| 2022 | CIBCB | Identification of Synthetic Engineering in Prokaryotic Genomes Using Evolved Neural Networks. | Gary B. Fogel, Enoch S. Liu, Brad Abramson, Semar Petrus, Tyler Barrus, Granger G. Sutton, Todd Michael, Sterling Thomas |
| 2021 | CIBCB | Using Evolved Neural Networks to Elucidate Nef Features Associated with HIV-1 Subtype Differentiation. | Enoch S. Liu, Gary B. Fogel, David J. Nolan, Susanna L. Lamers, Michael S. McGrath |
| 2020 | CIBCB | Using Neural Networks to Identify Features Associated with HIV Nef Protein and Cancer. | Enoch S. Liu, Gary B. Fogel, David J. Nolan, Susanna L. Lamers, Michael S. McGrath |
| 2015 | CEC | Ring optimization with extinction. | Daniel A. Ashlock, Sierra Gillis, Gary B. Fogel |
| 2015 | CIBCB | Evolving DNA classifiers with extinction based ring optimization. | Daniel A. Ashlock, Sierra Gillis, Jennifer Garner, Gary B. Fogel |
| 2014 | CEC | Evolved neural networks for HIV-1 co-receptor identification. | Gary B. Fogel, Enoch S. Liu, Marco Salemi, Susanna L. Lamers, Michael S. McGrath |
| 2013 | CEC | Functions for the analysis of exploration and exploitation. | Daniel A. Ashlock, Nikola Krsic, Gary B. Fogel |
| 2013 | CEC | Modeling the evolution of drug resistance in Plasmodium falciparum DHFR. | Gary B. Fogel, Carla Islas, David Hecht |
| 2012 | CEC | Evolutionary algorithms for supertree search. | Sevan G. Ficici, Enoch S. Liu, Gary B. Fogel |
| 2012 | CIBCB | Towards predictive structure-based models of evolved drug resistance. | David Hecht, Gary B. Fogel |
| 2011 | CEC | High-throughput toxicological classification of candidate drug compounds using gene expression, evolved neural networks, and a cell-based platform. | Gordon Vansant, Pat Pezzoli, Joseph Monforte, Gary B. Fogel |
| 2010 | CIBCB | Machine learning approaches for customized docking scores: Modeling of inhibition of Mycobacterium tuberculosis enoyl acyl carrier protein reductase. | Gary B. Fogel, Jonathan Tran, Stephen Johnson, David Hecht |
| 2009 | CEC | Docking scores and QSAR using evolved neural networks for the Pan-inhibition of wild-type and mutant PfDHFR by cycloguanil derivatives. | David Hecht, Mars Cheung, Gary B. Fogel |
| 2008 | CEC | Quantitative structure-property relationships for drug solubility prediction using evolved neural networks. | Mars Cheung, Stephen Johnson, David Hecht, Gary B. Fogel |
| 2008 | CIBCB | Classification of mouse fRNA genes using evolved neural networks. | Mars Cheung, Gary B. Fogel |
| 2006 | CEC | Evolved Neural Networks for High Throughput Anti-HIV Ligand Screening. | Connie Y. C. Ma, Susanna W. M. Wong, David Hecht, Gary B. Fogel |
| 2006 | CIBCB | Feature Selection Approach for Quantitative Prediction of Transcriptional Activities. | Ashish Anand, Gary B. Fogel, E. Ke Tang, Ponnuthurai N. Suganthan |
| 2006 | CIBCB | Determination of the Relative Importance of Gene Function or Taxonomic Grouping to Codon Usage Bias Using Cluster Analysis and SVMs. | Jianmin Ma, Minh Ngoc Nguyen, Gary B. Fogel, Jagath C. Rajapakse |
| 2005 | CEC | Derivation of quantitative structure-toxicity relationships for ecotoxicological effects of organic chemicals: evolving neural networks and evolving rules. | Gary B. Fogel, Mars Cheung |
| 2005 | CIBCB | Identification of Functional RNA Genes Using Evolved Neural Networks. | Mars Cheung, Gary B. Fogel |
| 2004 | CEC | Parameter optimization of an evolutionary algorithm for RNA structure discovery. | Gary B. Fogel, Dana G. Weekes, Rangarajan Sampath, David J. Ecker |
| 2004 | CEC | Noisy optimization problems - a particular challenge for differential evolution? | Thiemo Krink, Bogdan Filipic, Gary B. Fogel |
| 2003 | CEC | Improvement of clustal-derived sequence alignments with evolutionary algorithms. | Ren Thomsen, Gary B. Fogel, Thiemo Krink |
| 2002 | CEC | Evolved neural networks for quantitative structure-activity relationships of anti-HIV compounds. | Dana Landavazo, Gary B. Fogel |
| 2002 | CEC | A Clustal alignment improver using evolutionary algorithms. | Ren Thomsen, Gary B. Fogel, Thiemo Krink |
| 2000 | CEC | Evolutionary computation with extinction: experiments and analysis. | Gary B. Fogel, Garrison W. Greenwood, Kumar Chellapilla |
| 1999 | CEC | Multiple sequence alignment using evolutionary programming. | Kumar Chellapilla, Gary B. Fogel |
| 1999 | CEC | Simulated sequencing by hybridization using evolutionary programming. | Gary B. Fogel, Kumar Chellapilla |
| 1999 | CEC | A survey of recent work on evolutionary approaches to the protein folding problem. | Garrison W. Greenwood, Jae-Min Shin, Byungkook Lee, Gary B. Fogel |
| 1999 | CEC | Emphasizing extinction in evolutionary programming. | Garrison W. Greewood, Gary B. Fogel, Manuel Ciobanu |