COBRA’s experience

Engaged for 23 years at the interface of computational applications with life science research, both basic and applied

COBRA’s skill set

-- Computer-based models for analysis of biological systems and human diseases and disorders

-- Modeling and analysis of dynamic, nonlinearly interacting biological networks (assessed by gene chips and experimental studies of endocrine system function and interactions)

-- Physiologically-based mathematical modeling and analysis of rhythmic, episodic, and irregular temporal patterns of biological activities

-- Predictive, systems-level dynamical network models to describe functional properties of neuroendocrine regulatory interactions and inter- and intracellular mechanisms of temporal organization of biological processes

-- Development and implementation of automated, intelligent algorithms for analysis, interpretation, and screening of time series

-- Analysis and modeling of the biothermodynamics of protein, lipid, and nucleic acid systems

-- Principles of nonlinear least squares parameter estimation

-- Robust confidence interval estimation, propagation of uncertainty, analysis of residuals, and quantitative statistical interpretations of confidence

-- Analytical and statistical considerations for effective and optimal experimental protocol design and interpretation

Problem areas within COBRA’s experience domain

(i) membrane biophysics -- dynamic fluorescence techniques; novel, advanced, computationally-oriented analytical algorithms

(ii) computational biothermodynamics -- mathematical-modeling of oxygen-binding by human hemoglobin; linkage to protein subunit assembly; cooperative oxygen-binding energetics associated with hemoglobin’s protein conformational changes

(iii) protein biothermodynamics -- at Johns Hopkins for 4 years as an Assistant Professor of Research in Biology and Director of the NIH’s NCRR-funded Biocalorimetry Center; thorough immersion in the world of experimental and computational protein biothermodynamics

(iv) complex, nonlinear biological dynamics -- at the University of Virginia for 13 years as biomathematician of NSF’s Center for Biological Timing (Associate Professor of Research -- Medicine)

the basic science setting

(a) dynamic gene expression patterning

(b) neuronal electrical dynamics

(c) luciferase reporter gene analytics

(d) proteomics analytics

(e) rhythms in whole animal body temperature and locomotor activity patterning

the biomedical and clinical setting

(a) heart rate dynamics and neonatal sepsis

(b) dynamic scintigraphy & radiation-induced GI damage and individualized chronotherapy

(c) circadian biology and its intersection with epilepsy and seizure occurrence

(d) diverse endocrine secretory dynamics and associated human disorders and diseases

(e) circadian applications to a variety of sleep and human performance issues