Professor Patrick Cunningham
Chief Scientific Adviser to the Irish GovernmentProfessor of Animal Genetics, Trinity College, University of Dublin
Patrick Cunningham is Chief Scientific Adviser to the Irish Government and Professor of Animal Genetics in Trinity College, University of Dublin. He holds degrees in Agricultural Science and Animal Nutrition from the National University of Ireland and a PhD in Animal Genetics from Cornell University.
He was formerly Deputy Director (Research) in the Irish National Agriculture and Food Research Institute (1980 - 1988), visiting Professor at the Economic Development Institute, World Bank (1988) and Director of the Animal Production and Health Division, Food & Agriculture Organisation of the UN, Rome (1990 - 93).
He has published extensively on the genetics of domesticated animals. He is co-founder of the biotechnology company IdentiGEN. He has been President of the European and World Associations of Animal Production, and served on the European Life Sciences Group which advised Commissioner Busquin. In 2008 he led the Irish team behind the successful bid to host the “European City of Science (ESOF)” event in Dublin, in 2012.
He holds honorary doctorates from three universities, and in 1996 was awarded the Boyle Medal, Ireland’s premier award in science.
Link to Professor Cunningham's website
Plenary Speakers
Professor Elaine Mardis (Plenary Speaker)
Associate Professor of Genetics and Molecular Microbiology.Co-director, The Genome Institute at Washington University School of Medicine, USA.
Prof. Elaine Mardis graduated Phi Beta Kappa from the University of Oklahoma with a B.S. degree in zoology. She then completed her Ph.D. in Chemistry and Biochemistry in 1989, also at Oklahoma. Following graduation, Prof. Mardis was a senior research scientist for four years at BioRad Laboratories in Hercules, CA.
In 1993, Prof. Mardis joined The Genome Institute at Washington University School of Medicine. As Director of Technology Development, she helped create methods and automation pipelines for sequencing the Human Genome. She currently orchestrates the Institute’s efforts to explore next generation and third generation sequencing technologies and to transition them into production sequencing capabilities.
Prof. Mardis has research interests in the application of DNA sequencing to characterize cancer genomes. She also is interested in facilitating the translation of basic science discoveries about human disease into the clinical setting.
Prof. Mardis serves on several NIH study sections, is an editorial board member of Genome Research, and acts as a reviewer for Nature and Genome Research. She serves as chair of the Basic and Translational Sciences Committee for the American College of Surgeons Oncology Group, an NCI funded cooperative group. She serves on the scientific advisory boards of Pacific Biosciences, Inc. and Edge Biosciences, Inc. Prof. Mardis received the Scripps Translational Research award for her work on cancer genomics in 2010, and has been named a Distinguished Alumni of the University of Oklahoma College of Arts and Sciences for 2011.
Link to Professor Mardis' website
Professor Eckhard Wolf (Plenary Speaker)
Director of the Laboratory for Functional Genome Analysis (LAFUGA) at the Gene Center, University of Munich, Germany.Professor Eckhard Wolf is Head of the Institute of Molecular Animal Breeding and Biotechnology and Director of the Laboratory for Functional Genome Analysis (LAFUGA) at the Cene Center, University of Munich, Germany.
His research programme focuses on pre-implantation development of mammalian embryos and their interaction with the maternal environment, using molecular profiles as sensors for physiological developmental events and their disturbances in the context of assisted reproduction techniques or metabolic imbalances. Moreover, genetically tailored large animal models are generated for hypothesis-driven research projects in the fields of reproductive biology and biomedicine.
Link to Professor Wolf's website
Professor David A. Hume (Plenary Speaker)
Director of The Roslin Institute and Research Director of the Royal (Dick) School of Veterinary Studies at the University of Edinburgh, UK.Professor David Hume is Director of The Roslin Institute and Research Director of the Royal (Dick) School of Veterinary Studies at the University of Edinburgh.
Professor Hume holds the Chair of Mammalian Functional Genomics and his research programme focuses on the functional genomics and systems biology of macrophages - specialised cells of the immune system involved in infection, inflammatory disease and cancer.
Since joining the Roslin Institute from the University of Queensland in 2007, Professor Hume has extended his interests to encompass the control of innate immunity in major livestock species including chickens and pigs. He is a Fellow of the Royal Society of Edinburgh and the Society of Biology and holds a Royal Society Wolfson Research Merit Award.
Link to Professor Hume's website
Invited Speakers
Dr. Mario Calus (Invited Speaker)
Senior researcher at the Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, The Netherlands.Dr. Mario Calus is a senior researcher at the Animal Breeding and Genomics Centre at Wageningen UR Livestock Research in The Netherlands. His research during the past five years focuses on genomic selection in livestock, in particular on developing methods and software to allow estimation of genome-wide SNP effects and implementation of genomic selection in practical breeding programmes. He has been instrumental in the implementation of genomic selection for the breeding industry in the Netherlands.
Professor Paul M. Coussens (Invited Speaker and founder of the ISAFG meeting series)
Director, Center for Animal Functional Genomics, Michigan State University, USA.Dr. Paul M. Coussens is a Professor at the Department of Animal Science and Director of the Center for Animal Functional Genomics (CAFG) at Michigan State University. As Director of the MSU CAFG, Professor Coussens has been instrumental in securing funding and personnel to develop cDNA and oligonucleotide microarray facilities dedicated to physiology, immunology, nutrition, welfare and growth in livestock, companion, and wildlife animal species. The CAFG has since developed 12 microarrays for studies in pigs, cattle, dogs, zebra finches, and rainbow trout. The MSU CAFG continues to distribute microarrays to investigators throughout the world. Currently Professor Coussens’ research is focused on the immunology of mycobacterial diseases, survival of mycobacteria in macrophages, and development of influenza vaccine production systems. Most of this current work has grown out of previous functional genomics studies.
In 1995, Professor Coussens founded a biotechnology company focused on development of novel veterinary vaccines, diagnostics, and vaccine production systems. Professor Coussens began a three-year leave from MSU to serve as Chief Technology Officer within this company, raising over $1.5 million in venture funds and small business grants.
Professor Coussens has published over 75 peer-reviewed research articles, several book chapters, and numerous symposia papers, presented over 170 abstracts and invited talks, and authored 12 US patents, as well as several international patents.
Professor Alexander Evans (Invited Speaker)
Head of School and Director of the Reproductive Biology Research Cluster (RBRC), UCD School of Agriculture and Food Science, University College Dublin, Ireland.Alexander Evans was awarded a BSc in Animal Science by Nottingham University (UK), a PhD by the University of Saskatchewan (Canada) and a DSc (Published work) from the National University of Ireland. After spending three years as a postdoctoral fellow in Cornell University (USA) he joined the academic staff in University College Dublin in 1996. Professor Evans’ research interests are in reproductive physiology with emphasis on cattle in the areas of ovarian follicular development, oocyte and embryo development and the factors associated with the establishment of pregnancy.
Link to Professor Evans’ website
Professor Tom Freeman (Invited Speaker)
Group Leader, Systems Immunology, The Roslin Institute, University of Edinburgh, UK.For the last 15 years Professor Freeman has worked on various aspects of functional genomics and systems biology. In 1994 he began his long association with the Hinxton Genome Campus, where he first led the Gene Expression Group at Sanger Institute before moving on to lead the UK National Microarray Programme. His current work focuses on furthering the understanding of macrophage biology and its role in the control of infection and inflammation. In this respect his work combines the use of experimental technologies to examine macrophage activation, together with new and innovative approaches to the analysis of complex data and pathway modelling. He also leads the development of BioLayout Express3D a powerful network analysis program with a growing international user base.
Link to Professor Freeman’s website
Dr. Emmeline Hill (Invited Speaker)
Principal Investigator, UCD Equine Exercise Genomics Research Group and co-founder and Chairman of Equinome Ltd., UCD School of Agriculture and Food Science, University College Dublin, Ireland.Dr Emmeline Hill leads the Equine Exercise Genomics Research Group at the UCD School of Agriculture and Food Science, University College Dublin and is a co-founder and Chairman of Equinome Ltd., a world leader in the development and provision of genetic tests for the international Thoroughbred horse industry. She joined UCD in 2002 with a B.A. Genetics (1995) and a Ph.D. in Molecular Population Genetics (2000) from Trinity College, Dublin. Dr. Hill has been at the forefront of Thoroughbred performance genomics during the last decade and has published more scientific papers on equine exercise genomics than any other researcher worldwide. In 2004 she received a Science Foundation Ireland President of Ireland Young Researcher Award, Ireland's most prestigious award for young scientists, to develop the world’s first academic research programme dedicated to understanding the genomics of athletic performance in Thoroughbred racehorses. She is a member of the International Horse Genome Mapping Group, the International Equine Genetic Diversity Consortium and the International Horse Genome Sequencing Consortium.
Link to Dr. Hill’s website
Professor Haja Kadarmideen (Invited Speaker)
Group Leader of Quantitative and Systems Genetics, Department of Basic Animal and Veterinary Sciences, Faculty of Life Sciences, University of Copenhagen, Denmark.Haja Kadarmideen obtained a Doctor of Veterinary Medicine and Masters' degree in Veterinary Genetics (both from Tamil Nadu Veterinary and Animal Sciences University, Chennai, India) in 1989 and 1992, respectively. He obtained his PhD degree in Quantitative Genetics from The University of Guelph (Ontario, Canada) in 1998 after conducting a part of his PhD research at Wageningen University in the Netherlands. He was a dairy cattle geneticist for over three years at the Scottish Agricultural College of the University of Edinburgh, UK. He spent a short time as a visiting scientist at the University of Wisconsin-Madison, USA in 1999. He was then Head of the Statistical Animal Genetics Group at the Swiss Federal Institute of Technology (ETH) Zurich in Switzerland (2001-2006). In 2006, he was appointed as a Principal Scientist and Leader of the Quantitative Genetics and Systems Biology Group at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia where he worked until his move to the University of Copenhagen in January 2011. He has worked closely with animal breeding/genomics/biotech industries, international organisations and has led many international research projects in Europe, Africa and Asia. He has trained 24 graduate (MSc and PhD) students, nine postdocs and authored over 140 research articles.
Professor Kadarmideen’s research interests include the following: systems genetics and systems biology applied in animal models (pigs and dogs) for underpinning complex animal and human diseases; genome and transcriptome analysis for genetic- and bio-marker discovery; genomic evaluation and breeding of dairy cattle and pigs for improved health and disease resistance.
Link to Professor Kadarmideen’s website
Professor James N. MacLeod (Invited Speaker)
John and Elizabeth Knight Chair, Professor of Veterinary Science, Gluck Equine Research Center, University of Kentucky, USA.Professor James N. MacLeod is the Head of the Laboratory of Equine Musculoskeletal Sciences at the Gluck Equine Research Center. His research group studies articular cartilage, primarily focused on the cell biology of chondrocytes. Additional experiments focus on how the function of cartilage and synovial cells is regulated by cell/matrix interactions and influenced by intra-articular medications.
Professor MacLeod’s laboratory study changes in chondrocyte gene expression that occur during normal maturation, when joints develop arthritis, and associated with efforts to heal joint surface lesions. Physical exertion and the musculoskeletal stress of athletic events predispose both horses and humans to joint injuries. In fact, pain and lameness associated with joint disease is a primary variable that limits many athletic careers.
Professor MacLeod’s group are also interested in genomics and the identification of genetic determinants that influence both congenital and acquired musculoskeletal diseases. They have been at the forefront of recent developments in equine genomics and have been closely involved with the equine genome sequencing project and the development of functional genomics tools for the horse.
Link to Professor MacLeod’s website
Dr. Rebecca J. Oakey (Invited Speaker)
Reader in Epigenetics, Department of Medical and Molecular Genetics, King’s College London, London, UK.Rebecca Oakey completed her D.Phil. in the Department of Biochemistry at the University of Oxford in 1989 with Dr Chris Tyler-Smith and Professor E.M Southern, constructing a long-range physical map of the human centromere. Following graduation she moved to the United States for thirteen years, completing post-doctoral training in mouse genetics with Dr Michael Seldin at Duke University and in mammalian genetics with Dr Bob Nussbaum at the University of Pennsylvania. Dr Oakey established her independent group at the Children’s Hospital of Philadelphia in 1996 in the Division of Human Genetics before moving to the UK in 2002 to the Department of Medical & Molecular Genetics at King’s College London.
Dr Oakey’s interests are focussed on epigenetic mechanisms of imprinted gene regulation in mammals. In the mouse, this includes understanding how a group of imprinted retrogenes are regulated and especially how they are involved with alternative polyadenylation. In humans the group is interested in understanding the mechanisms associated with epigenetic causes of human disease. This is being addressed genome-wide using next generation sequencing of the methylome, the exome, the transcriptome and by interrogating DNA binding proteins across the genome. Essential to all of these approaches is the integration of bioinformatics research and development into these genome-wide data analyses.
Link to Dr Oakey’s website
Professor John Quackenbush (Invited Speaker)
Professor of Computational Biology and Bioinformatics, Harvard School of Public Health, USA.Professor John Quackenbush holds the Chair of Computational Biology and Bioinformatics at the Harvard School of Public Health. He earned his PhD in theoretical particle physics from UCLA in 1990 and then completed a postdoctoral fellowship in experimental high energy physics. After receiving a fellowship from the National Center for Human Genome Research, he worked with Glen Evans on the physical mapping of human chromosome 11, and later with Richard Myers and David Cox on large-scale DNA sequencing of chromosomes 21 and 4. In 1998 he joined the faculty at The Institute for Genomic Research (TIGR) where his work focused on the use of genomic and computational methods for the study of human disease.
Professor Quackenbush joined the Dana-Farber Cancer Institute in 2005 where his work has increasingly focused on the analysis of women's cancers although the methods he and his group develop can be broadly applied. In 2009 he launched the Center for Cancer Computational Biology (CCCB), a Dana-Farber Strategic Plan Center focused on providing computational support more broadly to the DFCI research community.
The goal of Professor Quackenbush’s research programme is to develop software, databases, and bioinformatics techniques that will allow the development of new diagnostics and a more complete understanding of the cellular networks that are responsible for diseases. His work in these areas is conceptually organized along the flow of information within the cell: from gene to RNA to protein to pathways and networks, and ultimately to disease.
Link to Professor Quackenbush’s website
Dr. Carl-Johan Rubin (Invited Speaker)
Scientist, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.Dr. Rubin received a M.S. in Biomedicine from Uppsala University in 2003 and a Ph.D. in Molecular Medicine from the Department of Medical Sciences at the same University in 2008. His PhD project involved functional genomics studies of bone metabolism using chicken models. As a post-doc at the Department of Medical Biochemistry and Microbiology at Uppsala University (2009-2011), his work involved mainly bioinformatics of sequence data (whole genome, target enrichment and RNA) and quantitative genetics, primarily in domestic animals such as chicken, pig and horse, but also human, mouse and other vertebrates. Dr. Rubin’s work is particularly focused on utilizing massively parallel sequencing data to unravel genes and molecular pathways altered in response to positive selection in animals and in monogenic human traits and diseases.
Link to Dr. Rubin’s website
Dr. Tad S. Sonstegard (Invited Speaker)
Research Geneticist, USDA, ARS Beltsville, USA.Dr. Sonstegard received a B.S. in Agricultural Biochemistry from Iowa State University (1987) and a Ph.D. from the University of Minnesota in Molecular Biology and Genetics (1995). After a post-doc at the USMARC (1995-97), he moved to his current position at USDA, ARS Beltsville (1997-present) focused on development of genomic tools to characterize the structure and function of ruminant livestock genomes, and the application of these tools to accelerate genetic improvement. Dr. Sonstegard has actively participated on the International BAC map and HapMap consortia for cattle, and led the Bovine Gene Atlas project characterizing the transcriptome in 100 different tissues. He was a co-leader of consortia that developed the BovineSNP50 chip and won the National Federal Labs technology transfer award and USDA Secretary of Agriculture’s Honour Award for helping revolutionize the US dairy industry. Most recently, he helped lead development of high and low density bovine SNP chips.
Link to Dr. Sonstegard’s website
Professor Christopher K. Tuggle (Invited Speaker)
Chair, Interdepartmental Genetics and Professor of Molecular Genetics, Department of Animal Science, Iowa State University, USA.Professor Tuggle is on the faculty in the Department of Animal Science at Iowa State University, where he has worked since 1991. His background is in Molecular Genetics and he holds a Ph.D. in Biochemistry and Molecular Biology; he also completed postdoctoral training at Columbia University in New York and the University of Southern California in Los Angeles.
His research programme at ISU from 1991-2001 focused on mapping and sequencing genes controlling important traits in food animals; since 2001 he has focused on the use of functional genomics and bioinformatics to understand gene pathways and networks relevant for finding targets for genetic improvement of pork safety and feed efficiency. He is especially interested in the promise of genomics and bioinformatics to create tools for prediction of phenotypes that are difficult or expensive to obtain such as quantitative disease resistance traits.
Professor Tuggle has published more than 100 papers in refereed journals. He currently serves as Functional Genomics Editor for Animal Genetics, and is on several Editorial Boards covering animal genomics and biotechnology. Professor Tuggle has won several regional and national awards for his research, including a 2011 Fulbright award that supported immunogenomics work at the Roslin Institute in Edinburgh, Scotland.
Link to Professor Tuggle’s website
