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Hakonarson has published numerous papers on genomic discoveries and their translations in scientific medical journals, including Nature (journal), Nature Medicine, Nature Genetics, Cell (journal), Science (journal) and The New England Journal of Medicine. Time Magazine listed Dr. Hakonarson’s autism gene discovery project, reported in Nature in 2009, among the top 10 medical breakthroughs of that year. Dr. Hakonarson’s Nature Medicine paper on a novel precision based therapy in rare lymphatic disorders was awarded among the Top 10 clinical/translational papers in 2019 by the Clinical Research Forum.