Combined the COAT partners have extensive skills and know-how in the research areas covered in this application. We value collaboration between the different partners, in particular between the wet and dry labs, since this is where the real potential for synergies is located. Every year the center personnel will gather at a meeting to discuss strategies, results and collaborations. A major objective of these meetings will be to establish a common “language” for the center participants and to encourage further collaboration among the partners. Two of these yearly meetings will be larger workshops with the participation of the US partners and other invited speakers.
Department of Biology, University of Copenhagen
The Department of Biology is committed to hosting the COAT and will provide facilities, administrative support and co-financing to the center. The center will be an integrated part of the research strategy of the Department (see support letter from Department Head Karsten Kristiansen, appendix D). COAT will be managed by Anders Krogh. Anders is recognized worldwide for introducing probabilistic modeling with Hidden Markov Models into bioinformatics and remains a leader in the field. Moreover, he has extensive management skills obtained through building and managing a large research group over the last decade. Throughout his career, Anders has prioritized management, both in practice and by taking a formal education in research management (Copenhagen Business School, 2008) and other smaller courses. These management competences have been absolutely required for Anders to establish the very successful Bioinformatics section at the Department of Biology, which currently employs about 40 scientists and regularly publishes in the most prestigious international journals. Included in the COAT budget is increased administrative support to Anders Krogh that will free time for research leadership. High through-put experimental techniques create massive amounts of data. The Krogh group has previously successfully mapped and assembled an entire human genome from high through-put sequencing data (Rasmussen et al., 2010) and has the infrastructure and know-how necessary to deal with this kind of data. Moreover, the section is a partner in the sequencing center being established at the Faculty of Science, which will contain at least 5 modern high-throughput sequencers on campus. The Vinther and Christiansen groups at the Department of Biology will coordinate the experimental efforts in WP1 and WP3. Jeppe Vinther is a talented young researcher that has successfully managed his own experimental group for the last four years and has during this period collaborated extensively with the Bioinformatics Section and this has resulted in several good publications on different aspects of posttranscriptional regulation with emphasis on miRNA regulation. Jan Christiansen’s group has conducted and published important research on Protein-RNA interactions for several decades, focusing on the IMP family of RNA-BPs. Jan’s experience and know-how will be extremely important for the success of center.
Santaris Pharma A/S
Santaris Pharma (founded in 2003) is a privately held biopharmaceutical company developing new classes of RNA medicines targeting disease-related mRNAs and miRNAs based on its proprietary locked nucleic acid (LNA) chemistry. The Company’s research and development activities focus on infectious diseases and metabolic disorders. Santaris Pharma is leveraging its highly effective and efficient Drug Discovery Engine to generate lead LNA drug candidates against a broad array of disease targets selected by strategic partners. The Company and its corporate partners currently have four compounds in clinical development and a full pipeline in late preclinical development. Santaris Pharma has since its inception raised nearly $100 million through private financing and upfront payments. As recipient of several large public grants, Director of microRNA Research Sakari Kauppinen has extensive experience successfully bridging academic and commercial research (Elmen et al., 2008; Lanford et al., 2010). Moreover, Santaris Pharma A/S has a strong systems biology and bioinformatics group, lead by Morten Lindow, which will contribute with its oligonucleotide expertise and exploit the know-how generate by COAT to improve LNA drug design.
Lund group, BRIC, University of Copenhagen
The Lund group studies gene regulation by epigenetic and post-transcriptional mechanisms. Technically, the lab spans from the identification of disease-relevant genes in functional screens or genome-wide studies, over genetic and biochemical studies in cell culture models to advanced mouse genetics. The group employs state-of-the-art methods and has access to the high-content screening facility present at BRIC. The group is well embedded in the Center with long-standing, productive collaborations with the groups of Krogh and Kauppinen.
Pedersen group, Department of Molecular Medicine (MOMA), Aarhus University
Jakob Skou Pedersen has more than eight years experience with computational RNA structure analysis. Based on contributions to the field, he has repeatedly been invited to contribute genomic RNA structure identification and analysis to prestigious international genomics projects, such as ENCODE and the ongoing 29 Mammals project. Experimental validation of his computational predictions has in several cases led to independent publications in top-ranking journals (Han et al., 2009). Jakob Skou Pedersen recently moved to MOMA, Aarhus University, establishing a group studying ncRNAs, cis-regulatory structures, and their implications on gene regulation using computational analysis and NGS-based methods.
Haussler group, University of California, Santa Cruz, US
The Haussler lab is a world leader in generation and analysis of cross-species comparative and high-throughput genomics data and makes this data available to the research community through the UCSC genome browser. David Haussler has been and continues to be one of the pioneers of the functional annotation of the human genome. Sofie Salama is leading the experimental efforts in the Haussler Lab, including the recent development of method for high throughput mapping of RNA structure, and is a principle investigator by her own right.
Sanford group, University of California, Santa Cruz, US
Jeremy Sanford recently established his own group at UCSC to investigate the role of RBP in mammalian gene expression with special focus on proteins that are related to human disease. The lab has extensive experience with the CLIP methodology for mapping of RNA-protein interactions.
Sander group, Memorial Sloan-Kettering Cancer Center, New York, US
The Sander group is world renown for their contribution to the computational analysis of biological processes at different levels of organization. The aim of the group is to use of different types of high throughput data to predict the results of interventions in biological systems, and improve the prevention, diagnosis, prognosis, and therapy of cancer.