Mining gene expression data by interpreting principal components. - Joseph C. Roden; Brandon W. King; Diane Trout; Ali Mortazavi; Barbara J. Wold; Christopher E. Hart (BMC Bioinform., 2006)

The common ground of genomics and systems biology. - Ana Conesa; Ali Mortazavi (BMC Syst. Biol., 2014)

Sizing and layout design of truss structures under dynamic and static constraints with an integrated particle swarm optimization algorithm. - Ali Mortazavi; Vedat Togan (Appl. Soft Comput., 2017)

Interactive search algorithm: A new hybrid metaheuristic optimization algorithm. - Ali Mortazavi; Vedat Togan; Ayhan Nuhoglu (Eng. Appl. Artif. Intell., 2018)

Progressive Clustering and Characterization of Increasingly Higher Dimensional Datasets with Living Self-organizing Maps. - Camden Jansen; Ali Mortazavi (WSOM+, 2019)

Solution of structural and mathematical optimization problems using a new hybrid swarm intelligence optimization algorithm. - Ali Mortazavi; Vedat Togan; Mahsa Moloodpoor (Adv. Eng. Softw., 2019)

TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts. - Dana Wyman; Ali Mortazavi (Bioinform., 2019)

Interactive fuzzy search algorithm: A new self-adaptive hybrid optimization algorithm. - Ali Mortazavi (Eng. Appl. Artif. Intell., 2019)

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps. - Camden Jansen; Ricardo N. Ramirez; Nicole C. El-Ali; David Gomez-Cabrero; Jesper Tegnér; Matthias Merkenschlager; Ana Conesa; Ali Mortazavi (PLoS Comput. Biol., 2019)

Large-scale structural optimization using a fuzzy reinforced swarm intelligence algorithm. - Ali Mortazavi (Adv. Eng. Softw., 2020)

A new fuzzy strategy for size and topology optimization of truss structures. - Ali Mortazavi (Appl. Soft Comput., 2020)

Best-case lower bounds in online learning. - Cristóbal Guzmán; Nishant A. Mehta; Ali Mortazavi (NeurIPS, 2021)

Bayesian Interactive Search Algorithm: A New Probabilistic Swarm Intelligence Tested on Mathematical and Structural Optimization Problems. - Ali Mortazavi (Adv. Eng. Softw., 2021)

Differential evolution method integrated with a fuzzy decision-making mechanism and Virtual Mutant agent: Theory and application. - Ali Mortazavi; Mahsa Moloodpoor (Appl. Soft Comput., 2021)

Swan: a library for the analysis and visualization of long-read transcriptomes. - Fairlie Reese; Ali Mortazavi (Bioinform., 2021)

Enhanced Butterfly Optimization Algorithm with a New fuzzy Regulator Strategy and Virtual Butterfly Concept. - Ali Mortazavi; Mahsa Moloodpoor (Knowl. Based Syst., 2021)

Optimization of Seismic Base Isolation System Using a Fuzzy Reinforced Swarm Intelligence. - Elif Cagda Kandemir; Ali Mortazavi (Adv. Eng. Softw., 2022)

Interactive fuzzy Bayesian search algorithm: A new reinforced swarm intelligence tested on engineering and mathematical optimization problems. - Ali Mortazavi (Expert Syst. Appl., 2022)

Novel Wearable HD-EMG Sensor With Shift-Robust Gesture Recognition Using Deep Learning. - Félix Chamberland; Étienne Buteau; Simon Tam 003; Evan Campbell; Ali Mortazavi; Erik J. Scheme; Paul Fortier; Mounir Boukadoum; Alexandre Campeau-Lecours; Benoit Gosselin (IEEE Trans. Biomed. Circuits Syst., 2023)

On the price of exact truthfulness in incentive-compatible online learning with bandit feedback: a regret lower bound for WSU-UX. - Ali Mortazavi; Junhao Lin; Nishant A. Mehta (AISTATS, 2024)

Single-Cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. - Lujia Chen; Xiangduo Kong; Kevin Gregory Johnston; Ali Mortazavi; Todd Holmes; Zhiqun Tan; Kyoko Yokomori; Xiangmin Xu (Zenodo, 2024)

Simultaneous optimization of capacity and topology of seismic isolation systems in multi-story buildings using a fuzzy reinforced differential evolution method. - Ali Mortazavi; Elif Cagda Kandemir (Adv. Eng. Softw., 2024)

A fuzzy reinforced Jaya algorithm for solving mathematical and structural optimization problems. - Ali Mortazavi (Soft Comput., 2024)

A novel type-2 decision mechanism for dynamic parameter adaptation: theory and application in mathematical and structural problems. - Ali Mortazavi (Neural Comput. Appl., 2024)

No-Regret Incentive-Compatible Online Learning under Exact Truthfulness with Non-Myopic Experts. - Junpei Komiyama; Nishant A. Mehta; Ali Mortazavi (EC, 2025)

A novel binomial-based fuzzy type-2 approach for topology and size optimization of skeletal structures. - Ali Mortazavi (Adv. Eng. Softw., 2025)