Research & Interests
From HMS Genetics Department Wiki
My background is in mathematics and computer science with a PhD in Cognitive and Neural Systems. I am interested in modeling scientific knowledge in order to make it more useful, either computationally reusable for other scientific research, or in practice, such as in medical decision support systems.
Individual (Personalized) Medical Treatment
My PhD research focused on mathematical models of unipolar depression that would provide insight into the underlying dynamics of depression in order to support clinicians, enabling them to make better treatment choices, drug or therapy, for their individual patients. This type of approach is now known as personalized medicine. I used neural networks and differential equation modeling in this work. These approaches are known as machine learning and systems biology, respectively.
Translational Medicine - from Clinical Research to Clinical Practice
While researching in this area, I became aware of the need to integrate knowledge from and across multiple disciplines in order utilize the knowledge within each domain from its unique perspective. I studied the use of ontologies for knowledge representation and as a way to further exploit description logics (the formalism underlying the OWL ontology language) as a mechanism in which the integration of heterogeneous life science data could be automated. I focused this initial work in the area of biological pathways (signal transduction, metabolic, gene regulatory, protein interactions, etc.) which apply to a number of disease areas; for example, biological pathways form the basis for identifying and relating chemical compounds with putative targets for drug therapies. In support of this theme, I took on the role as community liaison for the BioPathways Consortium and co-led the development of a community-based standard for the exchange of pathway information (BioPAX) leading to the establishment of the BioPAX initiative, a global consortium within which the standards work takes place.
The seamless integration of clinical research, outcomes and life science knowledge, remains the major challenge in being able to reap the rewards of our nations' research investments in biomedical research.
Throughout my research career, I have sought the engagement of clinicians and scientists from multiple disciplines. In fact, identification of the so-called stakeholders in the first step. In order to provide any solution one must first understand the problems and the issues that domain experts face. This is not possible without engaging with others - as no one is an expert in all areas.
The Methods from my dissertation research, which were subsequently patented were sold in 2009 in order to be put into use in clinical practice.
Teaching
In addition, I have a long-standing interest in teaching that I am looking to continue/develop further. Until now multidisciplinary research has meant that one finds oneself in departments where there isn't a direct fit and teaching isn't an option. Now with the growing recognition of the utility of in silico methods in enhancing clinical practice (the translational medicine movement), there is a better understanding of the contribution of each discipline in medical practice and much more support for it. Thus I look forward to being able to teach what I've learned in a multidisciplinary environment.
Research Projects
Biological Pathways Integration, Aggregation, and Inference
EMPWR: Computational Exploration of Molecules in the Context of Biological Pathway Networks \\ National Science Foundation Award Number IIS-0542041
BioPAX (http://www.biopaxwiki.org). Core Group Member involved in intimating the creation of a data exchange format for biological pathway databases. Procured partial support from the DOE and got it doubled in the second year. Represents BIOPAX at international conferences and workshops and coordinate development with the BioPathways Consortium and its constituents. (Since August 2002)
Major Depressive Disorder (Unipolar Depression)
My graduate work was in the area of predictive medicine and personalized medicine. I was awarded two patents based on my graduate work, one for predicting the therapeutic outcome of a treatment and the other for an automated treatment selection method. This work was based on analyzing clinical research and clinical trial data for antidepressant treatments including cognitive behavioral therapy.
I have a strong interest in integrating diverse sources of knowledge, data (from multiple technologies) and various modeling and analysis methodology to address clinical, medical, biological and scientific questions. I welcome opportunities to collaborate in any disease area.
I have a strong interest in education and in collaborative work. This is evidenced by my emphasis on including tutorials as introductory parts of workshops and my involvement in creating consortia and collaborations in health care and life sciences.
On going
BioPathways Consortium (http://www.biopathways.org) Co-organizer and Steering Committee. The mission of the BioPathways Consortium is to catalyze the emergence and development of computational pathways biology, by building up a strong and coherent scientific community, sharing knowledge, facilitating collaborations, and fostering the development of methods and tools of wide interest to the community.
W3C Semantic Web for Health Care and Life Science (HCLSIG)
Dean's Advisory Board Boston Univeristy Metropolitan College. Here's a photo from the meeting in November 2003 at Student Village Boston University and one from the Dean's Advisory Board Dinner, Veronique, Boston March 13, 2003
