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BMC Genomics|August 19, 2016
Computing energy landscape maps and structural excursions of proteinsEmmanuel Sapin, Daniel B Carr, Kenneth A De Jong, et al.IEEE/ACM Transactions on Computational Biology and Bioinformatics|January 24, 2017
From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy LandscapesEmmanuel Sapin, Kenneth A De Jong, Amarda ShehuJournal of Bioinformatics and Computational Biology|June 30, 2011
A two-stage evolutionary approach for effective classification of hypersensitive DNA sequencesUday Kamath, Amarda Shehu, Kenneth A De JongJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 16, 2017
Sample-Based Models of Protein Energy Landscapes and Slow Structural RearrangementsTatiana Maximova, Zijing Zhang, Daniel B Carr, et al.IEEE/ACM Transactions on Computational Biology and Bioinformatics|April 18, 2012
An evolutionary algorithm approach for feature generation from sequence data and its application to DNA splice site predictionUday Kamath, Jack Compton, Rezarta Islamaj-Doğan, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 30, 2015
idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein DockingIrina Hashmi, Amarda ShehuIEEE Transactions on Nanobioscience|February 11, 2016
A General, Adaptive, Roadmap-Based Algorithm for Protein Motion ComputationKevin Molloy, Amarda ShehuJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 24, 2015
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy LandscapesRudy Clausen, Amarda ShehuProteome Science|February 26, 2014
HopDock: a probabilistic search algorithm for decoy sampling in protein-protein dockingIrina Hashmi, Amarda ShehuBMC Structural Biology|February 26, 2014
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired methodKevin Molloy, Amarda ShehuPageof 21