Medical research aims to improve health for everyone. While its advances are undeniable, the pace and cost of the progress are not optimal. For example, independent analyses concluded that at least half of the published biomedical research findings are irreproducible, and most scientific papers are never read or cited. This paper examines biomedical research holistically, as a system of incentives that shape the behavior of scientists, administrators, publishers, and funders, and are detrimental to medical progress. We identify opportunities to change and improve those incentives by altering the way research output is disseminated and evaluated, and recommend transparent, data-driven measures of methodological rigor, reproducibility, and societal value of scientific discoveries. Embracing these opportunities would maximize our investments in biomedical research and optimize its value to human health, while simultaneously increasing freedom, creativity, and satisfaction of the scientific workforce.