Computational Biology & Medicine

With the increasing availability of data and the improved understanding of system-level interactions in biological systems, computational methods have found many applications in biology and medicine. Research in CISE develops algorithms for long-standing problems in computational biology, such as predicting and characterizing protein interactions, optimizing metabolic networks, and developing computational neuroscience models. Another line of research develops computational methods to advance experimental observation techniques used in biology, from imaging methods to atomic force microscopy. A burgeoning area of research applies Artificial Intelligence (AI) methods to medical data, leading to disease/outcome prediction models and medical decision-making tools.

QuBBD: From Personalized Predictions to Better Control of Chronic Health Conditions

The United States spends twice as much annually on health care than the next-highest spender but significantly under-performs in quality of care metrics, such as life expectancy and infant mortality. Hospital care accounts for about a third of U.S. health care spending. It has been estimated that nearly $30 billion in hospital care costs each […]

Joint Estimation Of Motion Model, Model Parameters, And Particle Trajectories In Single Particle Tracking

Single particle tracking (SPT) is a powerful class of techniques for understanding biomolecular motion at the subcellular level in the crowded environments of the plasma membrane, cytoplasm, and nucleus. The basic scheme is to acquire image sequences, typically through wide-field fluorescence imaging, produce trajectories from these images, and finally to estimate motion parameters from the […]

NSF, CISE Look to the Future of Smart Healthcare at Campus Workshop

By Sara Cody As the National Science Foundation looks to the future of science in smart and connected health, the agency partnered with the Center for Information and Systems Engineering to convene a gathering of principal investigators and other research leaders on the BU campus this month. The interdisciplinary researchers discussed their progress and identified […]

Analysis and Prediction of Molecular Interactions

The research in our lab focuses on molecular recognition using computational methods and follow-up validation experiments. Our primary target areas are (1) protein-protein docking and (2) exploring binding properties of proteins by computational solvent mapping. Protein docking methods are needed because many important interactions occur in weak, transient complexes that are not amenable to direct […]

AF: Small: Manifold optimization algorithms for protein-protein docking

Proteins are the major building blocks of the cell. Many proteins perform their function by interacting with other proteins. In a typical cell hundreds of thousands of different protein interactions take place. Characterizing these interactions helps elucidate how living organisms function at the molecular level, contributes towards the development of treatments against diseases such as […]

ABI Development: Utilization of Diverse Data in Exploring Protein-Protein Interactions

Each living cell is packed with proteins that continuously interact with each other in response to envirtonmental and other signals to control the cell’s growth and eventual fate. The analysis of such interactions is crucial for understanding signal transduction pathways that drive cell differentian during development and throughout the life an an organism. These pathways […]


Recent developments in nanotechnology and synthetic biology have enabled a new direction in biological engineering: synthesis of collective behaviors and spatio-temporal patterns in multi-cellular bacterial and mammalian systems. This will have a dramatic impact in such areas as amorphous computing, nano-fabrication, and, in particular, tissue engineering, where patterns can be used to differentiate stem cells […]

Interdisciplinary Team Sheds Light on How Proteins Bind

Finding Could Open Up New Drug Discovery Opportunities   Over the past six years, an interdisciplinary team of College of Engineering faculty members—Professor Sandor Vajda (BME, SE), Research Assistant Professor Dima Kozakov (BME), Professor Yannis Paschalidis (ECE, SE) and Associate Professor Pirooz Vakili (ME, SE)—have been developing a set of powerful optimization algorithms for predicting the structures of complexes that form when […]

2012 IEEE International Symposium on Biomedical Imaging Travel Support Barcelona, Spain

The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI) is a forum that has traditionally focused on the computational and modeling aspects of biomedical imaging. It emphasizes methodologies that have the potential to be applicable to multiple imaging modalities and to imaging at different scales. Topics include physical, biological and statistical modeling […]

Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ

All successful state-of-the-art protein docking methods employ a so called multistage approach. At the first stage of such approaches a rough energy potential is used to score billions of conformations. At a second stage, thousands of conformations with the best scores are retained and clustered based on a certain similarity metric. Cluster centers correspond to […]