Refereed Journal Articles

  • 1. Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., ..., AstraZeneca-Sanger Drug Combination DREAM Consortium, … & Nguyen, T. (2019). Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature communications, 10(1), 2674. (Soufan, O. is a member of AstraZeneca-Sanger Drug Combination DREAM Consortium).
  • 2. Soufan, O., Ewald, J., Viau, C., Crump, D., Hecker, M., Basu, N., & Xia, J. (2019). T1000: A reduced toxicogenomics gene set for improved decision making. Under peer review in PeerJ.
  • 3. Zhou, G., Soufan, O., Ewald, J., Hancock, R. E., Basu, N., & Xia, J. (2019). NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic acids research.
  • 4. Zhao, H., Soufan, O., Xia, J., Tang, R., Li, L., & Li, D. (2019). Transcriptome and physiological analysis reveal alterations in muscle metabolisms and immune responses of grass carp (Ctenopharyngodon idellus) cultured at different stocking densities. Aquaculture, 503, 186-197.
  • 5. Alazmi, M., Kuwahara, H., Soufan, O., Ding, L., & Gao, X. (2018). Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions. Bioinformatics.
  • 6. Chong, J., Soufan, O., Li, C., Caraus, I., Li, S., Bourque, G., Wishart, D.S. and Xia, J., 2018. MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. Nucleic Acids Research (Web Server issue).
  • 7. Soufan, O., Ba-alawi, W., Magana-Mora, A., Essack, M., & Bajic, V. B. (2018). DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. Scientific Reports.
  • 8. Alshahrani, M., Soufan, O., Magana-Mora, A., & Bajic, V. B. (2017). DANNP: an efficient artificial neural network pruning tool. PeerJ Computer Science, 3, e137.
  • 9. Soufan, O., Ba-Alawi, W., Afeef, M., Essack, M., Kalnis, P., & Bajic, V. B. (2016). DRABAL: Novel Method for Mining Large High-throughput Screening Assays using Bayesian Active Learning. Journal of Cheminformatics.
  • 10. Ba-alawi, W., Soufan, O., Essack, M., Kalnis, P., & Bajic, V. B. (2016). DASPfind: new efficient method to predict drug–target interactions. Journal of Cheminformatics, 8(1), 1.
  • 11. Soufan, O., Ba-Alawi, W., Afeef, M., Essack, M., Rodionov, V., Kalnis, P., & Bajic, V. B. (2015). Mining Chemical Activity Status from High-Throughput Screening Assays. PLOS ONE, 10(12), e0144426.
  • 12. Soufan, O., Kleftogiannis, D., Kalnis, P., & Bajic, V. B. (2015). DWFS: A Wrapper Feature Selection Tool Based on a Parallel Genetic Algorithm. PLOS ONE, 10(2), e0117988.
  • Proceedings of Conferences, Posters and Talks

  • 1. Chang, L., Huiting Ou J., Soufan, O., Zhou, G., & Xia, J. (2019). mGWAS-DB: elucidating genetically influenced metabotypes for mGWAS studies – 8th Annual Canadian Human and Statistical Genetics Meeting (Poster).
  • 2. Soufan, O., Zhou, G., Fan, Y., Ewald, J., Hacariz, O., Head, J., Crump, D., Hecker, M., Basu, N. & Xia., J. (2019). EcoToxXplorer: a visual analytics and signature development platform for comprehensive toxicogenomic analysis – SETAC North America 40th Annual Meeting (Talk).
  • 3. Soufan, O., Ewald, J., Liu, P., Boulanger, E., Head, J., Crump, D., Hecker, M., Basu, N. & Xia, J. (2019). EcoToxDB: a toxicogenomics knowledgebase to query, browse and interrogate chemical-gene-exposure networks of EcoToxChip experiments – SETAC North America 40th Annual Meeting (Talk).
  • 4. Soufan, O., Dhariwal, A., Fan, Y., Crump, D., Hecker, M., Basu, N., & Xia, J. (2017). ToxMine: A novel toxicogenomics tool integrating chemical structures and gene expression profiles via network methods for improved toxicity assessment. Paper presented at the SETAC Minneapolis – SETAC North America 38th Annual Meeting (Talk).
  • 5. Soufan, O., Dhariwal, A., Fan, Y., Crump, D., Hecker, M., Basu, N., & Xia, J. (2017). ToxMine: A novel toxicogenomics tool integrating chemical structures and gene expression profiles via network methods for improved toxicity assessment. Paper presented at the SETAC Minneapolis – SETAC North America 38th Annual Meeting (Poster).
  • 6. Soufan, O., and Arafat, S.: ‘Arrhythmia Detection using Mutual Information Based Integration Method’. Proc. World Conference on Soft Computing, San Francisco, USA 2011.
  • 7. Bellegdi, S., Mohandes, S., Soufan, O., and Arafat, S.: ‘Computational Intelligence for Cardiac Arrhythmia Classification’. Proc. The 11th UK Workshop on Computational Intelligence, University of Manchester 2011 pp. 93-97.
  • Patents and Invention Disclosures

  • • Wail Ba-alawi, Othman Soufan, Panos Kalnis, Vladimir Bajic, “A method to predict and rank new edges in a network”. United States Provisional Patent Application No. 62/287,471, Filed January 27, 2016, Applicant: KAUST
  • • Vladimir Bajic, Othman Soufan, Panos Kalnis, Wail Ba-alawi, A method to predict and rank new edges in a network, Invention #2015-091, Submitted 2015-08-18