Combining Expression Data and Knowledge Ontology for Gene Clustering and Network Reconstruction

Towards integrative gene functional similarity measurement

(2014) Jiajie Peng et al.   BMC BIOINFORMATICS

A new cluster validity measure based on general type-2 fuzzy sets: Application in gene expression data clustering

(2014) Abolfazl Doostparast Torshizi et al.   KNOWLEDGE-BASED SYSTEMS

Novel Biologically Inspired Approaches to Extracting Online Information from Temporal Data

(2014) Zeeshan Khawar Malik et al.   Cognitive Computation

Modular Composite Representation

(2014) Javier Snaider et al.   Cognitive Computation

Sparse-Representation-Based Classification with Structure-Preserving Dimension Reduction

(2014) Jin Xu et al.   Cognitive Computation

Analysing microarray expression data through effective clustering

(2013) E. Masciari et al.   INFORMATION SCIENCES

Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources

(2013) Paurush Praveen et al.   PLoS One

Information Content-Based Gene Ontology Semantic Similarity Approaches: Toward a Unified Framework Theory

(2013) Gaston K. Mazandu et al.   Biomed Research International

Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method

(2012) Yu-Ting Hsiao et al.   BMC BIOINFORMATICS

Machine learning approaches for the discovery of gene-gene interactions in disease data

(2012) R. Upstill-Goddard et al.   BRIEFINGS IN BIOINFORMATICS

Clustering of high throughput gene expression data

(2012) Harun Pirim et al.   COMPUTERS & OPERATIONS RESEARCH

BiMine+: An efficient algorithm for discovering relevant biclusters of DNA microarray data

(2012) Wassim Ayadi et al.   KNOWLEDGE-BASED SYSTEMS

Boolean modeling of biological regulatory networks: A methodology tutorial

(2012) Assieh Saadatpour et al.   METHODS

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes

(2012) Padhraig Gormley et al.   Cognitive Computation

Principal component analysis based methods in bioinformatics studies

(2011) S. Ma et al.   BRIEFINGS IN BIOINFORMATICS

An Adaptive GA--PSO Approach with Gene Clustering to Infer S-system Models of Gene Regulatory Networks

(2011) W.-P. Lee et al.   COMPUTER JOURNAL

An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks

(2011) B. Vasic et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Learning gene regulatory networks using the bees algorithm

(2011) Gonzalo A. Ruz et al.   NEURAL COMPUTING & APPLICATIONS

Construction of gene regulatory networks using biclustering and bayesian networks

(2011) Fadhl M Alakwaa et al.   Theoretical Biology and Medical Modelling

Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network

(2011) Jérémie Bourdon et al.   PLoS Computational Biology

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

Data-Fusion in Clustering Microarray Data: Balancing Discovery and Interpretability

(2010) R. Kustra et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

An ontology-based measure to compute semantic similarity in biomedicine

(2010) Montserrat Batet et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A roadmap of clustering algorithms: finding a match for a biomedical application

(2009) B. Andreopoulos et al.   BRIEFINGS IN BIOINFORMATICS

Influence of Prior Knowledge in Constraint-Based Learning of Gene Regulatory Networks

(2009) Mehmet Tan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Inferring gene regulatory networks by thermodynamic modeling

(2008) Chieh-Chun Chen et al.   BMC GENOMICS

Reverse engineering the cell

(2008) Nicholas T. Ingolia et al.   NATURE

A clustering-based approach for inferring recurrent neural networks as gene regulatory networks

(2007) Wei-Po Lee et al.   NEUROCOMPUTING