N. Khuri, K. Virginia Lehmkhul-Dakhwe, Miri Vanhoven, Wendy Lee, S. Khuri. Interdisciplinary Minor in Bioinformatics: First Results and Outlook. Accepted for publication and presentation at the ACM SIGCSE, Portland, Oregon, March 11 -- March 14, 2020.
N. Khuri. Mining Environmental Chemicals with Boosted Trees. Accepted for publication and presentation at the ACM SAC, Brno, Czech Republic, March 30--April 3, 2020.
S. Deshmukh, P. Heller, N. Khuri. A Long-Short Term Memory Network for Detecting CRISPR Arrays. Accepted for publication and oral presentation at the 2019 IEEE International Conference on Machine Learning and Applications (ICMLA 2019), Boca Raton, Florida, December 16 -- 19, 2019.
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, nqz255, November 25, 2019.
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 (student). Machine Learning for Classification of Inhibitors of Hepatic Drug Transporters. IEEE 17th International Conference on Machine Learning and Applications (ICMLA 2018), pp. 181--186, Orlando, Florida, December 17--20, 2018.
V. Kannan (student) and N. Khuri. Creating Digital Collages Inspired by English Texts. Proceedings of the 13th International Conference on Digital Information Management (ICDIM 2018), pp. 228-233, Berlin, September 24--26, 2018. Best paper award.
S. Deshmukh (student) and N. Khuri. PediatricDB: Data Analytics Platform for Pediatric Healthcare. Proceedings of the 13th International Conference on Digital Information Management (ICDIM 2018), pp. 216-221, Berlin, September 24--26, 2018.
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, Seattle, March 8-11, 2017.
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.
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