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Krainer received a 2019 Breakthrough Prize in Life Sciences for his contributions to the understanding of the RNA gene-splicing process and, in collaboration with fellow Prize Laureate Dr. Frank Bennet of Ionis Pharmaceuticals, the development of medical interventions that target the RNA-splicing process, including Spinraza, which is the first treatment for the genetic disorder Spinal Muscular Atrophy.. Other honors include: Cold Spring Harbor Fellow (1986-89); Pew Scholar in the Biomedical Sciences (1992-96); National Institute of General Medical Sciences MERIT Award (2012-2022); New York Intellectual Property Law Association Inventor of the Year Award (2017); FE Bennett Award of the American Neurological Association (2017); Herbert & Esther Bennett Brandwein Award in Genetic Research (2018); Bermuda Principles Award (2019); RNA Society Lifetime Achievement Award (2019); Doctor Philosophiae Honoris Causa, Tel Aviv University (2019); Klaus Joachim Zülch Prize in Basic Neurological Research (2019); Peter Speiser Award in Pharmaceutical Sciences (2019); Ross Prize in Molecular Medicine (2020); Gregor Johann Mendel Medal for Outstanding Achievements in Science (2020); Fellow of the American Academy of Arts & Sciences (2016); Fellow of the National Academy of Inventors (2018); Member of the National Academy of Medicine (2019). In 2020, Krainer was elected to the National Academy of Sciences.

From 1986-1989, Krainer conducted postdoctoral research as the first Cold Spring Harbor Fellow at the Cold Spring Harbor Laboratory. Krainer worked as an Assistant Professor from 1989-1990, Associate Professor from 1990-1994, and Professor since 1994. Krainer is a faculty member of the graduate programs in Genetics, Molecular and Cellular Biology, and Molecular Genetics and Microbiology at State University of New York, Stony Brook. Krainer holds the St. Giles Foundation Professorship at Cold Spring Harbor Laboratory. His former students include Ewan Birney. Krainer is a co-founder and Director of Stoke Therapeutics, based in Bedford, MA.

Krainer was born in Montevideo, Uruguay to a Jewish family of Hungarian and Romanian descent. He has one older brother, who is a chemical engineer. His father did forced labor for two years in a Romanian labor camp (Ferma Alba) during World War II. After the war, his father's original surname, Kreiner changed to Krainer due to a clerical error when he was a refugee in Italy. His parents owned a small leather business in Montevideo. Krainer attended a private bilingual French-Spanish elementary school. He later attended a public school for two years before completing his pre-college education with four years at a private Spanish-Hebrew school. Krainer lived through political unrest during his teenage years, including urban guerrilla and military dictatorship. Krainer received a full scholarship from Columbia University and completed a Bachelor of Arts degree in Biochemistry in 1981. He graduated cum laude and Phi Beta Kappa. In 1986, he earned a Doctor of Philosophy degree in Biochemistry from Harvard University in 1986.