Genomic engineering: moving beyond DNA sequence to function. - J. Patrick Fitch; Bahrad A. Sokhansanj (Proc. IEEE, 2000)

Matrix formulation of a universal microbial transcript profiling system. - J. Patrick Fitch; Jefferson Ng; Bahrad A. Sokhansanj (ICASSP, 2001)

Linear fuzzy gene network models obtained from microarray data by exhaustive search. - Bahrad A. Sokhansanj; J. Patrick Fitch; Judy N. Quong; Andrew A. Quong (BMC Bioinform., 2004)

An indexed modeling and experimental strategy for biosignatures of pathogen and host. - Andrew A. Quong; J. R. Kercher; Paula M. McCready; Judy N. Quong; Bahrad A. Sokhansanj; J. Patrick Fitch (J. Frankl. Inst., 2004)

Visualization of protein-protein interaction network for knowledge discovery. - Weizhong Zhu; Xia Lin; Xiaohua Hu 001; Bahrad A. Sokhansanj (GrC, 2005)

Mining and Dynamic Simulation of Sub-Networks from Large Biomolecular Networks. - Xiaohua Hu 001; Fang-Xiang Wu; Michael K. Ng 001; Bahrad A. Sokhansanj (IC-AI, 2007)

Accelerated search for biomolecular network models to interpret high-throughput experimental data. - Suman Datta; Bahrad A. Sokhansanj (BMC Bioinform., 2007)

Integrated modeling methodology for microtubule dynamics and Taxol kinetics with experimentally identifiable parameters. - He Zhao; Bahrad A. Sokhansanj (Comput. Methods Programs Biomed., 2007)

A Novel Approach for Mining and Fuzzy Simulation of Subnetworks From Large Biomolecular Networks. - Xiaohua Hu 001; Bahrad A. Sokhansanj; Daniel Duanqing Wu; Yuchun Tang (IEEE Trans. Fuzzy Syst., 2007)

Metagenome Fragment Classification Using N-Mer Frequency Profiles. - Gail L. Rosen; Elaine Garbarine; Diamantino Caseiro; Robi Polikar; Bahrad A. Sokhansanj (Adv. Bioinformatics, 2008)

Mining, Modeling, and Evaluation of Subnetworks From Large Biomolecular Networks and Its Comparison Study. - Xiaohua Hu 001; Michael K. Ng 001; Fang-Xiang Wu; Bahrad A. Sokhansanj (IEEE Trans. Inf. Technol. Biomed., 2009)

Scalable Dynamic Fuzzy Biomolecular Network Models for Large Scale Biology. - Bahrad A. Sokhansanj; Suman Datta; Xiaohua Hu 001 (Fuzzy Systems in Bioinformatics and Computational Biology, 2009)

Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. - Zhengqiao Zhao; Bahrad A. Sokhansanj; Charvi Malhotra; Kitty Zheng; Gail L. Rosen (PLoS Comput. Biol., 2020)

Incremental & Semi-Supervised Learning for Functional Analysis of Protein Sequences. - Mali Halac; Bahrad A. Sokhansanj; William L. Trimble; Thomas Coard; Norman C. Sabin; Emrecan Ozdogan; Robi Polikar; Gail L. Rosen (SSCI, 2021)

Incremental and Semi-Supervised Learning of 16S-rRNA Genes For Taxonomic Classification. - Emrecan Ozdogan; Norman C. Sabin; Thomas Gracie; Steven Portley; Mali Halac; Thomas Coard; William L. Trimble; Bahrad A. Sokhansanj; Gail Rosen; Robi Polikar (SSCI, 2021)

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network. - Zhengqiao Zhao; Stephen Woloszynek; Felix Agbavor; Joshua Chang Mell; Bahrad A. Sokhansanj; Gail L. Rosen (PLoS Comput. Biol., 2021)

Semi-supervised and Incremental VSEARCH for Metagenomic Classification. - Emrecan Ozdogan; Adriana Fasino; Rachel Nguyen; Bahrad A. Sokhansanj; Gail Rosen; Robi Polikar (SSCI, 2022)

Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. - Bahrad A. Sokhansanj; Gail L. Rosen (Comput. Biol. Medicine, 2022)

Semi-Supervised and Incremental Sequence Analysis for Taxonomic Classification. - Adriana Fasino; Emrecan Ozdogan; Bahrad A. Sokhansanj; Gail Rosen; Robi Polikar (SSCI, 2023)

Predicting Anti-microbial Resistance using Large Language Models. - Hyunwoo Yoo; Bahrad A. Sokhansanj; James R. Brown; Gail Rosen (CoRR, 2024)

Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening. - Rohan Chandraghatgi; Hai-Feng Ji; Gail L. Rosen; Bahrad A. Sokhansanj (J. Chem. Inf. Model., 2024)

Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis. - Mohammad S. Refahi; Mahdi Abavisani; Bahrad A. Sokhansanj; James R. Brown; Gail Rosen (CoRR, 2025)

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN. - Mohammad S. Refahi; Gavin L. A. Hearne; Harrison Muller; Kieran Lynch; Bahrad A. Sokhansanj; James R. Brown; Gail Rosen (CoRR, 2025)