Classification of Mouse fRNA Genes Using Evolved Neural Networks (2009)
Mars Cheung, Gary B. Fogel, Senior Member
Abstract-Functional RNAs (fRNAs) play a key role in gene regulation, at both the transcriptional and translational levels. Identification of fRNA genes can be difficult, given that some classes of...
Fogel G: Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks (2009)
Susanna L. Lamers, Marco Salemi, Michael S. Mcgrath, Gary B. Fogel
Abstract—The HIV-1 genome is highly heterogeneous. This variation affords the virus a wide range of molecular properties, including the ability to infect cell types, such as macrophages and...
Prediction of Transcription Factor Families Using DNA Sequence Features (2009)
Ashish An, Gary B. Fogel, Ganesan Pugalenthi, P. N. Suganthan
Abstract. Understanding the mechanisms of protein-DNA interaction is of critical importance in biology. Transcription factor (TF) binding to a specific DNA sequence depends on at least two factors: A...
2005) “Identification of functional RNA genes using evolved neural networks (2009)
Mars Cheung, Gary B. Fogel, Senior Member
Abstract-Functional RNAs (fRNAs) play a key role in gene regulation, at both the transcriptional and translational levels. Identification of fRNA genes can be difficult, given that some classes of...
High-Throughput Ligand Screening via Preclustering and Evolved Neural Networks (2008)
Abstract—The pathway for novel lead drug discovery has many major deficiencies, the most significant of which is the immense size of small molecule diversity space. Methods that increase the search...
Evolutionary optimization, backpropagation, and (2008)
data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives
Special section on machine intelligence approaches to systems biology (2008)
Fogel, Gary B, Bullinger, Eric, Su, Shun-Feng, Azuaje, Francisco
Computational intelligence approaches for pattern discovery in biological systems (2008)
Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as...
Evolutionary computation for discovery of composite transcription factor binding sites (2008)
Fogel, Gary B., Porto, V. William, Varga, Gabor, Dow, Ernst R., Craven, Andrew M., Powers, David M., ...
Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it...
Evolved Neural Networks for High Throughput Anti-HIV (2006)
David Hecht, Gary B. Fogel, Senior Member
Abstract—The pathway for novel lead drug discovery has many major deficiencies, the most significant of which is the astronomically large size of small molecule diversity space. Methods that...
Discovery of sequence motifs related to coexpression of genes using evolutionary computation (2004)
Gary B. Fogel, Dana G. Weekes, Gabor Varga, Ernst R. Dow, Harry B. Harlow, Jude E. Onyia, ...
genes using evolutionary computation
Parameter Optimization of an Evolutionary (2004)
Algorithm For Rna, Gary B. Fogel, Dana G. Weekes
This paper focuses on the optimization of population and selection parameters of an evolutionary algorithm for similar RNA structure discovery. The effects of population settings such as the number...
Discovery of sequence motifs related to coexpression of genes using evolutionary computation (2004)
Fogel, Gary B., Weekes, Dana G., Varga, Gabor, Dow, Ernst R., Harlow, Harry B., Onyia, Jude E., ...
Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding site (TFBS) motifs in the upstream region of coexpressed genes is therefore...
A Clustal Alignment Improver using Evolutionary Algorithms (2002)
Ny Munkegade, Gary B. Fogel, Thiemo Krink, Evalife Group, Evalife Group
Abstract- Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this study we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the...
BioSystems 65 (2002) 37 -- 47 (2002)
Quantitative Structure Activity, Dana G. L, Gary B. Fogel, David B. Fogel
Evolutionary computation provides a useful method for training neural networks in the face of multiple local optima. This paper begins with a description of methods for quantitative structure...
Discovery of RNA structural elements using (2002)
Evolutionary Computation Gary, Gary B. Fogel, V. William Porto, Dana G. Weekes, David B. Fogel, Richard H. Griffey, ...
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures, or certain structural motifs within them,...
Discovery of RNA structural elements using evolutionary computation (2002)
Fogel, Gary B., Porto, V. William, Weekes, Dana G., Fogel, David B., Griffey, Richard H., McNeil, John A., ...
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures, or certain structural motifs within them,...
Multiple-Vector Self-Adaptation in Evolutionary Algorithms (2001)
Gary B. Fogel, Gary B. Fogel, Kazuhiro Ohkura
Self-adaptation is a common method for learning online control parameters in an evolutionary algorithm. In one common implementation, each individual in the population is represented as a pair of...
Evolutionary computation with extinction: Experiments and analysis (2000)
Gary B. Fogel, Garrison W. Greenwood, Kumar Chellapilla
Abstract- Under a species-level abstraction of classical evolutionary programming, the standard tournament selection model is not appropriate. When viewed in this manner, it is more appropriate to...
A survey of recent work on evolutionary approaches to the protein folding problem (1999)
Garrison W. Greenwood, Byungkook Lee, Gary B. Fogel
Abstract- A problem of immense importance in computational biology is the determination of the functional conformations of protein molecules. With the advent of faster computers, it is now possible...
Simulated sequencing by hybridization using evolutionary programming (1999)
Sequencing of DNA is among the most important tasks in molecular biology. DNA chips are considered to be a more rapid alternative to more common gel-based methods of sequencing. Previously, we...
Gary B. Fogel, Clifford F. Brunk
Relative growth is often used as a phenotypic measure to distinguish mutant and wild-type yeast or bacterial strains. Differential growth as a function of temperature is a convenient and accurate...
Gary B. Fogel, Clifford F. Brunk
Histone H4 is one of the most conserved proteins known. The very low rate of nonsynonymous substitution in H4 suggests that it fulfills an essential function in virtually all eukaryotes. While the...
Discovery of RNA structural elements using evolutionary computation
Fogel, Gary B., Porto, V. William, Weekes, Dana G., Fogel, David B., Griffey, Richard H., McNeil, John A., ...
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures, or certain structural motifs within them,...
Discovery of sequence motifs related to coexpression of genes using evolutionary computation
Fogel, Gary B., Weekes, Dana G., Varga, Gabor, Dow, Ernst R., Harlow, Harry B., Onyia, Jude E., ...
Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding site (TFBS) motifs in the upstream region of coexpressed genes is therefore...
Discovery of RNA structural elements using evolutionary computation
Fogel, Gary B., Porto, V. William, Weekes, Dana G., Fogel, David B., Griffey, Richard H., McNeil, John A., ...
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures, or certain structural motifs within them,...
Discovery of sequence motifs related to coexpression of genes using evolutionary computation
Fogel, Gary B., Weekes, Dana G., Varga, Gabor, Dow, Ernst R., Harlow, Harry B., Onyia, Jude E., ...
Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding site (TFBS) motifs in the upstream region of coexpressed genes is therefore...
Evolutionary computation for discovery of composite transcription factor binding sites
Fogel, Gary B., Porto, V. William, Varga, Gabor, Dow, Ernst R., Craven, Andrew M., Powers, David M., ...
Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it...
Extensive HIV-1 Intra-Host Recombination Is Common in Tissues with Abnormal Histopathology
Lamers, Susanna L., Salemi, Marco, Galligan, Derek C., De Oliveira, Tulio, Fogel, Gary B., Granier, Sara C., ...
There is evidence that immune-activated macrophages infected with the Human Immunodeficiency Virus (HIV) are associated with tissue damage and serve as a long-lived viral reservoir during therapy. In...