Team

Dr. Aaron Adler is a Senior Scientist at BBN. Dr. Adler’s expertise includes synthetic biology, artificial intelligence, machine learning, and human computer interaction. He has served as the PI and PM of several AFRL and DARPA-funded projects. He has developed analytical tools and interfaces for flow cytometry, and an API for a liquid handling robot as part of the TASBE project. Dr. Adler has organized several workshops at the intersection of AI and synthetic biology. He received his Ph.D. in Computer Science from the Massachusetts Institute of Technology.

Dr. Bryan Bartley is a Scientist at BBN. His research interests include computational modeling and data integration for systems and synthetic biology. His background includes biomedical research in diabetes, kidney disease, and cancer, and he has helped developed biosimulation applications for the biotech industry. He received a PhD in Bioengineering from the University of Washington.

 

Dr. Jacob Beal is a Senior Scientist at BBN where he leads research on analyzing and engineering complex aggregates, such as engineered and natural cells, genetic regulatory networks, sensor networks, and robot swarms. Dr. Beal has a strong record in synthetic biology, computer science, biological representation, and organization and management of complex cross-disciplinary efforts. He has been PI for several DARPA-funded projects, including the Toolchain for Assisting Synthetic Biology Engineering (TASBE), which demonstrated the first end-to-end automation toolchain for engineering cells from high-level designs. On the Living Computing Project, an NSF Expeditions grant, Dr. Beal leads metrology, standardization, and device characterization, coordinating across a group of eight leading synthetic biology PIs at MIT and Boston University. Dr. Beal is an active contributor to the Synthetic Biology Open Language (SBOL) standards community, which focuses on representation and exchange of biological design information. Dr. Beal has also developed of methods for calibrated flow cytometry, applied in the DARPA CCM program to develop high-precision engineering of RNA replicon expression in cell populations and prediction of transcriptional regulatory networks from models of individual components, as well as to develop modular in-cell protein sensors and CRISPR-based repressor devices. His work on fluorescence calibration is being standardized in collaboration with NIST, and has been validated through deployment in inter-laboratory studies involving more than 150 laboratories around the world. Dr. Beal also developed the Proto BioCompiler—the first method for automatically generating genetic regulatory topologies from high-level computational specifications—and is a member of the Executive Committee of the SRC Semiconductors and Synthetic Biology Roadmap Project. Dr. Beal also leads research on aggregate programming, which focuses on efficient engineering of complex global phenomena from local interactions, and is co-creator of field calculus, a foundational theory for global-local relations, as well as its implementations in the Proto and Protelis programming languages, and a number of algorithmic and application contributions. Dr. Beal has a Ph.D. from the Massachusetts Institute of Technology.

Ms. Susan Katz, is a senior software engineer and an experienced technical PM, with extensive experience running large teams of subcontractors (both industry and academic) for research and production programs. She has led numerous software and hardware research projects. Ms. Katz has developed a deep technical understanding in diverse technology areas such as computational neuroscience, federated database systems, user interfaces, quantum computing, signature detection algorithms, and assistive design for robotics systems.

Dr. Nicholas Roehner is a Scientist at BBN. His research interests include the development of software tools to automate genetic and experimental design and the development of domain-specific languages to help make synthetic biology more reproducible and accessible as a field. He earned his Ph.D. in Bioengineering at the University of Utah in 2014 and was most recently a postdoctoral researcher at Boston University and the Broad Institute. He is a twice-elected editor for the Synthetic Biology Open Language (SBOL), a standard for the electronic representation and exchange of biological design data.

Dr. Allison Taggart is a Scientist at BBN. Her research interests are in computational molecular biology and include the use of genomic data to study mechanisms of gene expression and RNA processing with applications in synthetic biology. Her previous research includes development of algorithms for probing RNA intermediates in sequencing data and research into splicing and intron turnover. She received her PhD in Molecular Biology, Cell Biology and Biochemistry from Brown University.

Dr. Fusun Yaman is a Senior Scientist at BBN. Her research interests are in artificial intelligence, with a focus on multi-agent plan assessment and planning. She has applied her background in machine learning and knowledge representation to solve synthetic biology problems. Dr. Yaman has been the PI and PM for several projects. In synthetic biology, Dr. Yaman has been a technical lead on two DARPA- funded projects: on the TASBE project she developed the MatchMaker system for automatic selection of genetic devices for transcriptional computations, and in the Controlling Cellular Machinery (CCM) program she developed machine-learning methods to identify combinations of miRNA expression levels associated with particular disease states. Dr. Yaman has a Ph.D. in Computer Science from the University of Maryland.