S.M. Short, M.D. Perez, A. Morse, R. Dameron Jennings, D.S. Howard, C. David, L. Blaha, Y. Shaw, C. J. Lee, N. Park, C Marsac, Z. McIver, N. Khuri and J.M. Grayson. High Dimensional Immune Profiles and Machine Learning May Predict AML Relapse Early Following Transplant., accepted for publication in The Journal of Immunology, November 2024.

K. Zhao, S. Bhandari, N.P. Whitener, J. M. Grayson, and N. Khuri. An Ensemble Machine Learning Approach for Benchmarking and Selection of scRNA-seq Integration Methods, 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, September 2023, pp. 1--10.

K. Zhao, J. M. Grayson, and N. Khuri. Multi-Objective Genetic Algorithm for Cluster Analysis of Single-Cell Transcriptomes. Journal of Personalized Medicine, 2023, 13(2), 183.

N. Khuri, S. Bhandari, E. Murillo Burford, N.P. Whitener and K. Zhao. An Evolutionary Approach to Data Valuation. 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 2022, pp. 1--10.

S. Bhandari, N.~P. Whitener, K. Zhao and N. Khuri. Multi-Target Integration and Annotation of Single-Cell RNA-Sequencing Data. 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 2022, pp. 1--6.

S. Parsons, N. P. Whitener, S. Bhandari and N. Khuri. Interpretable Hierarchical Bayesian Modeling of Cell-Type Distributions in COVID-19 Disease. Proceedings of the 56th Annual Conference on Information Sciences and Systems, March 2022.

X. Wang and N. Khuri. Generative Adversarial Network for the Segmentation of Ground Glass Opacities and Consolidations from Lung CT Images. Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3 -- BIOINFORMATICS. February 2022, pp. 27--37.

N. Khuri, E. Murillo Burford, S. Parsons, C. Xu. A Game-Theoretical Approach for Data Acquisition From Fitness Tracking Devices. Proceedings of the IEEE Symposium on Networks, Computers and Communications. November 2021, pp. 1--6.

N. Khuri and S. Parsons. A Value-Based Approach for Training of Classifiers with High-Throughput Small Molecule Screening Data. BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 2021, pages 1–-10.

E. C. Salcedo, M. B. Winter, N. Khuri, G. M. Knudsen, A. Sali, C. S. Craik. Global Protease Activity Profiling Identifies Breast Cancer Subtype-Associated Proteolysis. ACS Chemical Biology, 16(4), March 2021, pages 712–-723.

N. Khuri and A. Prasanna. Using Game Theory to Guide the Classification of Inhibitors of Human Iodide Transporters. Proceedings of the 36th ACM/SIGAPP Symposium on Applied Computing, virtual, 2021, pages 916--923.

T. Liu and N. Khuri. Classification of Drug Prescribing Information Using Long Short-Term Memory Networks. Proceedings of the 36th ACM/SIGAPP Symposium on Applied Computing, 2021, pages 1086--1089.

N. Bhagwat and N. Khuri. Predicting Targets for Genome Editing with Long Short Term Memory Networks. Transactions on Computational Science & Computational Intelligence, Springer Nature -- Advances in Computer Vision and Computational Biology, 2021, pages 657--670.

T. Yun, D. Garg and N. Khuri. Mining Biomedical Texts for Pediatric Information. Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, volume 3: BIOINFORMATICS, 2021, pages 60--71.

S. Parsons and N. Khuri. Discovery of Research Trends in Computer Science Education on Ethics Using Topic Modeling. Proceedings of the 2020 International Conference on Computational Science and Computational Intelligence (CSCI'20), 2020, pages 885--891.

L. Zou, P. Spanogiannopoulos, L. Pieper, H.-C. Chien, W. Cai, N. Khuri, J. Pottel, B. Vora, Z. Ni, E. Tsakalozou, X. Zhang, W. Zhang, B. K. Shoichet, K. M. Giacomini, P. J. Turnbaugh. Bacterial metabolism rescues the inhibition of intestinal absorption by food and drug additives. Proceedings of the National Academy of Sciences, 117(27), July 2020, pages 16009--16018.

N. Khuri. Mining Environmental Chemicals with Boosted Trees. Proceedings of the 35th Annual ACM Symposium on Applied Computing, 2020, pp. 1082--1089.

N. Khuri, K.V. Lehmkhul-Dakhwe, M. Vanhoven, W. Lee, S. Khuri. Interdisciplinary Minor in Bioinformatics: First Results and Outlook. Proceedings of the 51st ACM Technical Symposium on Computer Science Education, 2020, pp. 407--412.

Z. Zou, J. Pottel, N. Khuri, H. Ngo, Z. Ni, E. Tsakalozou, M. Warren, Y. Huang, B. Shoichet, Brian, K. Giacomini. Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP. Journal of Molecular Pharmaceutics. 17(3), pp. 748--756 , March 2, 2020.

B. Vora, E.A.E. Green, N. Khuri, F. Ballgren, M. Sirota, K. M. Giacomini. Drug-nutrient interactions: discovering prescription drug inhibitors of the thiamine transporter, ThTR-2 (SLC19A3). The American Journal of Clinical Nutrition, Volume 111, Issue 1, January 2020, Pages 110–-121.

S. Deshmukh, P. Heller, N. Khuri. A Long-Short Term Memory Network for Detecting CRISPR Arrays. Proceedings of the 2019 IEEE International Conference on Machine Learning and Applications (ICMLA 2019), 2019, pp. 619--624.

L.C. Pereira, D.V.R. Sturzenegger, J. Ortiz, N.M.E. Ayad, W.A. Cortopassi, L.P. Safatle, N. Khuri. Challenges in the regulation of high cost treatments -- An overview from Brazil. Value in Health Journal Regional Issues, pp. 191--195, Volume 20, December 2019.

D. Schneidman-Duhovny, N. Khuri, G.Q. Dong, M. Winter, E. Shifrut, N. Friedman, C. Craik, P. Paz, F. Aswad, A. Sali. Predicting T-cell epitopes by integrated modeling of APC processing, MHCII presentation, and TCR recognition. PLoS One. 2018 Nov 6;13(11)

N. Khuri and S. Deshmukh. Machine Learning for Classification of Inhibitors of Hepatic Drug Transporters. Proceedings of the 17th IEEE International Conference on Machine Learning and Applications (ICMLA 2018), 2018, pp. 181--186.

V. Kannan and N. Khuri. Creating Digital Collages Inspired by English Texts. Proceedings of the 13th International Conference on Digital Information Management (ICDIM 2018), 2018, pp. 228-233. Best paper award.

S. Deshmukh and N. Khuri. PediatricDB: Data Analytics Platform for Pediatric Healthcare. Proceedings of the 13th International Conference on Digital Information Management (ICDIM 2018), 2018, pp. 216-221.

N. Khuri, A. Zur, M. Wittwer, L. Lin, S.W. Yee, A. Sali, K. Giacomini. Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. Journal of Chemical Information and Modeling, May 31, 2017.

E. C. Chen, N. Khuri, X. Liang, A. Stecula, Y. Huang, A. Sali, K. M. Giacomini. Discovery of orthosteric and allosteric ligands of the Organic Cation Transporter, OCT1. Journal of Medicinal Chemistry, February 23, 2017.

S. Khuri, M. Van Hoven, N. Khuri. Increasing the Capacity of STEM Workforce: Minor in Bioinformatics. Proceedings of 2017 ACM SIGCSE, 2017, pp. 315--320.

R. Altman, S. Prabhu, A. Sidow, J. Zook, R. Goldfeder, D. Litwack, E. Ashley, G. Asimenos, C. Bustamante, K. Donigan, K. Giacomini, E. Johansen, N. Khuri, E. Lee, X. Liang, M. Salit, O. Serang, Z. Tezak, D. Wall, E. Mansfield, T. Kass-Hout. A research roadmap for next-generation sequencing informatics. Science Translational Medicine volume 8 (335), pp. 335ps10, 2016.

R. Altman, N. Khuri, M. Sali, K. Giacomini. Unmet needs: Research helps regulators do their jobs. Science Translational Medicine volume 7, Issue 315, pp. 315ps22, 2015.

B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G. Dong, A. Sali. Comparative Modeling of Drug Target Proteins. Chemistry, Molecular Sciences and Chemical Engineering. Ed: J. Reedijk, Elsevier, Waltham, MA, 2014.

U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research, 2014 Jan 1;42(1):D336-46.

A. Schlessinger, N. Khuri, K. Giacomini, A. Sali. Molecular modeling and ligand docking for Solute Carrier (SLC) transporters. Current Topics in Medicinal Chemistry 13, 843-856, 2013.

M.B. Wittwer, A.A. Zur, N. Khuri, Y. Kido, A. Kosaka, X. Zhang, K.M. Morrissey, A. Sali, Y. Huang, K.M. Giacomini. Discovery of potent, selective multidrug and toxin extrusion Transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling. Journal of Medicinal Chemistry 56, 781-795, 2013.

A. Schlessinger, M.B. Wittwer, A. Dahlin, N. Khuri, M. Bonomi, H. Fan, K. Giacomini, A. Sali. High Selectivity of the gamma-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach. Journal of Biological Chemistry 287, 37745-37756, 2012.

D. Bhaya, A.R. Grossman, A.S. Steunou, N. Khuri, F.M. Cohan, N. Hamamura, M. C. Melendrez, M. M. Bateson, D. M. Ward, J.F. Heidelberg. Genomic, metagenomic and functional analyses of cyanobacteria from hot-spring microbial mats reveal an unexpected diversity in nutrient utilization strategies. ISME J: 1(8):703-13, 2007.