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POST CONFERENCE WORKSHOP

CV: www.roslin.ed.ac.uk/dave-burt/curriculum-vitae/

Professor David W. Burt, Chair in Comparative Genomics and Head of Avian Genomics, at the Roslin Institute, Edinburgh University (UK). He received his BSc (1st class) in Molecular Biology at Edinburgh University (1977) and PhD in Molecular Genetics at Leicester University (1980). His post-doctoral training included research on molecular genetics of a wide range of species (bacteriophage lambda, bacteria, mouse, rat and human) and research areas (transcription circuits, cDNA cloning of growth factors, renin-angiotensin system and hypertension, QTL mapping, bioinformatics, phylogenetics and avian genomics). He has worked in the ICI-Joint Lab at Leicester University, Harvard Medical School (USA), Clinical Research Centre (London) and the Roslin Institute at Edinburgh University.

His current research is focused on applications in avian genetics and comparative genomics. Current projects include: (i) Assembly and annotation of the chicken genome, (ii) Development of bioinformatics tools and resources to determine the complete transcriptome of the chicken genome, (iii) Creation of an atlas of gene expression in the chicken, (iv) Characterization of the genome variation and predicted consequences in chicken populations, (v) Evolution of avian genomes, and (vi) Avian host susceptibility towards viral infections.

He is active in promoting livestock and avian genomics as co-chair in various avian genome consortia and international meetings, including the International Chicken Genome Consortium, the Functional Annotation of Animal Genomes (FAANG), and the Avian Phylogenomics Group and Bird10K.

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Title: CRAVAT 4.0: Informatics Tools for High-throughput Analysis of Exome Variants

Christopher Douville¹, David Masica¹, Collin Tokheim¹, Rohit Bhattacharya¹,Rick Kim², Derek Gygax², Michael Ryan² and Rachel Karchin<sup>1,3

1</sup>Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
²In Silico Solutions, Fairfax, VA, USA
³Department of Oncology, Johns Hopkins Medical Institutions, Baltimore MD, USA

Abstract: CRAVAT provides high-throughput services for researchers to annotate and prioritize small-scale variants and genes discovered in normal tissues and cancers. The services are publicly available and free for non-commercial use through both a graphical web interface and a RESTful web services API. If users establish a CRAVAT account (optional), we provide a new graphical interface for exploratory results browsing and retrieval of previous jobs.

Variants can be submitted either as a Variant Call File (vcf) or in a simple tab-delimited format, based on genome coordinates. Variant- and gene-level annotations and bioin-formatic scores are provided to enable interpretation and prioritization of variants identified in sequencing studies. In the new interactive interface, sortable tabular views of results in worksheet format are enhanced with graphical displays that highlight significant properties of variants and genes, including protein-domain based lollipop displays and viewing on annotated 3D protein structures and theoretical models. For users interested in cancers, TCGA mutations from 32 cancer types in 2D and 3D, and statistically significant 3D mutation clusters identified with the HotMAPS algorithm can be viewed for each cancer type and for TCGA's PanCan12 study.

Pathogenicity scores are provided for all non-silent mutation types, including frameshift and in-frame insertions/deletions, splice site and nonsense. Analytical p-values integrated across mutation types enable one-pass sorting and enhance score interpretability. Annotations include TARGET drug associations, 1000 Genomes, Exome Variant Server and Exome Aggregation Consortium (ExAC) minor allele frequencies by population. Variant zygosity, pileup coverage and variant allele frequencies are provided when users submit vcf files. Cancer-specific annotations include COSMIC mutation frequencies by tumor type, Vogelstein/Kinzler oncogene/tumor suppessor gene assignments and PubMed hits.

CRAVAT 4.0 was designed to interoperate with many popular bioinformatics tools. It has an enhanced web services interface to enable very fast programmatic retrieval of results for a single variant or full variant batch processing and has an available Galaxy tool. CRAVAT annotations and visualization tools are used in the TRINITY transcript discovery pipeline, Xena cancer browser. Integration efforts are underway with the IGV Genomics Viewer and the NDex Network Data Exchange.

Availability: http://cravat.us
Funding: NCI's Informatics Tools for Cancer Researchers initiative U01CA180956-03

Biography: Rachel Karchin received a PhD in Computer Science from the University of California Santa Cruz in 2003 and did postdoctoral research in the Department of Biopharmaceutical Sciences at University of California San Francisco. She joined the faculty of Johns Hopkins University in 2006, where she is currently an Associate Professor with joint appointments in the Departments of Biomedical Engineering and Oncology. She was appointed as the Whiting School of Engineering William R. Brody Faculty Scholar in 2013. Dr. Karchin’s lab develops computational and statistical methods to interpret and predict the impact of individual variation in the genome, transcriptome, and proteome. These methods are being applied to discovery and clinical translation in cancer, cystic fibrosis and psychiatric disorders. The lab is deeply embedded in collaborations that include geneticists, oncologists, pathologists, psychiatrists and surgeons.

http://karchinlab.org/

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ERIC KARSENTI

Title: TARA OCEANS: Characterisation of Global Oceans Plankton Ecosystems

Abstract: Over a 3 years expedition carried out onboard the 36 m schooner TARA, an international and interdisciplinary team of scientists has sampled quantitatively plankton organisms from viruses to small metazoans, including unicellular protists with associated environmental parameters. The idea was to get large data sets in order to better understand the evolution and robustness of these ecosystems that are our ancestors, that generated the atmosphere we breathe, and at the base of the oceanic food chain.

The analysis pipeline involves high throughput sequencing, and imaging methods, bioinformatics and oceanography, all integrated in an innovative manner.

During the presentation I will present the expedition, the analysis strategy and the initial results obtained using the first series of stations analysed.

Biography: On September 27, 2015, Eric Karsenti was awarded the Centre National de la Recherche Scientifique (CNRS) gold medal, France's highest scientific distinction that recognizes a French scientist in any field covered by the CNRS.

Former recipients include Nobel Laureates such as Jules Hoffmann (Physiology or Medicine, 2011) or Jean Tirole (Economics, 2014). The press release and a complete list of honorees is available at: www2.cnrs.fr/en/2625.htm.

Eric Karsenti obtained a PhD in Immunology and cell Biology at the Pasteur Institute in Paris in 1979. Then he moved to San Francisco to work on the cell cycle and mitosis in the laboratory of Marc Kirschner between 1981 and 1984, before establishing his own group in the Cell Biology department at EMBL, Heidelberg in 1985. Since then he contributed to the understanding of the cell cycle clock and developed a new approach to Cell Biology involving statistical physics and modeling to understand how cell shapes and the mitotic spindle form. Over the past 15 years and before starting the TARA OCEANS expedition, he created the Cell Biology and Biophysics unit at EMBL when the former head, Kai Simons, left. He hired an interdisciplinary team of group leaders having a background in genetics, imaging, statistical physics and biophysics, with common interests in cell and organisms morphogenesis. He worked also on the application of self-organization principles at the scale bridging molecular mechanisms and the emergence of cellular functions like the mitotic spindle.

Research director at the CNRS and Senior Scientist at EMBL, he is a member of EMBO and of the French Academy of Sciences. Since 2009 he is the Scientific Director of the TARA OCEANS expedition.

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Biography: Suzanna E. Lewis is a scientist and Principal Investigator (PI) at the Berkeley Bioinformatics Open-source Project (BBOP) based at Lawrence Berkeley National Laboratory. Lewis leads the development of open standards and software for genome annotation and ontologies.

She led the team responsible for the systematic annotation of the Drosophila melanogaster genome, which included development of the chado annotation pipeline and database framework, and the annotation curation tool Apollo. Lewis' work in genome annotation also includes playing instrumental roles in the GASP community assessment exercises to evaluate the state of the art in genome annotation, development of the Gbrowse, Jbrowse, and Web Apollo genome browsers, and the data coordination center for the modENCODE project. In addition to her work in genome annotation, Lewis has been a leader in the development of interoperable biological ontologies, now collected under the Open Biomedical Ontologies (OBO) effort. These include the original founding of the Gene Ontology (for which she remains a Principal Investigator), the Sequence Ontology, Uberon anatomy ontologies, and developing open software for editing and navigating ontologies such as AmiGO, OBO-Edit and Phenote. Most recently her team is developing methods for discovery of genotype to phenotype relationships as part of the Monarch Initiative.

In 2005 Lewis was elected a fellow of the American Association for the Advancement of Science in recognition of her contributions to science in the fields of Information, Computing, and Communication.

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