TRICLUSTER: an effective algorithm for mining coherent clusters in 3D microarray data
Proceedings of the 2005 ACM SIGMOD international conference on Management of data
Analyzing Gene Expression Time-Courses
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Discovering Gene Networks with a Neural-Genetic Hybrid
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The wavelet-based cluster analysis for temporal gene expression data
EURASIP Journal on Bioinformatics and Systems Biology
Inferring time-varying network topologies from gene expression data
EURASIP Journal on Bioinformatics and Systems Biology
Inferring biomolecular interaction networks based on convex optimization
Computational Biology and Chemistry
Methodological Review: Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Spectral similarity for analysis of DNA microarray time-series data
International Journal of Data Mining and Bioinformatics
Creating gene set activity profiles with time-series expression data
International Journal of Bioinformatics Research and Applications
Polynomial models of gene dynamics
Neurocomputing
SlopeMiner: An Improved Method for Mining Subtle Signals in Time Course Microarray Data
FAW '08 Proceedings of the 2nd annual international workshop on Frontiers in Algorithmics
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Identifying Non-random Patterns from Gene Expression Profiles
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Finding Significantly Expressed genes from time-course expression profiles
International Journal of Bioinformatics Research and Applications
Bayesian models for two-sample time-course microarray experiments
Computational Statistics & Data Analysis
Detection of unique temporal segments by information theoretic meta-clustering
Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining
Gene Specific Co-regulation Discovery: An Improved Approach
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
Subspace sums for extracting non-random data from massive noise
Knowledge and Information Systems
Comments on selected fundamental aspects of microarray analysis
Computational Biology and Chemistry
CEC'09 Proceedings of the Eleventh conference on Congress on Evolutionary Computation
An application of kernel methods to gene cluster temporal meta-analysis
Computers and Operations Research
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Significance analysis of time-course gene expression profiles
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Discovering relations among GO-annotated clusters by Graph Kernel methods
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Evaluating graph kernel methods for relation discovery in GO-annotated clusters
KES'07/WIRN'07 Proceedings of the 11th international conference, KES 2007 and XVII Italian workshop on neural networks conference on Knowledge-based intelligent information and engineering systems: Part III
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
The temporal logic of causal structures
UAI '09 Proceedings of the Twenty-Fifth Conference on Uncertainty in Artificial Intelligence
Efficiently mining time-delayed gene expression patterns
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
IEEE Transactions on Information Technology in Biomedicine
Genetic Networks and Soft Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Markov-Blanket-Based Model for Gene Regulatory Network Inference
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring Nonstationary Gene Networks from Longitudinal Gene Expression Microarrays
Journal of Signal Processing Systems
Unravelling the yeast cell cycle using the TriGen algorithm
CAEPIA'11 Proceedings of the 14th international conference on Advances in artificial intelligence: spanish association for artificial intelligence
Representing unevenly-spaced time series data for visualization and interactive exploration
INTERACT'05 Proceedings of the 2005 IFIP TC13 international conference on Human-Computer Interaction
Mining time-delayed coherent patterns in time series gene expression data
ADMA'06 Proceedings of the Second international conference on Advanced Data Mining and Applications
Dynamic modeling, prediction and analysis of cytotoxicity on microelectronic sensors
FSKD'05 Proceedings of the Second international conference on Fuzzy Systems and Knowledge Discovery - Volume Part II
Temporal gene expression profiles reconstruction by support vector regression and framelet kernel
ISNN'10 Proceedings of the 7th international conference on Advances in Neural Networks - Volume Part II
Order preserving clustering over multiple time course experiments
EC'05 Proceedings of the 3rd European conference on Applications of Evolutionary Computing
Efficient matching and retrieval of gene expression time series data based on spectral information
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part III
A patient-gene model for temporal expression profiles in clinical studies
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Hybrid method for the analysis of time series gene expression data
Knowledge-Based Systems
BiMine+: An efficient algorithm for discovering relevant biclusters of DNA microarray data
Knowledge-Based Systems
Reverse engineering of gene regulatory networks from biological data
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
IDA'12 Proceedings of the 11th international conference on Advances in Intelligent Data Analysis
ACSC '11 Proceedings of the Thirty-Fourth Australasian Computer Science Conference - Volume 113
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Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. However, when analyzing these experiments researchers face many new computational challenges. Algorithms that are specifically designed for time series experiments are required so that we can take advantage of their unique features (such as the ability to infer causality from the temporal response pattern) and address the unique problems they raise (e.g. handling the different non-uniform sampling rates). Results: We present a comprehensive review of the current research in time series expression data analysis. We divide the computational challenges into four analysis levels: experimental design, data analysis, pattern recognition and networks. For each of these levels, we discuss computational and biological problems at that level and point out some of the methods that have been proposed to deal with these issues. Many open problems in all these levels are discussed. This review is intended to serve as both, a point of reference for experimental biologists looking for practical solutions for analyzing their data, and a starting point for computer scientists interested in working on the computational problems related to time series expression analysis.