Sean Simmons
MIT Mathematics
Berger Lab

About Me

I am a joint postdoc between Cenk Sahinalp (SFU and Indiana) and Bonnie Berger (MIT). My research is focused on privacy in genomic analysis and on computational genomics more broadly. Before starting my postdoc I was an Applied Mathematics PhD student at MIT. I worked in Professor Bonnie Berger's Computational Biology research group, focusing on privacy preserving analysis of biomedical data. Before coming to MIT, I attended the University of Texas (go Longhorns!), where I majored in Mathematics (and occasionally flirted with majoring in computer science) through the Dean Scholar's Honors Program.


It is no secret that recent years have produced a deluge of data in almost all aspects of our lives. In particular, the rise of numerous large databases in the realm of biomedicine (Genetics databases like TCGA, medical databases like MIMIC, EHRs, etc), as well as nontraditional data sources (health apps, online forums, etc), holds much promise to generate new insights for biomedicine and the everyday consumer of medical information. At the same time there is risk of abuse, due to both the sensitive nature of the data, as well as the effects of spurious results. My research is focused on how to balance these risks with the possible rewards.

My thesis work mainly focused on how to best use computational methods to protect the privacy of participants in biomedical studies.

I have also been working on problems related to using simple machine learning approaches to look at RNA-seq data and RNA protein interactions (with Professor Berger, Dr. Jadwiga Bienkowska at Biogen Idec and Dr. Jian Peng in the Berger lab), as well as having played around with statistical medical genomics (with George Tucker now at Amazon, focusing on Mixed Linear Models, etc.).

Before joining Professor Berger's group, most of my focus in graduate school was on optimization, theoretical computer science, and combinatorics.

Undergraduate Research

Before coming to graduate school my research experiences were related to more traditional areas of pure and applied mathematics. I spent three summers (two as a participant, one as a graduate assistant) working on problems related to combinatorics on partial words under Francine Blanchet-Sadri at the UNCG REU on partial words.

I also spent the summer after my freshman year working on problems related to Algebraic Cryptography under Chris Christensen and Jintai Ding at NKU.

Finally, as part of a capstone project at the University of Texas I worked on problems related to knot theory under Cameron Gordon.