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. Joseph Loyall is a Principal Scientist at BBN. Dr. Loyall is the lead of the Intelligent Software and Systems (ISS) business unit at BBN, which performs research and development in a variety of areas, including the engineering of biological systems, application of machine intelligence to synthetic biology, and the development of languages and tools for predictable and controllable biological systems. Dr. Loyall has been the PI and PM for numerous DARPA and AFRL research projects, is the author of over 100 technical papers, and holds four patents. Dr. Loyall has a Ph.D. in Computer Science from the University of Illinois.
Tom Mitchell is a Senior Software Engineer at BBN. He is a software generalist who has worked across the BBN footprint during his 30-year tenure. He has helped to deliver prototype and fielded systems to both government and commercial customers. His customers have included DARPA, IARPA, IRS, ERDC, NSF, ConEdison, The New York Stock Exchange, and Blue Cross Blue Shield of Massachusetts. He has worked in a diverse set of domains including simulation and modeling, expert systems, fraud detection, signal processing, speech and language processing, distributed systems, healthcare, geographic information systems, and future networking testbeds. Most recently Tom has been involved in three synthetic biology projects for both DARPA and IARPA. Tom holds a B.A. in Cognitive Science from the University of Rochester.
Dr. Tramy Nguyen is a Scientist at BBN. She received her Ph.D. in Electrical and Computer Engineering at the University of Utah. Her main research interest includes the design automation for synthetic biology. This involves developing Computer Aided Design (CAD) tools that will assist biologist in dealing with complex biological designs. She is also a big advocate towards standards development for synthetic biology.
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. Miles Rogers is a Scientist at BBN. His research interests are in protein engineering and the creation of novel biosensors, as well as the development of microphysiological human organ systems for use as disease models. His background includes research in host-pathogen interactions in human disease as well as disease transmissibility by insect vectors. Dr. Rogers received his Ph.D.in Biological Sciences from Western Michigan University.
Ms. Helen Scott is a staff scientist at BBN. Her research interests include modeling biological systems, and the use of computational techniques to better understand the expression of the genome. Her previous research includes development of photosynthetic models for use in Earth System Modeling, genome and breeding system evolution in trees, and predictive models for the effects of climate change on vector borne diseases. She received both her B.S. in Biology, and M.S. in Biotechnology from Texas Tech University.
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.
Dan Wyschogrod is a Senior Scientist at BBN. For many years he has been working in cyber security in fields including network traffic monitoring and formal methods for code analysis. Recently, he has applied some of the techniques he developed for network packet inspection to inspection of DNA samples for both pathogen sequences and evidence of engineering for both the FAST-NA and FELIX projects. These methods are based on previous work in the cyber realm using string matching and application of Bloom filters to large corpora of data. His past work includes development of high speed regular expression matching in hardware, malware signature extraction, image guided robotics and image processing for tracking of aircraft on airport surface among other fields. His name appears on nine patents and provisional patents.
Dr. Fusun Yaman is a Lead 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.