Dr. Alexander Ioannidis (PhD, MPhil) graduated summa cum laude from Harvard University in Chemistry and Physics and earned an M.Phil in Computational Biology and Diploma in Greek from the University of Cambridge. His Ph.D. from Stanford University was in Computational and Mathematical Engineering, where he still teaches machine learning and data science as an Adjunct Lecturer in the School of Engineering. He also has an M.S. in Mgmt. Sci. and Eng. (Optimization) from Stanford. Prior to Stanford, he worked in superconducting computing logic and quantum computing at Northrop Grumman. As a current research fellow in the Stanford School of Medicine (Department of Biomedical Data Science), his work focuses on applying computational methods to problems in genomics and population genetics.


I work on novel algorithm design (particularly ancestry related) for several large-scale genomic studies that aim at understanding genetic causes of disease.

I also focus on projects at the intersection of history and population genetics, including work with native communities. As the grandson of Cappadocian refugees expelled from their native land, I try to engage with the complex sentiments of displaced indigenous peoples in these projects. Pain over the disruption of community heritage and over dispossession from traditional sites often remains raw. If engagement with descendant communities is lacking, research into our past can often feel like a continuation, even a legitimation, of dispossession. Combined alongside a dialogue with native communities, however, genetics can play a small role in helping to reclaim ancestral stories and dispersed ancestral connections. I hope our work in this area plays a constructive role in that process.

As written by the poet Rumi in the language of the Cappadocians (Rûm),
پیمی تیِ پَاثیِسْ پیمی تی خاسِس
“Tell me what happened to you, tell me what you have lost.”
[Rumi; Konya ms 67; translit. πε με τι έπαθες, πε με τι έχασες]

Professional Education

  • Doctor of Philosophy, Stanford University, CME-PHD (2018)
  • Master of Science, Stanford University, MGTSC-MS (2018)
  • Master of Philosophy, University of Cambridge, Computational Biology (2005)
  • Bachelor of Arts, Harvard University, Chemistry and Physics (2003)


2020-21 Courses


All Publications

  • Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients. Journal of biomedical informatics Lopez Pineda, A., Pourshafeie, A., Ioannidis, A., McCloskey Leibold, C., Chan, A. L., Bustamante, C. D., Frankovich, J., Wojcik, G. L. 2020: 103664


    OBJECTIVE: Pediatric acute-onset neuropsychiatric syndrome (PANS) is a complex neuropsychiatric syndrome characterized by an abrupt onset of obsessive-compulsive symptoms and/or severe eating restrictions, along with at least two concomitant debilitating cognitive, behavioral, or neurological symptoms. A wide range of pharmacological interventions along with behavioral and environmental modifications, and psychotherapies have been adopted to treat symptoms and underlying etiologies. Our goal was to develop a data-driven approach to identify treatment patterns in this cohort.MATERIALS AND METHODS: In this cohort study, we extracted medical prescription histories from electronic health records. We developed a modified dynamic programming approach to perform global alignment of those medication histories. Our approach is unique since it considers time gaps in prescription patterns as part of the similarity strategy.RESULTS: This study included 43 consecutive new-onset pre-pubertal patients who had at least 3 clinic visits. Our algorithm identified six clusters with distinct medication usage history which may represent clinician's practice of treating PANS of different severities and etiologies i.e., two most severe groups requiring high dose intravenous steroids; two arthritic or inflammatory groups requiring prolonged nonsteroidal anti-inflammatory drug (NSAID); and two mild relapsing/remitting group treated with a short course of NSAID. The psychometric scores as outcomes in each cluster generally improved within the first two years.DISCUSSION: and conclusion Our algorithm shows potential to improve our knowledge of treatment patterns in the PANS cohort, while helping clinicians understand how patients respond to a combination of drugs.

    View details for DOI 10.1016/j.jbi.2020.103664

    View details for PubMedID 33359113

  • Native American gene flow into Polynesia predating Easter Island settlement. Nature Ioannidis, A. G., Blanco-Portillo, J., Sandoval, K., Hagelberg, E., Miquel-Poblete, J. F., Moreno-Mayar, J. V., Rodriguez-Rodriguez, J. E., Quinto-Cortes, C. D., Auckland, K., Parks, T., Robson, K., Hill, A. V., Avila-Arcos, M. C., Sockell, A., Homburger, J. R., Wojcik, G. L., Barnes, K. C., Herrera, L., Berrios, S., Acuna, M., Llop, E., Eng, C., Huntsman, S., Burchard, E. G., Gignoux, C. R., Cifuentes, L., Verdugo, R. A., Moraga, M., Mentzer, A. J., Bustamante, C. D., Moreno-Estrada, A. 2020


    The possibility of voyaging contact between prehistoric Polynesian and Native Americanpopulations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1-6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South Americanpopulations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesianindividuals with Native Americanindividuals (around AD 1200) contemporaneouswith the settlement of remote Oceania13-15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesianindividuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.

    View details for DOI 10.1038/s41586-020-2487-2

    View details for PubMedID 32641827

  • Reconstructing admixture and migration dynamics of post-contact Mexico Esteban Rodriguez-Rodriguez, J., Blanco-Portillo, J., Ioannidis, A., Moreno-Estrada, A. WILEY. 2018: 228
  • Integrated Power Divider for Superconducting Digital Circuits IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY Oberg, O. T., Herr, Q. P., Ioannidis, A. G., Herr, A. Y. 2011; 21 (3): 571–74
  • Ultra-low-power superconductor logic JOURNAL OF APPLIED PHYSICS Herr, Q. P., Herr, A. Y., Oberg, O. T., Ioannidis, A. G. 2011; 109 (10)

    View details for DOI 10.1063/1.3585849

    View details for Web of Science ID 000292115900092

  • Digital circuits using self-shunted Nb/NbxSi1-x/Nb Josephson junctions APPLIED PHYSICS LETTERS Olaya, D., Dresselhaus, P. D., Benz, S. P., Herr, A., Herr, Q. P., Ioannidis, A. G., Miller, D. L., Kleinsasser, A. W. 2010; 96 (21)

    View details for DOI 10.1063/1.3432065

    View details for Web of Science ID 000278183200086

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