Bonnie Berger

Academic Achievements

Professor Bonnie Berger received her undergraduate degree from Brandeis University in Waltham, MA and then went on to earn her Ph.D. from MIT under Turing Award winner, Silvio Micali. In 1989, she wrote a paper on parallel algorithms with John Rompel, which won her the Machtey Award which is given to the students with the best paper.

Berger holds a joint appointment in Electrical Engineering and Computer Science. She currently serves as the head of Computation and Biology group at MIT CSAIL. Her most recent work focuses on designing algorithms to gain biological insights from advances in automated data collection and the subsequent large data sets drawn from them.

I started to learn biology on a need to know basis, by getting in touch with famous biologists here at MIT, such as Peter Kim and Jonathan King, and they taught me biology and I taught them computer science.”
Bonnie Berger
Modern Cryptographic Tools Combined with Computational Biology

Berger’s work really took focus when she combined her knowledge of computer science and biology. Her interest in biology began when her postdoc professor Danny Kleitman, came back from a conference in Washington D.C. and said, “Proteins. That’s what you should do.” Combining her computer science background with new interest in biology began Berger’s educational experience in the world of Computational Biology. With the help of her colleagues, Peter S. Kim and Jonathan King, Berger began to learn biology on what she describes as a “need to know” basis.

As her research furthered in computational biology, she realized that they were generating massive amounts of data sets. Berger understood that if they could access these data sets, then they could use them to discover patterns in the underlying processes. She and her students introduced "Compressive Genomics," a framework for computing on compressed genomic data without having to decompress it. While studying these data sets could lead to breakthroughs in understanding the roles of genes in disease, there are also security concerns. Berger and her group began leveraging cryptographic techniques and designing computational platforms that allowed them to do secure crowdsourcing at scale.

Genomes are essentially akin to your electronic health record, meaning they tie back directly to an individual. If it’s released and happens to get into the wrong hands, then it’s permanently leaked. This makes people reluctant to release their genomes. Berger’s goal is to work with the genomes to do some form of computation in order to see patterns and clues that come from different genomes. To do this, she and her team created a provably secure server that researchers can tap into the massive amounts of human genomes that are being sequenced in order to come up with a genetic basis for disease. With access to genomes, Berger could complete a genome-wide association study that finds associations between mutations in genomes and disease. From there they could find statistical correlations between mutations in many genomes with diseases or complex phenotypes such as height, weight, etc. Allowing individuals to feel that they can securely share their genomes will allow Berger and her team, as well as other researchers, to employ computation on the genomic data sets and possibly determine improved medical treatments.

We provide a framework, that’s provably secure so that researchers can tap into the massive amounts of human genomes that are being sequenced to come up with the genetic basis for important human conditions such as cancer and diabetes.”
Bonnie Berger
Awards and Research

Berger was one of the pioneer researchers in the area of computational molecular biology and, together with the many students she has mentored, has had a massive impact and value in defining the field. She works on a diverse set of problems, including compressive genomics, network integration, structural bioinformatics, genomic privacy, and medical genomics. She often collaborates closely with biologists in order to design experiments to leverage the power of computation for biological explorations.

Professor Berger has won many awards including a National Science Foundation Career Award and the Biophysical Society’s Dayhoff Award for research. In 1999, Berger was named one of Technology Review Magazine’s inaugural TR100, as a top young innovator of the twenty-first century. Five years later, Berger was elected as a Fellow of the Association for Computing Machinery (ACM), and in 2010, received the RECOMB Test of Time Award. More recently, Berger received International Society for Computational Biology's 2019 Senior Scientist Award - the highest award given by the 3500-member society. She is also an elected member of the American Academy of Arts and Sciences. In addition, she received the Margaret Pittman Director's Award at the NIH, was elected as a Fellow of the International Society for Computational Biology (ISCB), American Institute of Medical and Biological Engineering (AIMBE), and American Mathematical Society (AMS), and received an Honorary Doctorate from EPFL. She was elected to serve as Vice President of the ISCB, Head of the steering committee for RECOMB, and as a Member-at-Large of the Section on Mathematics at the American Association of the Advancement of Science (AAAS). She is a recent member of the Sloan Fellowship Selection committee. She also serves on the Executive Editorial Board of Journal of Computational Biology and as a member of the editorial boards of Annual Reviews for Biomedical Data Science, Genome Biology, Bioinformatics, IEEE/ACM TCBB, and Cell Systems. In addition, Professor Berger is an Associate Member of the Broad Institute, Faculty member of Harvard/MIT Health Science & Technology, and Affiliated Faculty of Harvard Medical School.

As I have gotten more and more into computational biology, I realized that we are currently generating massive data sets. So massive that if we can effectively access these data sets, then we can use them to discover patterns that provide clues to the underlying processes.”
Bonnie Berger