In 2006, Bakken joined the Columbia University Institute of Medicine. Her research combines informatics, evidence-based nursing and health equity.[3] At Columbia, she led the Center for Evidence-based Practice in the Underserved and the pre-/post-doctoral program on Reducing Health Disparities through Informatics (RHeaDI).[4][5]
Bakken worked on the representation of nursing concepts and terminology in Systematized Nomenclature of Medicine and LOINC.[6] She showed that using formal vocabularies to express patient problems enhanced the generalizability of research, improved the quality of health outcomes and improved the traineeship of informatics and nursing researchers.[6] She has argued that digital infrastructure is a critical component of a health ecosystem, and that new clinical tools could be used for self-management and care.[7] However, to make the digital infrastructure fair and equitable, it is key to improve public trust such that individuals contribute personal data and clinical experiences. Bakken developed community engagement projects to improve public trust amongst urban Latino populations.[7]
Bakken is known for her contributions to biomedical informatics, with a focus on visual analytic innovations, training of informatics students and knowledge formalization.[citation needed] She spent 2015 as a Scholar in Residence at the National Academy of Medicine.[4] During the COVID-19 pandemic, Bakken was supported by the National Institutes of Health to create a visualization toolbox to address COVID-19 misinformation and hesitation around testing and vaccination.[8]