BOOKS

  1. Bill Campbell, Swami Iyer, Bahar Akbal-Delibas, Introduction to Compiler Construction in a Java World (CRC Press, 2012)

Publications

 

JOURNAL PAPERS AND BOOK CHAPTERS

  1. R. Farhoodi, B. Akbal-Delibas, and N. Haspel, "Machine Learning Approaches for Predicting Protein Complex Similarity." Journal of Computational Biology, 24(1), 40-51, 2017.


  1. B. Akbal-Delibas, Roshanak Farhoodi, Marc Pomplun and N. Haspel, “Accurate Refinement of Docked Protein Complexes Using Evolutionary Information and Deep Learning ”, J Bioinform Comput Biol (JBCB), 14(3):1642002, 2016.


  1. B. Akbal-Delibas, Marc Pomplun and N. Haspel, “Accurate Prediction of Docked Protein Structure Similarity”, Journal of Computational Biology (JCB) 22(9), 2015.


  1. B. Akbal-Delibas and N. Haspel, "A Conservation and Biophysics Guided Stochastic Approach to Refining Docked Multimeric Proteins", BMC Structural Biology, 13(Suppl 1):S7, 2013.

  2. B. Akbal-Delibas, F. Jagodzinski, and N. Haspel, "A Conservation and Rigidity Based Method for Detecting Critical Protein Residues", BMC Structural Biology, 13(Suppl 1):S6, 2013.

  3. B. Akbal-Delibas, P. Boonma and J. Suzuki, "Baobab: A Model-Driven Development Framework for Autonomous and Adaptive Wireless Sensor Network Applications," In International Journal of Autonomous and Adaptive Communications Systems, Special Issue on Self-* Systems, Inderscience, to appear.

  4. B. Akbal-Delibas, I. Hashmi, A. Shehu and N. Haspel, "An Evolutionary Conservation Based Method for Refining and Reranking Protein Complex Structures", Journal of Bioinformatics and Computational Biology (JBCB),  10(3):1242002, 2012.

  5. I. Hashmi, B. Akbal-Delibas, N. Haspel and A. Shehu, "Guiding protein docking with geometric and evolutionary information", Journal of Bioinformatics and Computational Biology (JBCB), 10(3):1242008, 2012.

  6. B. Akbal-Delibas, P. Boonma, and J. Suzuki, "Precise Application Development for Wireless Sensor Networks", In J. Suzuki (ed.) Service Composition, Business Process Engineering and Domain-Specific Challenges in Service Oriented Architecture: Engineering Non-Functional Requirements, IGI Global, est. publishing date in 2012.


CONFERENCE AND WORKSHOP PAPERS

  1. R. Farhoodi, B. Akbal-Delibas, and N. Haspel. “Accurate Prediction of Docked Protein Structure Similarity Using Neural Networks and Restricted Boltzmann Machines”, CSBW IEEE BIBM, Washington D.C., 2015


  1. B. Akbal-Delibas, M. Pomplun, and N., Haspel. "AccuRefiner: A Machine Learning Guided Refinement Method for Protein-Protein Docking", 7th International Conference on Bioinformatics and Computational Biology (BICoB), Honolulu, Hawaii, 2015.


  1. B. Akbal-Delibas, M. Pomplun, and N., Haspel. “AccuRMSD: A Machine Learning Approach to Predicting Structure Similarity of Docked Protein Complexes”, In Proc. of the ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB), Newport Beach, CA, 2014.


  1. F. Jagodzinsky, B. Akbal-Delibas and N., Haspel. "An Evolutionary Conservation and Rigidity Analysis Machine   Learning Approach for Detecting Critical Protein Residues", In Proc. of the Computational Structural Biology Workshop (CSBW), ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB), Washington DC, 2013.


  1. B. Akbal-Delibas and N., Haspel. "Refining Multimeric Protein Complexes Using Conservation, Electrostatics and Probabilistic Selection", In Proc. of the Computational Structural Biology Workshop (CSBW), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Philadelphia, PA, 2012

  2. B. Akbal-Delibas, F. Jagodzinski and N., Haspel. "Towards a Hybrid Method for Detecting Critical Protein Residues", In Proc. of the Computational Structural Biology Workshop (CSBW), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Philadelphia, PA, 2012.

  3. B. Akbal-Delibas, I. Hashmi, A. Shehu and N. Haspel, "Refinement of Docked Protein Complex Structures Using Evolutionary Traces", In Proc. of the Computational Structural Biology Workshop (CSBW), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Atlanta, GA, 2011.

  4. I. Hashmi, B. Akbal-Delibas, A. Shehu and N. Haspel, "Protein Docking with Information on Evolutionary Conserved Interfaces", In Proc. of the Computational Structural Biology Workshop (CSBW), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Atlanta, GA, 2011.

  5. B. Akbal-Delibas, P. Boonma, and J. Suzuki, "Extensible and Precise Modeling for Wireless Sensor Networks", In Proc. of the 2nd International Workshop on Model-Based Software and Data Integration (MBSDI), Sydney, Australia, April 2009.


POSTERS

  1. B. Akbal-Delibas, M. Pomplun, N. Haspel, “An Artificial Neural Network to Predict RMSDs of Docked Protein Complexes”, 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA, July 2014.


  1. B. Akbal-Delibas, P. Boonma, and J. Suzuki, "Extensible Modeling for Wireless Sensor Networks", 2nd Coastal Environmental Sensing Networks Conference, Boston, MA, July 2009.


INVITED TALKS

  1. S.E.T. in the City College/Grad Student Panel, Microsoft NERD Center, Cambridge, MA, April 2014


  1. "Using Evolutionary Conservation Information for Protein Complex Refinement and Detecting Critical Residues", UMass Boston Colloquium Talk, December 12, 2012.

  2. "An Evolutionary Conservation Based Method for Refining and Reranking Protein Complex Structures", Graduate Students' Research Symposium, UMass Boston, MA, May 4, 2012.

  3. "Refining and Reranking Protein Complex Structures Using Evolutionary Information", Fifth Annual Meeting of the North East Turkish American (NETA) Scholars at Harvard University, Boston, MA, April 28, 2012.

  4. "Exploration of Protein Complex Structures", Women in Science Workshop, Boston, MA, December 8, 2010