Hasin Afzal Ahmed

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The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. Co-expression network have become popular in the analysis of microarray data, such as for detecting functional gene modules. This paper presents a method to build a co-expression(More)
The existence of various types of correlations among the expressions of a group of biologically significant genes poses challenges in developing effective methods of gene expression data analysis. The initial focus of computational biologists was to work with only absolute and shifting correlations. However, researchers have found that the ability to handle(More)
Construction of co-expression network and extraction of network modules have been an appealing area of bioinformatics research. This article presents a co-expression network construction and a biologically relevant network module extraction technique based on fuzzy set theoretic approach. The technique is able to handle both positive and negative(More)
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch-mode(More)
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch mode(More)
Triclustering techniques extract genes that have similar expression patterns in a set of samples across a set of time points. A challenge in triclustering is to account for both inter-temporal and intra-temporal gene coherence. Other challenges include avoidance of time-dominated and sample-dominated results and detection of time latent triclusters. This(More)
Measurement of gene expression using DNA microarrays have revolutionized biological and medical research. This paper presents a divisive clustering algorithm that produces a tree of genes called GERC tree along with the generated clusters. Unlike a dendrogram, a GERC tree is a general tree and it is an ample resource for biological information about the(More)
Mining microarray data sets is important in bioinformatics research and biomedical applications. Recently, mining triclusters or 3D clusters in a Gene Sample Time or 3D microarray data is an emerging area of research. Each tricluster contains a subset of genes and a subset of samples such that the genes are coherent on the samples along the time series.(More)
Complex biological systems are often represented as networks and studied computationally. In protein–protein interaction networks, interactions give rise to certain compounds known as protein complexes. Identifying functional protein complexes is an emerging field of study in system biology. Several machine learning methods have been proposed so far to(More)
Discretization techniques are widely used as preprocessing task in different classification techniques specially in the area of machine learning. These techniques have also been used as a preprocessing task for computational construction of regulatory networks in gene expression data analysis. We analyze the use of some widely used discretization techniques(More)