Browne, Fiona, Wang, Haiying, Zheng, Huiru, Azuaje, Francisco
Abstract Background Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug...
Computational biology for cardiovascular biomarker discovery (2009)
Azuaje, Francisco, Devaux, Yvan, Wagner, Daniel
Computational biology is essential in the process of translating biological knowledge into clinical practice, as well as in the understanding of biological phenomena based on the resources and...
Permutation – based statistical tests for multiple hypotheses (2008)
Camargo, Anyela, Azuaje, Francisco, Wang, Haiying, Zheng, Huiru
Abstract Background Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false...
Clustering-based approaches to SAGE data mining (2008)
Wang, Haiying, Zheng, Huiru, Azuaje, Francisco
Abstract Serial analysis of gene expression (SAGE) is one of the most powerful tools for global gene expression profiling. It has led to several biological discoveries and biomedical applications,...
A knowledge-driven approach to cluster validity assessment (2008)
Gene Expression, Nadia Bolshakova, Francisco Azuaje, Pádraig Cunningham
doi:10.1093/bioinformatics/bti317
Francisco Azuaje, Haiying Wang, Olivier Bodenreider
similarity approaches to supporting gene functional assessment
Self-Adaptive Neural Networks Based on a Poisson Approach for Knowledge Discovery (2008)
Haiying Wang, Huiru Zheng, Francisco Azuaje
The ability to learn from data and to improve its performance through incremental learning makes self-adaptive neural networks (SANNs) a powerful tool to support knowledge discovery. However, the...
Ontology-Based Similarity: An Assessment of Quantitative Relationships (2008)
Haiying Wang, Francisco Azuaje, Olivier Bodenreider, Joaquín Dopazo
the S. cerivisiae Genome Database were analyzed to calculate functional similarity of gene products. Three methods for measuring similarity (including a distance-based approach) were implemented....
Francisco Azuaje, Olivier Bodenreider
This research explores the feasibility of semantic similarity approaches to supporting predictive tasks in functional genomics. It aims to establish potential relationships between ontology-based...
Haiying Wang, Francisco Azuaje, Olivier Bodenreider
The Gene Ontology (GO) is an important knowledge resource for biologists and bioinformaticians. This paper explores the integration of similarity information derived from GO into clustering-based...
Special section on machine intelligence approaches to systems biology (2008)
Fogel, Gary B, Bullinger, Eric, Su, Shun-Feng, Azuaje, Francisco
BioData Mining BioMed Central Review Clustering-based approaches to SAGE data mining (2008)
Haiying Wang, Huiru Zheng, Francisco Azuaje
© 2008 Wang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
A Computational Evolutionary Approach to Evolving Game Strategy and Cooperation (2007)
Abstract-- This paper describes an approach to the co-evolution of competing virtual creatures. Pairs of individuals enter one-on-one contests in which they contend to establish contact with a common...
In silico approaches to microarray-based disease classification and gene function discovery
BMC Bioinformatics BioMed Central (2007)
Francisco Azuaje, Francisco Azuaje
Research article Genomic data sampling and its effect on classification performance assessment
The automated interpretation of data originating from the human genome may play a crucial role in cancer treatment. Here a new computational approach to the discovery and analysis of gene expression...
discovery of gene function and classes (2007)
A computational neural approach to support the
Review of "Data Mining: Practical Machine Learning Tools and Techniques" by Witten and Frank (2006)
No abstract available.
Jafari, Peyman, Azuaje, Francisco
Abstract Background The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such...
Wang, Haiying, Zheng, Huiru, Simpson, David, Azuaje, Francisco
Abstract Background Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of...
Advancing Post-Genome Data and System Integration Through Machine Learning (2006)
Research on biological data integration has traditionally focused on the development of systems for the maintenance and interconnection of databases. In the next few years, public and private...
Browne, Fiona, Wang, Haiying, Zheng, Huiru, Azuaje, Francisco
Protein-protein interactions (PPI) play a key role in many biological systems. Over the past few years, an explosion in availability of functional biological data obtained from high-throughput...
Predictive integration of Gene Ontology-driven similarity and functional interactions (2006)
Francisco Azuaje, Haiying Wang, Huiru Zheng, Olivier Bodenreider, Alban Chesneau
There is a need to develop methods to automatically incorporate prior knowledge to support the prediction and validation of novel functional associations. One such important source is represented by...
BMC Medical Informatics and Decision Making (2006)
Biomed Central, Peyman Jafari, Francisco Azuaje
Research article An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors
Review of "Gene Regulation and Metabolism" edited by Julio Collado-Vides and Ralf Hofestädt (2005)
No abstract available.
Review of "Mining Imperfect Data" by Ronald K. Pearson (2005)
No abstract available.
Review of "Statistical Analysis and Data Display" by Richard M. Heiberger and Burt Holland (2005)
No abstract available.
Non-linear mapping for exploratory data analysis in functional genomics (2005)
Azuaje, Francisco, Wang, Haiying, Chesneau, Alban
Abstract Background Several supervised and unsupervised learning tools are available to classify functional genomics data. However, relatively less attention has been given to exploratory,...
Cc Olivier Bodenreider, F. Azuaje, O. Bodenreider, H. Wang, H. Zheng, ...
During this visit we have expanded our investigations on the application of Gene Ontology-driven similarity (GOS) to functional genomics. We focused on two specific problems: • Study of significant...
A knowledge-driven approach to cluster validity assessment (2005)
Bolshakova, Nadia, Azuaje, Francisco, Cunningham, Pádraig
Summary: This paper presents an approach to assessing cluster validity based on similarity knowledge extracted from the Gene Ontology. Availability: The program is freely available for non-profit use...
A knowledge-driven approach to cluster validity assessment (2005)
Bolshakova, Nadia, Azuaje, Francisco, Cunningham, Pádraig
Summary: This paper presents an approach to assessing cluster validity based on similarity knowledge extracted from the Gene Ontology. Availability: The program is freely available for non-profit use...
An integrated tool for microarray data clustering and cluster validity assessment (2005)
Bolshakova, Nadia, Azuaje, Francisco, Cunningham, Pádraig
Summary: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality...
BIOINFORMATICS ORIGINAL PAPER (2004)
Nadia Bolshakova, Francisco Azuaje, Pádraig Cunningham
doi:10.1093/bioinformatics/bti190 An integrated tool for microarray data clustering and cluster validity assessment
Estimating the Number of Clusters in DNA Microarray Data (2004)
Nadia Bolshakova, Francisco Azuaje
ds may support the prediction of the optimal partition and computational diagnosis. A weighed voting technique was used to improve the prediction of the number of clusters based on different data...
An integrated tool for microarray data clustering and cluster validity assessment (2004)
Bolshakova, Nadia, Azuaje, Francisco, Cunningham, Pádraig
Summary: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality...
An integrated tool for microarray data clustering and cluster validity assessment (2004)
Bolshakova, Nadia, Azuaje, Francisco, Cunningham, Pádraig
Summary: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality...
Machaon CVE: Cluster validation for gene expression data (2003)
Bolshakova, Nadia, Azuaje, Francisco
This paper presents a cluster validation tool for gene expression data. Machaon-CVE (Clustering and Validation Environment) system aims to partition samples or genes into groups characterised by...
A markup language for electrocardiogram data acquisition and analysis (ecgML) (2003)
Wang, Haiying, Azuaje, Francisco, Jung, Benjamin, Black, Norman
Abstract Background The storage and distribution of electrocardiogram data is based on different formats. There is a need to promote the development of standards for their exchange and analysis. Such...
Genomic data sampling and its effect on classification performance assessment (2003)
Abstract Background Supervised classification is fundamental in bioinformatics. Machine learning models, such as neural networks, have been applied to discover genes and expression patterns. This...
BMC Medical Informatics and Decision Making (2003)
Haiying Wang, Francisco Azuaje, Benjamin Jung, Norman Black
A markup language for electrocardiogram data acquisition and analysis (ecgML)
Machaon CVE: cluster validation for gene expression data (2003)
Bolshakova, Nadia, Azuaje, Francisco
Summary: This paper presents a cluster validation tool for gene expression data. Machaon CVE (Clustering and Validation Environment) system aims to partition samples or genes into groups...
Clustering-based approaches to discovering and visualising microarray data patterns (2003)
This article focuses on clustering techniques for the analysis of microarray data and discusses contributions and applications for the implementation of intelligent diagnostic systems and therapy...
Discovering Genome Expression Patterns With Self-Organizing Neural Networks (2002)
Azuaje F. “Discovering Genome Expression Patterns With Self-Organizing Neural Networks”, in Understanding and Using Microarray Analysis Techniques: A Practical Guide, Berrar D, Dubitzky W and...
Discovering genome expression patterns with self-organizing neural networks (2002)
Originally published: Azuaje F. “Discovering Genome Expression Patterns With Self-Organizing Neural Networks”, in Understanding and Using Microarray Analysis Techniques: A Practical Guide, Berrar...
Kevin Dunne, Padraig Cunningham, Francisco Azuaje
It is generally accepted that Wrapper approaches will outperform Filter-based approaches to feature selection, particularly in situations where an adequate amount of data is available. What is often...
Clustering genome expression data: design and evaluation principles (2002)
Francisco Azuaje, Nadia Bolshakova
The analysis of expression data is based on the idea that genes that are involved in a particular pathway, or respond to a common environmental stimulus, should be co-regulated and therefore should...
Self-organizing neural networks represent a family of useful clusteringbased classification methods in several application domains. One such technique is the Kohonen Self-Organizing Feature Map (SOM)...
Advancing Post-Genome Data and System Integration through Machine Learning (2002)
Research on biological data integration has traditionally focused on the development of systems for the maintenance and interconnection of databases. In the next few years, public and private...
With more than 30 years of experimental research, there have been no generic models to classify tumours and identify new types of cancer. Similarly, advances in molecular classification of tumours...
A markup language for electrocardiogram data acquisition and analysis (ecgML)
Wang, Haiying, Azuaje, Francisco, Jung, Benjamin, Black, Norman
A markup language for electrocardiogram data acquisition and analysis (ecgML)
Wang, Haiying, Azuaje, Francisco, Jung, Benjamin, Black, Norman
Advancing Post-Genome Data and System Integration Through Machine Learning
Research on biological data integration has traditionally focused on the development of systems for the maintenance and interconnection of databases. In the next few years, public and private...
Clustering-based approaches to SAGE data mining
Wang, Haiying, Zheng, Huiru, Azuaje, Francisco
Serial analysis of gene expression (SAGE) is one of the most powerful tools for global gene expression profiling. It has led to several biological discoveries and biomedical applications, such as the...
Permutation – based statistical tests for multiple hypotheses
Camargo, Anyela, Azuaje, Francisco, Wang, Haiying, Zheng, Huiru
Innovative methods in assessing political risk for business internationalization
Rios-Morales, Ruth, Gamberger, Dragan, Smuc, Tom, Azuaje, Francisco
Political risk assessment, together with portfolio analysis, has become an important part of international business investment decision making. In this paper, by using different knowledge discovery...