Najafian, K., Ghanbari, A., Stavness, I., Jin, L., Shirdel, G. H., & Maleki, F. (2021). A Semi-Self-Supervised Learning Approach for Wheat Head Detection Using Extremely Small Number of Labeled Samples. In Proceedings of the IEEE/CVF International Conference on Computer Vision (pp. 1342-1351).

Maleki, F., Ovens, K., McQuillan, I., & Kusalik, A. J. (2021). Silver: Forging almost Gold Standard Datasets. Genes, 12(10), 1523.

Maleki, F., Cote, K., Najafian, K., Ovens, K., Miao, Y., Zakarian, R., ... & Gao, Z. H. (2021, September). A Deep Learning-Based Pipeline for Celiac Disease Diagnosis Using Histopathological Images. In International Conference on Computer Analysis of Images and Patterns (pp. 206-214). Springer, Cham.

Mascarella, M. A., Muthukrishnan, N., Maleki, F., Kergoat, M. J., Richardson, K., Mlynarek, A., ... & Forghani, R. (2021). Above and Beyond Age: Prediction of Major Postoperative Adverse Events in Head and Neck Surgery. Annals of Otology, Rhinology & Laryngology, 00034894211041222.

Finch, S. L., Rosenberg, A. M., Kusalik, A. J., Maleki, F., Rezaei, E., Baxter-Jones, A., ... & BBOP Study Group. (2021). Higher Concentrations of Vitamin D in Canadian Children with Juvenile Idiopathic Arthritis Compared to Healthy Controls are Associated with More Frequent Use of Vitamin D Supplements and Season of Birth. Nutrition Research.

Liu, X., Maleki, F., Muthukrishnan, N., Ovens, K., Huang, S.H., Pérez-Lara, A., Romero-Sanchez, G., Bhatnagar, S.R., Chatterjee, A., Pusztaszeri, M.P., Spatz, A., Batist, G., Payabvash, S., Haider, S.P., Mahajan, A., Reinhold, C., Forghani, B., O’Sullivan, B., Yu, E. & Forghani, R.(2021). Site-Specific Variation in Radiomic Features of Head and Neck Squamous Cell Carcinoma and Its Impact on Machine Learning Models. Cancers.

Ovens, K., Maleki, F., Eames, B. F. & McQuillan, I (2021). Juxtapose: a gene-embedding approach for comparing co-expression networks. BMC Bioinformatics.

Maleki, F., Le, W. T., Sananmuang, T., Kadoury, S. & Forghani, R. (2020). Machine Learning Applications for Head and Neck Imaging. Neuroimaging Clinics.

Maleki, F., Muthukrishnan, N., Ovens, K., Reinhold, C. & Forghani, R. (2020). Machine Learning Algorithm Validation: From Essentials to Advanced Applications and Implications for Regulatory Certification and Deployment. Neuroimaging Clinics

Maleki, F., Ovens, K., Najafian, K., Forghani, B., Reinhold, C. & Forghani, R. (2020). Overview of Machine Learning Part 1: Fundamentals and Classic Approaches. Neuroimaging Clinics of North America.

Le, W. T. , Maleki, F. , Romero, F. P., Forghani, R. & Kadoury, S. (2020). Overview of machine learning: part 2: deep learning for medical image analysis. Neuroimaging Clinics

Maleki, F., Ovens, K., Hogan, D. J., & Kusalik, A. J. (2020). Gene Set Analysis: Challenges, Opportunities, and Future Research. Frontiers in Genetics, 11, 654.

Sananmuang, T., Agarwal, M., Maleki, F., Muthukrishnan, N., Marquez, J. C., Chankowsky, J., & Forghani, R. (2020). Dual Energy Computed Tomography in Head and Neck Imaging: Pushing the Envelope. Neuroimaging Clinics of North America, 30(3), 311-323.

Mardanisamani, S., Maleki, F., Hosseinzadeh Kassani, et al. (2019, June). Crop Lodging Prediction from UAV-acquired Images of Wheat and Canola using a DCNN Augmented with Handcrafted Texture Features. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Long Beach, CA, USA.

Maleki, F., Ovens, K. L., Hogan, D. J., Rezaei, E., Rosenberg, A. M., & Kusalik, A. J. (2019). Measuring consistency among gene set analysis methods: A systematic study. Journal of Bioinformatics and Computational Biology, 17(5), 1940010.

Maleki, F., Ovens, K., McQuillan, I., & Kusalik, A. J. (2019). Size matters: how sample size affects the reproducibility and specificity of gene set analysis. Human Genomics, 13(1), 42.

Ovens, K., Hogan, D., Maleki, F., McQuillan, I., & Kusalik A. pineplot: An R package for visualizing symmetric relationships. In Proceedings of the Tenth International Conference on Computational Systems-Biology and Bioinformatics (CSBio ’19). Association for Computing Machinery, New York, NY, USA, (pp. 1–8) ACM.

Maleki, F., Ovens, K., McQuillan, I., Rezaei, E., Rosenberg, A.M., Kusalik, A.J. (2019 September). Gene Set Databases: A Fountain of Knowledge or a Siren Call? In the 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Niagara Falls, NY, USA.

Maleki, F., Ovens, K.L., Rezaei, E., Rosenberg, A.M., Kusalik, A.J. (2019 February). Method Choice in Gene Set Analysis has Important Consequences for Analysis Outcome. In the 10th International Conference on Bioinformatics Models, Methods, and Algorithms. Prague, Czech Republic.

Maleki, F. & Kusalik, A.J. (2019, February). Gene Set Overlap: An Impediment to Achieving High Specificity in Over-representation Analysis. In the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019). Prague, Czech Republic.

Maleki, F., Ovens, K., McQuillan, I., & Kusalik, A. J. (2018, December). Sample Size and Reproducibility of Gene Set Analysis. In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 122-129). IEEE.

Trost, B., Maleki, F., Kusalik, A., & Napper, S. (2016). DAPPLE 2: A Tool for the Homology-based Prediction of Post-translational Modification Sites. Journal of Proteome Research, 15(8), 2760-2767.

Maleki, F., & Kusalik, A. (2015). A Synthetic Kinome Microarray Data Generator. Microarrays, 4(4), 432-453.

Farazi, H., Ahmadinejad, F., Maleki, F., & Shiri, M. E. (2013, April). Evolutionary Approach for Developing Fast and Stable Offline Humanoid Walk. In 3rd Joint Conference of AI & Robotics and 5th RoboCup Iran Open International Symposium (pp. 1-6). IEEE.

Maleki, F., Bijari, A., Mohades, A., & Shiri, M. E. (2010, June). Rule Discovery for Pseudorandom Number Generator based on Cellular Automata. In the 2010 International Symposium on Information Technology (Vol. 2, pp. 739-744). IEEE.

Maleki, F., Mohades, A., Shiri, M. E., & Bijari, A. (2010). A CA Randomizers based on Parallel CAs with Balanced Rules. Procedia Computer Science, 1(1), 417-425.

Maleki, F., Mohades, A., Hashemi, S. M., & Shiri, M. E. (2008, March). An Image Encryption System by Cellular Automata with Memory. In Third International Conference on Availability, Reliability and Security (pp. 1266-1271). IEEE.