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Publications

Journals, Conferences and Posters

JOURNALS

Behkamal, B., Naghibzadeh, M., Pagnani, A., Reza Saberi, M., Al Nasr, K., "Solving the α-Helix Correspondence Problem at Medium-Resolution Cryo-EM Map". Journal of Molecular Graphics and Modelling, vol. 103, 2021.

Abu Al-Haija, Q., Al Nasr, K., "Forecasting Model for the Annual Growth of Cryogenic Electron Microscopy Data". Lecture Notes in Computer Science, Springer, vol 12029, 2020, pp. 147-158.

Mardugalliamov, R., Al Nasr, K., Hayes, M., "A Hidden Markov Model-based approach to reconstructing double minute chromosome amplicons". International Journal of Computational Biology and Drug Design. Vol. 13, No. 1, January 2020, pp. 5-20.

Al Nasr, K., Abu Al-Haija, Q., "Forecasting the growth of structures from NMR and X-Ray Crystallography experiments released per year". Journal of Information and Knowledge Management. Vol. 19, No. 1, March 2020, pp: 1-12.

Abu Al-Haija, Q., Marouf, I., Asad, M., Al Nasr, K., "Cost-Effective FPGA Implementation of Parallel Schmidt-Samoa Cryptosystem (SSC)". Journal of Theoretical and Applied Information Technology. Vol. 97, No. 15, August 2019.

Thapa, S., Li, H., OHair, J., Bhatti, S., Chen, F., Al Nasr, K., Johnson, T., Zhou, Z., "Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives". Molecular Biotechnology. June 2019, pp.1-23.

Abu Al-Haija, Q., Marouf, I., Asad, M., Al Nasr, K., "Implementing a lightweight Schmidt-Samoa cryptosystem (SSC) for sensory communications". International Journal on Smart Sensing and Intelligent Systems. Vol. 12, No. 1, May 2019

Abu Al-Haija, Q., Mao, Q., Al Nasr, K., "Forecasting the Number of Monthly Active Facebook and Twitter Worldwide Users Using ARMA Model". Journal

Al Nasr, K. , Yousef, F., Jebril, R., Jones, C., "Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem". Molecules, 23(2), 28. January 2018.

Al Nasr, K. , Jones, C., Yousef, F., Jebril, R., "PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models". Journal of Computational Biology. Vol. 25, Issue 1. January 2018.

Biswas, A., Ranjan, D., Zubair, M., Zeil, S., Al Nasr, K., He, J., "An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images". IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. PP, No. 99. March 2016.

Al Nasr, K., He, J., "Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions– Beyond the Protein Loop Closure Problem". Robotica-Cambridge University Press, Vol. 34, No. 8, August 2016, 1777-1790.

Biswas, A., Ranjan, D., Zubair, M., Zeil, S., Al Nasr, K., He, J., "An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images". IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Vol. PP, No. 99. March 2016.

Al Nasr, K., Ranjan, D., Zubair, M., Chen, L., He, J., "Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph Algorithm", IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. 11, No. 2, March-April 2014, pp. 419-430.

Al Nasr, K., Liu, C., Rwebangira, M., Burge, L., He, J., "Intensity-Based Skeletonization of CryoEM Grayscale Images Using a True Segmentation-Free Algorithm", IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). Vol. 10, No. 5, September-October 2013, pp. 1289-1298..

McKnight, A., Si, D., Al Nasr, K., Chernikov, A., Chrisochoides, N., He, J., "Estimating Loop Length from CryoEM Images at Medium Resolutions", BMC Structural Biology, 13(Suppl 1):S5, November 2013.

Biswas, A., Si, D., Al Nasr, K., Ranjan, D., Zubair, M., He, J., "Improved Effeciency in CryoEM Secondary Structure Topology Determination from Inaccurate Data", Journal of Bioinformatics and Computational Biology (JBCB), Vol. 10, No. 3, June 2012.

Si, D., Ji, S., Al Nasr, K. He, J., "A Machine Learning Approach for the Identification of Protein Secondary Structure Elements from cryoEM Density Maps", Biopolymers, Vol. 97, No. 9, September 2012, pp. 698-708.

Al Nasr, K., Ranjan, D., Zubair, M., He, J., "Ranking valid topologies of the Secondary Structure Elements Using A Constraint Graph", Journal of Bioinformatics and Computational Biology (JBCB), Vol. 9, No. 3, June 2011, pp. 415-430.

Al Nasr, K., Ranjan, D., He, J., "Enumeration of the Geometrically Constrained Assignments of the Secondary Structure Using the Constraints Graph", Systemics and Informatics World Network (SIWN), Vol. 10, July 2010, pp.68-76.

Al Nasr, K., Sun, W., He, J., "Structure prediction for the helical skeletons detected from the low resolution protein density map", BMC Bioinformatics, Vol.11, (Suppl. 1):S44, 2010.

Al Nasr, K., He, J, "An Effective Convergence Independent Loop Closure Method using Forward-backward Cyclic Coordinate Descent", Int. J. Data Mining and Bioinformatics, Vol. 3, No. 3, 2009, pp. 346-361.

CONFERENCE PROCEEDINGS

Al Sallal, M., Chen, W., Al Nasr, K., "Machine Learning Approach to Assign Protein Secondary Structure Elements from Cα Trace". 2020 IEEE International Conference on Bioinformatics & Biomedicine (BIBM), San Diego, CA, USA, pp. 35-41, 2020.

Jebril, R., Zhu, Y., Chen, W., Al Nasr, K., "A Divide and Conquer Algorithm for Electron Microscopy Segmentation", Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Atlanta, GA, Article No.102, Pages 1–7, September 2020.

Chen, L., Jebril, R., Al Nasr, K., "Segmentation based Feature Extraction for Cryo Electron Microscopy at Medium Resolution", Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Atlanta, GA, Article No. 113, Pages 1–9, September 2020.

Abu Al-Haija, Q., Al Nasr, K., "Supervised Regression Study for Electron Microscopy Data". 2019 IEEE International Conference on Bioinformatics & Biomedicine (BIBM), San Diego, CA, USA, November 2019.

Mardugalliamov, R., Al Nasr, K., Hayes, M., "A Hidden Markov Model-based approach to reconstructing double minute chromosome amplicons", International Conference on Intelligent Biology and Medicine (ICIBM 2018), Los Angeles, CA, USA, June 2018.

Al Nasr, K., Yousef, F., Jones, C., Jebril, R., "Geometry Analysis for Protein Secondary Structures Matching Problem", The 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Boston, MA August 2017.

Al Nasr, K., Jones, C., "An efficient tool for protein models assessment", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China, December 2016.

Yang, T., Qian, K., Lo, D., Al Nasr, K., Qian, Y., "Spam Filtering using Association Rules and Naive Bayes Classifier", The 2015 International Conference on Progress in Informatics and Computing (PIC-2015), Nanjing, China, December 2015.

Al Nasr, K., He, J., "Deriving Protein Backbone Using Traces Extracted From Density Maps at Medium Resolutions", The 11th International Symposium on Bioinformatics Research and Applications (ISBRA 2015), Norfolk, VA, June 2015.

Al Nasr, K., He, J., "Construction of Protein Backbone Pieces Using Segment-based FBCCD and Cryo-EM Skeleton", Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Newport Beach CA, September 2014.

Al Nasr, K., Chen, L., He, J., "A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps", Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Washington DC, September 2013, pp. 479-455.

Al Nasr, K., Liu, C., Rwebangira, M., Burge, L., "A Graph Approach to Bridge the Gaps in the Volumetric Electron Cryo-Microscopy Skeletons", The 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC, May 2013, Lecture Notes in Computer Science, 7875: 211-223.

Chen, L., Al Nasr, K., He, J. "Using Constraints in Modeling the Protein β-Sheet Topology". Modeling, Simulation, and Visualization Student Capstone Conference. Suffolk, VA, 2013.

McKnight, A., Al Nasr, K., Si, D., Chernikov, A., Chrisochoides, N., He, J., "CryoEM Skeleton Length Estimation using a Decimate Curve", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, October 2012, pp. 109-113.

Al Nasr, K., Chen, L., Si, D., Ranjan, D., Zubair, M., He, J., "Building the Initial Chain of the Proteins Through De Novo
Modeling of the Cryo-Electron Microscopy Volume Data at the Medium Resolutions", Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando, FL, October 2012, pp.490-497.

Biswas, A., Si, D., Al Nasr, K., Ranjan, D., Zubair, M., He, J., "A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from Cryo-EM Density Data in Presence of Errors", The IEEE international conference on Bioinformatics and Biomedicine Workshops (BIBM), Atlanta, GA, November 2011, pp. 160-163.

He, J., Al Nasr, K., "An Approximate Robotics Algorithm to Assemble a Loop between Two Helices", The IEEE international conference on Bioinformatics and Biomedicine Workshops (BIBM), Silicon Valley, CA, November 2007, pp. 74-79.

Posters

Al Nasr, K.,Begna, G., Liu, C., "A Graph Approach to Bridge the Gaps in Volumetric Electron Cryo-Microscopy Skeletons", The First Annual Howard University Research Day, Howard University, Washington, DC, April 1, 2013. Best Poster Award in Computation & Biology Modeling.

Al Nasr, K., Liu, C., "De novo modeling of protein structure", Workshop held on NSF Center for Science of Information, Purdue University. West Lafayette, IN. December 2012.

Al Nasr, K., Chen, L., Si, D., Ranjan, D., Zubair, M., He, J., "Building the Initial Chain of the Proteins Through De Novo Modeling of the Cryo-Electron Microscopy Volume Data at the Medium Resolutions", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, October 2012.

Al Nasr, K., He, J., "Structure Prediction for Helical Skeletons from Low Resolution Protein Density Map", The IEEE international conference on Bioinformatics and Biomedicine Workshops (BIBM), Washington, D.C., November 2009.

Al Nasr, K., He, J., "Parallelized Simulated Annealing for protein topology prediction", NMSU Graduate Research and Arts Symposium (GRAS), Las Cruces, NM, April 2009.

Al Nasr, K., He, J., Sun, W., "Structure Prediction for helix skeletons from a low resolution density map", The IEEE international conference on Bioinformatics and Biomedicine Workshops (BIBM), Philadelphia, PA, November 2008.

Al Nasr, K., and He, J., "An Effective Convergence Independent Loop Closure Method using Forward-backward Cyclic Coordinate Descent", NMSU Graduate Research and Arts Symposium (GRAS), Las Cruces, NM, USA, April 2007.