has been fundamentally misunderstood for the past 50 years, because of the assumption that most genetic information is transacted by proteins. Working in conjunction with collaborators in Japan, Europe and the United States, we are working to characterise and understand the functions of the mammalian transcriptome, and to validate the prediction that most genetic information in mammals is conveyed by RNAs that control the trajectories of our differentiation and development. We also participated in the international ENCODE project to functionally analyse 1% of the human genome, and further characterised unusual features of the non-coding landscape of the genome, including ultraconserved sequences and transposon-free regions. We use advanced computational and experimental methods, integrating in silico, in vitro and in vivo approaches. The outcomes of our research will be to refine our understanding of the genomic factors underpinning human development, diversity and disease, with practical implications in medicine, genetic engineering and advanced programming of self-assembling information systems.  Rebecca Doerge Director, Statistical Bioinformatics Center, Purdue University, USA Statistical Genomics Professor Doerge has played an integral role in the establishment of Genomics at Purdue University, and continues to forge new ground in the exciting areas of statistical genomics, quantitative genetics, and bioinformatics. Her research is currently involved in assessing genomic based questions - Statistical genomics. Current research programs: development of statistical methodology for genetic mapping and quantitative trait loci (QTL) location; applying up to date genetic mapping and (e-)QTL methodology to real experimental data; assessing genetic variation and diversity of populations and germplasm collections; and understanding and analyzing gene expression, protein expression, and epigenomic data for the purpose of statistically designing and then testing (epi-)genomic/biologically based questions. Rebecca has won numerous awards for both teaching and research. She was elected Fellow of the American Statistical Association in 2007. 
Gene regulation and DNA methylation Epigenetic mechanisms of gene regulation impact genome organization and inheritance, as well as the specification and maintenance of cell fate. These mechanisms are conserved in eukaryotes and provide an additional layer of information superimposed on the genetic code. We are using model plants and yeast to investigate epigenetic mechanisms of transposon silencing, gene regulation and stem cell fate via functional genomics and developmental genetics. Cold Spring Harbor Laboratory is part of global consortia of researchers involved in the comprehensive sequencing of the Arabidopsis and rice genomes. The complete sequence of Arabidopsis will be available by the end of the year and promises to be a landmark event in plant biology.
Tell-Tale Genes: Harnessing Genomics for Breast Cancer Prognosis and Oncogene Discovery Using genomics technologies such as DNA microarrays, my laboratory investigates the transcriptional dynamics and genomic architectures of primary tumors and cell lines at various stages of the oncogenic process and in different clinical contexts. Integrative analysis of gene expression patterns, copy number alterations, and clinicopathologic features allows us to define transcriptional programs of mechanistic and clinical relevance. This strategy has led to the identification and validation of gene expression signatures in liver, breast, ovarian and lung cancers that 1) reflect the activity of specific growth-regulating pathways, 2) define known and novel tumor subtypes, and 3) predict clinical outcomes such as disease recurrence and therapeutic response. Recent examples include prognostic signatures in breast cancer that reflect the operational configuration of the TP53 pathway and delineate new clinical tumor subtypes based on “genetic grade”. We have also pioneered novel data mining strategies that integrate several forms of clinico-genomic information (expression, copy number, patient survival) capable of pinpointing known and candidate oncogenes.  Heather Cunliffe Head, Breast & Ovarian Cancer Research Lab Translational Genomics Research Institute (T-Gen), Phoenix, Arizona, USA New molecular targets in breast cancer Tumors of the breast and ovary are extremely heterogeneous and genetically complex, which is evident in their diverse and often unpredictable response to standard of care therapy. Early diagnosis and the ability to define optimal treatment strategies for each individual patient remains a significant challenge in oncology. The advent of microarray-based technologies has rapidly given rise to the identification of characteristic subclasses of breast tumors. Tumors within each molecular subclass have more predictable responses to therapy, which is most likely due to shared or similar underlying disease biology. Molecular sub-classifications are also being identified in ovarian and other solid tumors. These promising discoveries are not only revolutionizing development of more accurate diagnostic and prognostic assays, but also guiding therapeutic decision-making based on identifiable drivers of disease biology that can be exploited through novel targeted therapy.
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. We are now entering an era in which it will be feasible to catalogue every genetic event in a cancer. Next generation sequencing platforms already offer the capacity to generate gigabases (Gb) of sequence each week at a cost of less than 1 cent per kilobase (kb). Techniques have been developed which allow the detection of genomic rearrangements, copy number changes, point mutations and small insertions and deletions as well as epigenetic alterations on a single instrument. This will be a significant advance on existing approaches to cancer genomics. The analysis will be genuinely genome-wide, cataloguing genetic changes not only in coding sequence but also the other 98% of the human genome including, for example, promoters, enhancers and non-coding RNAs. At the Cancer Genome Project, we have developed protocols for mapping acquired rearrangements to the base-pair level, providing insights into the diversity of aberrant processes sculpting the genome which underlie the evolution and development of cancer.
DNA sequencing: Genome doesn't start with 'G'
David was previously Head of Human Genetics and founding Member of the Board of Management at the Wellcome Trust Sanger Institute, where he played leading roles in the Institute's contribution to the human genome reference sequence, The SNP Consortium and the International HapMap Project. With a DPhil in molecular biology from Oxford, he was a postdoctoral fellow at Guy's and St Thomas's Hospital in London, where he studied the mutations that cause genetic diseases such as haemophilia.
Dan Belluoccio (Australia) ~ Whole Genome Expression Analysis from Micro-dissected Mouse Cartilage Tissues
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John Mattick, AO
Rob Martienssen 
Lance Miller
Peter Campbell 
David Bentley
