Welcome to our Computational Biology lab

Predicted structure of pB119L (red) over known native structure (blue).

Our lab focuses on developing algorithms to bridge between computer science and the life sciences. Our research contributions are in computational structural biology, biophysics, and bioinformatics. We investigate from a computational perspective problems concerning sequence, structure, dynamics, function, and interactions of biological molecules.

Our methods build on probabilistic search, optimization, and machine learning approaches, often combining ideas from sampling-based robot motion planning and evolutionary computation. Our research projects are diverse, detailed under Research. Recent highlights include:

Evolutionary Search Strategies for Sampling Local Minima of the Protein Energy Surface:

  • This work appears in: Brian Olson and Amarda Shehu. Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface. ACM Bioinformatics and Computational Biology (BCB), Washington, D.C., 2013, pg. 430-439.

Probabilistic Path Sampling to Connect Protein Functional States:

  • This work appears in: Kevin Molloy and Amarda Shehu. Elucidating the Ensemble of Functionally-relevant Transitions in Protein Systems with a Robotics-inspired Method. BMC Structural Biology J 2013, 13(Suppl1):S8.

Evolutionary- and Geometry-driven Search of Protein-protein Structural Assemblies:

  • This work appears in: Irina Hashmi and Amarda Shehu. HopDock: A Probabilistic Search Algorithm for Decoy Sampling in Protein-protein Docking. Proteome Sci 2013, 11(Suppl1):S6.

Adaptive Probabilistic Tree-based Search to Sample Conformations of the Protein Native State:

  • This work appears in: Kevin Molloy, Sameh Saleh, and Amarda Shehu. Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab-initio Protein Structure Prediction. IEEE/ACM Trans Comp Biol and Bioinf 2013, 10(5):1162-1175.

Evolutionary Algorithms For Feature Generation and SVM Kernel Optimization:

  • This work appears in: Uday Kamath, Jack Compton, Rezarta Islamaj Dogan, Kenneth A. De Jong, and Amarda Shehu, An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and its Application to DNA Splice-Site Prediction, Trans Comp Biol and Bioinf 2012, 9(5):1387-1398.

Spatially-structured Evolutionary Algorithms for Parallel Machine Learning:

  • This work appears in: Uday Kamath, Johan Kaers, Amarda Shehu, and Kenneth A. De Jong. "A Spatial EA Framework for Parallelizing Machine Learning Methods." Intl Conf on Parallel Problem Solving From Nature (PPSN), LNCS vol. 7491, pg. 206-215, Taormina, Italy, 2012.