The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
Evolutionary algorithms in theory and practice: evolution strategies, evolutionary programming, genetic algorithms
Neural Networks: A Comprehensive Foundation
Neural Networks: A Comprehensive Foundation
Rough Sets: Theoretical Aspects of Reasoning about Data
Rough Sets: Theoretical Aspects of Reasoning about Data
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
A Tutorial on Support Vector Machines for Pattern Recognition
Data Mining and Knowledge Discovery
Rough Sets: Mathematical Foundations
Rough Sets: Mathematical Foundations
Challenges for Intelligent Systems in Biology
IEEE Intelligent Systems
A Statistical Method for Profiling Network Traffic
Proceedings of the Workshop on Intrusion Detection and Network Monitoring
Gene Clustering Using Self-Organizing Maps and Particle Swarm Optimization
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Cluster ensemble and its applications in gene expression analysis
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bioinformatics—an introduction for computer scientists
ACM Computing Surveys (CSUR)
Interactive Gene Clustering--A Case Study of Breast Cancer Microarray Data
Information Systems Frontiers
Partitioned optimization algorithms for multiple sequence alignment
AINA '06 Proceedings of the 20th International Conference on Advanced Information Networking and Applications - Volume 02
A fast learning algorithm for deep belief nets
Neural Computation
Self-organizing neural networks to support the discovery of DNA-binding motifs
Neural Networks - 2006 Special issue: Advances in self-organizing maps--WSOM'05
Rough Discretization of Gene Expression Data
ICHIT '06 Proceedings of the 2006 International Conference on Hybrid Information Technology - Volume 02
Pattern classification in DNA microarray data of multiple tumor types
Pattern Recognition
Genetic programming neural networks: A powerful bioinformatics tool for human genetics
Applied Soft Computing
Fuzzy rough sets hybrid scheme for breast cancer detection
Image and Vision Computing
Fuzzy-Granular Gene Selection from Microarray Expression Data
ICDMW '06 Proceedings of the Sixth IEEE International Conference on Data Mining - Workshops
Gene Selection with Rough Sets for Cancer Classification
FSKD '07 Proceedings of the Fourth International Conference on Fuzzy Systems and Knowledge Discovery - Volume 03
International Journal of Hybrid Intelligent Systems
Microarray Image Converted Database - Genetic Algorithm Application in Bioinformatics
BMEI '08 Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01
Algorithm Note: PK-means: A new algorithm for gene clustering
Computational Biology and Chemistry
Classification using discriminative restricted Boltzmann machines
Proceedings of the 25th international conference on Machine learning
Evaluating Switching Neural Networks for Gene Selection
WILF '07 Proceedings of the 7th international workshop on Fuzzy Logic and Applications: Applications of Fuzzy Sets Theory
A Complex Artificial Immune System
ICNC '08 Proceedings of the 2008 Fourth International Conference on Natural Computation - Volume 06
Applications of Computational Intelligence in Biology: Current Trends and Open Problems
Applications of Computational Intelligence in Biology: Current Trends and Open Problems
An expert system to classify microarray gene expression data using gene selection by decision tree
Expert Systems with Applications: An International Journal
Guest editorial: Computational intelligence and machine learning in bioinformatics
Artificial Intelligence in Medicine
Fuzzy ensemble clustering based on random projections for DNA microarray data analysis
Artificial Intelligence in Medicine
Computers in Biology and Medicine
Computational Intelligence in Bioinformatics
Computational Intelligence in Bioinformatics
Knowledge-assisted recognition of cluster boundaries in gene expression data
Artificial Intelligence in Medicine
GUEST EDITORIAL: Computational intelligence in solving bioinformatics problems
Artificial Intelligence in Medicine
Granular support vector machines with association rules mining for protein homology prediction
Artificial Intelligence in Medicine
Multiple Sequence Alignment Based on a Binary Particle Swarm Optimization Algorithm
ICNC '09 Proceedings of the 2009 Fifth International Conference on Natural Computation - Volume 03
Applications of artificial intelligence in bioinformatics: A review
Expert Systems with Applications: An International Journal
A method of tumor classification based on wavelet packet transforms and neighborhood rough set
Computers in Biology and Medicine
A new local search algorithm for the DNA fragment assembly problem
EvoCOP'07 Proceedings of the 7th European conference on Evolutionary computation in combinatorial optimization
Roughfication of numeric decision tables: the case study of gene expression data
RSKT'07 Proceedings of the 2nd international conference on Rough sets and knowledge technology
Ensemble gene selection for cancer classification
Pattern Recognition
A method for multiple sequence alignment based on particle swarm optimization
ICIC'09 Proceedings of the Intelligent computing 5th international conference on Emerging intelligent computing technology and applications
Expert Systems with Applications: An International Journal
Gene expression data classification using locally linear discriminant embedding
Computers in Biology and Medicine
International Journal of Approximate Reasoning
New inspirations in swarm intelligence: a survey
International Journal of Bio-Inspired Computation
Incorporating cellular sorting structure for better prediction of protein subcellular locations
Journal of Experimental & Theoretical Artificial Intelligence - Advances in knowledge discovery and data analysis for artificial intelligence
Disease gene prioritization based on topological similarity in protein-protein interaction networks
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
GPU computation in bioinspired algorithms: a review
IWANN'11 Proceedings of the 11th international conference on Artificial neural networks conference on Advances in computational intelligence - Volume Part I
Gene selection using rough set theory
RSKT'06 Proceedings of the First international conference on Rough Sets and Knowledge Technology
Comparison of neural network optimization approaches for studies of human genetics
EuroGP'06 Proceedings of the 2006 international conference on Applications of Evolutionary Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
DNA fragment assembly by ant colony and nearest neighbour heuristics
ICAISC'06 Proceedings of the 8th international conference on Artificial Intelligence and Soft Computing
Using fuzzy patterns for gene selection and data reduction on microarray data
IDEAL'06 Proceedings of the 7th international conference on Intelligent Data Engineering and Automated Learning
Bioinformatics with soft computing
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Evolutionary Rough Feature Selection in Gene Expression Data
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Protein annotation from protein interaction networks and Gene Ontology
Journal of Biomedical Informatics
Heteroscedastic linear feature extraction based on sufficiency conditions
Pattern Recognition
Learning Rough Set Classifiers from Gene Expressions and Clinical Data
Fundamenta Informaticae
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Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included.