Trainee Profile

Analysis and Modeling Group, Division of Sleep Medicine, Brigham and Women's Hospital
Neuroscience Statistics Laboratory, Massachusetts General Hospital - Massachusetts Institute of Technology
Machine Learning Group, Department of Computer Science, University of Massachusetts (Director, Gary Livingston, PhD)

My research focuses on developing tools and methods that facilitate the guided/automatic extraction of mathematical models from data. Traditionally, model building is a manpower intensive process that involves data analysis, formulating a model class, fitting parameters, and validating with alternate data sources. Whereas considering these steps separately made sense before the age of the personal computer, I would argue the availability of low cost computational hardware offers an opportunity to develop methods that can be used to interactively create and validate mathematical models.

My approach to developing interactive systems is to specify precise analytical links between formal methods used in computer science theory and machine learning with methods used in current mathematical modeling techniques. Analytical links between computer science and mathematics are essential, since they allow for algorithms based on mathematical models to be analyzed formally.

The objective of my research is to develop mathematical models that facilitate a deeper understanding of the effects of circadian phase and sleep on neurobehavioral performance. Developing tools that reduce the time needed to develop models and allows for more time to consider underlying physiological mechanisms.

Emery N. Brown, MD, PhD
Elizabeth Klerman, MD, PhD
Gary Livingston, PhD

Interactive Lecture and Computer Laboratory. Using principles of circadian physiology to design work schedules with Shifter. Presented as part of the Harvard Continuing Education Summer School course titled ”Circadian Biology: From clock genes and cellular rhythms to sleep”. (2008)

Interactive Lecture and Computer Laboratory. Using the Circadian Performance Simulation Software to Understand Circadian rythmns and Performance. Presented as part of the Chautauqua Short Course Program sponsored by the National Science Foundation. (2003 -2007)

Lecture. Using Simulations in Circadian Research. Presented at Circadian Biology: From Cellular Oscillators to Sleep Regulation (MCB 186), Department of Cellular and Molecular Biology, Harvard College (2003)

Related Link
CV (long; pdf, 84kb)
CV (1 page; pdf; 47 KB)

Honors and Awards
2009 Best Algorithm Poster Presentation Award, Conference of African American Researchers in the Mathematical Sciences
2009 Travel Sponsorship, Society of Applied Mathematics Annual Conference sponsored by the National Science Foundation
2008 Travel Sponsorship, Statistical Analysis of Neuronal Signals
2007 Elevated to Senior Member of the IEEE
2007 Best Modeling Poster Presentation award at the Conference for African American Researchers in the Mathematical Sciences
2006 Partners Healthcare Service Award
2005 Association of Multi-cultural Members at Partners Educational Scholarship
2005 Travel Sponsorship, Case Studies in Bayesian Statistics 8
2002 Trainee Research Merit Award, Association of Professional Sleep Societies Meeting
2001 First Time Travel Award, Association of Professional Sleep Societies Meeting
1999 Inducted into Upsilon Pi Epsilon, Computer Science Honor Society
1999 Northeastern University Minority Research Fellowship
1998 Northeastern University Research Fellowship

Dean II DA, Forger DB, Klerman EB. Taking the Lag out of Jet Lag through Model Based Schedule Design.
PLoS Comput Biol. 2009 Jun;5(6):e1000418. [PMID: 19543382]

Dean II DA, Fletcher A, Hursh SR, Klerman EB. Developing Mathematical Models of Neurobehavioral Performance for the "Real World".
J Biol Rhythms. 2007; 22:246-258. [PMID: 17517914]

Indic, P, Forger, DB, M.A. St. Hilaire, Dean II, DA, Brown, EN, Kronauer, RE, Klerman, EB, Jewett, ME, Comparison of amplitude recovery dynamics of two limit cycle oscillator models of the human circadian pacemaker.
Chronobiology International. 2005;22(4):613-29. [PMID: 16147894]

Forger, D.B., Dean II, D.A., Gurdziel, K., Leloup, J-C., Lee, C., von Gail, C. , Etchegary, J-P., Kronauer, R.E., Goldbeter, A., Peskin, C. S., Jewett, M.E. and Weaver, D.R. Development and Validation of Computational Models for Mammalian Circadian Oscillators.
OMICS. 2003 Winter;7(4):387-400. [PMID: 14683611]