| 2024 | CIBCB | AGED-ViT: A Novel Transformer-Based Framework for Diagnosis of Alzheimer's Disease by Leveraging Gene Expression Data. | Albert Guo, Megan Fowler, Kay C. Wiese |
| 2023 | AI | Navitas/Optimus: A Novel Computational Tool for enhanced CRISPR/Cas Genome Editing. | Amirhossein Daneshpajouh, Megan Fowler, Kay C. Wiese |
| 2023 | CIBCB | A Comparison of Machine Learning Models for Predicting CRISPR/Cas On-target Efficacy. | Megan Fowler, Amirhossein Daneshpajouh, Kay C. Wiese |
| 2022 | CIBCB | EvoDNN - Evolving Weights, Biases, and Activation Functions in a Deep Neural Network. | Peiyu Cui, Kay C. Wiese |
| 2019 | CEC | EvoDNN - An Evolutionary Deep Neural Network with Heterogeneous Activation Functions. | Peiyu Cui, Boris Shabash, Kay C. Wiese |
| 2018 | GECCO | EvoNN: a customizable evolutionary neural network with heterogenous activation functions. | Boris Shabash, Kay C. Wiese |
| 2013 | GECCO | pEvoSAT: a novel permutation based genetic algorithm for solving the boolean satisfiability problem. | Boris Shabash, Kay C. Wiese |
| 2012 | CIBCB | Non-coding RNA gene finding with combined partial covariance models. | Wenbo Jiang, Kay C. Wiese |
| 2011 | CEC | Improving splice-junctions classification employing a novel encoding schema and decision-tree. | Amin Yazdani Salekdeh, Kay C. Wiese |
| 2011 | CIBCB | Secondary structure element voting for RNA gene finding. | Nicholas George Erho, Kay C. Wiese |
| 2011 | CIBCB | Combined covariance model for non-coding RNA gene finding. | Wenbo Jiang, Kay C. Wiese |
| 2010 | CEC | A study of RNA secondary structure prediction using different mutation operators. | Herbert H. Tsang, Tiancheng Jiang, Kay C. Wiese, Christian Jacob |
| 2010 | CIBCB | An exploration of individual RNA structural elements in RNA gene finding. | Nicholas George Erho, Kay C. Wiese |
| 2010 | CIBCB | Expanded study of efn2 thermodynamic model performance on RnaPredict, an evolutionary algorithm for RNA folding. | Kay C. Wiese, Andrew Hendriks |
| 2009 | CEC | RNA pseudoknot prediction via an evolutionary algorithm. | Kay C. Wiese, Andrew Hendriks |
| 2009 | CEC | Impact of an enhanced thermodynamic model on RnaPredict, an evolutionary algorithm for RNA secondary structure prediction. | Kay C. Wiese, Andrew Hendriks |
| 2009 | CIBCB | rnaDesign: Local search for RNA secondary structure design. | Denny C. Dai, Herbert H. Tsang, Kay C. Wiese |
| 2009 | CIBCB | Performance prediction for RNA design using parametric and non-parametric regression models. | Denny C. Dai, Kay C. Wiese |
| 2009 | CIBCB | SARNA-ensemble-predict: The effect of different dissimilarity metrics on a novel ensemble-based RNA secondary structure prediction algorithm. | Herbert H. Tsang, Kay C. Wiese |
| 2008 | CIBCB | SARNA-Predict-pk: Predicting RNA secondary structures including pseudoknots. | Herbert H. Tsang, Kay C. Wiese |
| 2008 | CIBCB | A hybrid clustering/evolutionary algorithm for RNA folding. | Kay C. Wiese, Andrew Hendriks |
| 2007 | CEC | The significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing. | Herbert H. Tsang, Kay C. Wiese |
| 2007 | CIBCB | SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules. | Herbert H. Tsang, Kay C. Wiese |
| 2006 | CBMS | Graph Drawing Tools for Bioinformatics Research: An Overview. | Kay C. Wiese, Christina Eicher |
| 2006 | CBMS | jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots. | Kay C. Wiese, Edward Glen |
| 2006 | CEC | A Detailed Analysis of Parallel Speedup in P-RnaPredict - An Evolutionary Algorithm for RNA Secondary Structure Prediction. | Kay C. Wiese, Andrew Hendriks |
| 2006 | CIBCB | SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction. | Herbert H. Tsang, Kay C. Wiese |
| 2006 | CIBCB | Analysis of Thermodynamic Models and Performance in RnaPredict - An Evolutionary Algorithm for RNA Folding. | Kay C. Wiese, Andrew Hendriks, Alain Deschnes |
| 2005 | CEC | Significance of randomness in P-RnaPredict - a parallel evolutionary algorithm for RNA folding. | Kay C. Wiese, Andrew Hendriks, Alain Deschnes, Belgacem Ben Youssef |
| 2005 | CEC | Algorithms for RNA folding: a comparison of dynamic programming and parallel evolutionary algorithms. | Kay C. Wiese, Andrew Hendriks, Jagdeep Poonian |
| 2005 | GECCO | The impact of pseudorandom number quality on | Kay C. Wiese, Andrew Hendriks, Alain Deschnes, Belgacem Ben Youssef |
| 2004 | AI | Comparison of Permutation-Based and Binary Representation in a Genetic Algorithm for RNA Secondary Structure Prediction. | Alain Deschnes, Kay C. Wiese, Edward Glen |
| 2004 | AI | Comparison of Parallel and Serial Genetic Algorithms for RNA Secondary Structure Prediction. | Andrew Hendriks, Kay C. Wiese, Edward Glen |
| 2004 | AI | Genetic Algorithm Based OSPF Network Routing Using LEDA. | Lenny Tang, Kay C. Wiese, Vive Kumar |
| 2004 | CEC | Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures. | Alain Deschnes, Kay C. Wiese |
| 2004 | CIBCB | Comparison of dynamic programming and evolutionary algorithms for RNA secondary structure prediction. | Alain Deschnes, Kay C. Wiese, Jagdeep Poonian |
| 2004 | CIBCB | A parallel evolutionary algorithm for RNA secondary structure prediction using stacking-energies (INN and INN-HB). | Andrew Hendriks, Alain Deschnes, Kay C. Wiese |
| 2003 | CEC | A distributed genetic algorithm for RNA secondary structure prediction. | Andrew Hendriks, Kay C. Wiese, Edward Glen, Alain Deschnes |
| 2003 | CEC | Permutation-based RNA secondary structure prediction via a genetic algorithm. | Kay C. Wiese, Alain Deschnes, Edward Glen |
| 2003 | ISMIS | RNA Structure as Permutation: A GA Approach Comparing Different Genetic Sequencing Operators. | Kay C. Wiese, Edward Glen |
| 2002 | HIS | A Permutation Based Genetic Algorithm for RNA Secondary Structure Prediction. | Kay C. Wiese, Edward Glen |
| 2000 | AI | ASERC - A Genetic Sequencing Operator for Asymmetric Permutation Problems. | Kay C. Wiese, Scott D. Goodwin, Sivakumar Nagarajan |
| 1999 | SAC | Convergence Characteristics of Keep-Best Reproduction. | Kay C. Wiese, Scott D. Goodwin |
| 1998 | AI | The Effect of Genetic Operator Probabilities and Selection Strategies on the Performance of a Genetic Algorithm. | Kay C. Wiese, Scott D. Goodwin |
| 1998 | FlAIRS | Parallel Genetic Algorithms for Constrained Ordering Problems. | Kay C. Wiese, Sivakumar Nagarajan, Scott D. Goodwin |
| 1998 | SAC | Keep-best reproduction: a selection strategy for genetic algorithms. | Kay C. Wiese, Scott D. Goodwin |