AIMC Topic: Computational Biology

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The quantitative prediction of HLA-B*2705 peptide binding affinities using Support Vector Regression to gain insights into its role for the Spondyloarthropathies.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Computational methods are increasingly utilised in many immunoinformatics problems such as the prediction of binding affinity of peptides. The peptides could provide valuable insight into the drug design and development such as vaccines. Moreover, th...

Adaptive Fuzzy Consensus Clustering Framework for Clustering Analysis of Cancer Data.

IEEE/ACM transactions on computational biology and bioinformatics
Performing clustering analysis is one of the important research topics in cancer discovery using gene expression profiles, which is crucial in facilitating the successful diagnosis and treatment of cancer. While there are quite a number of research w...

Randomized Subspace Learning for Proline Cis-Trans Isomerization Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
Proline residues are common source of kinetic complications during folding. The X-Pro peptide bond is the only peptide bond for which the stability of the cis and trans conformations is comparable. The cis-trans isomerization (CTI) of X-Pro peptide b...

Unsupervised Structure Detection in Biomedical Data.

IEEE/ACM transactions on computational biology and bioinformatics
A major challenge in computational biology is to find simple representations of high-dimensional data that best reveal the underlying structure. In this work, we present an intuitive and easy-to-implement method based on ranked neighborhood compariso...

Supervised Variational Relevance Learning, An Analytic Geometric Feature Selection with Applications to Omic Datasets.

IEEE/ACM transactions on computational biology and bioinformatics
We introduce Supervised Variational Relevance Learning (Suvrel), a variational method to determine metric tensors to define distance based similarity in pattern classification, inspired in relevance learning. The variational method is applied to a co...

A New Semantic Functional Similarity over Gene Ontology.

IEEE/ACM transactions on computational biology and bioinformatics
Identifying functionally similar or closely related genes and gene products has significant impacts on biological and clinical studies as well as drug discovery. In this paper, we propose an effective and practically useful method measuring both gene...

P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations.

IEEE/ACM transactions on computational biology and bioinformatics
Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between...

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.

IEEE/ACM transactions on computational biology and bioinformatics
We introduce RLIMS-P version 2.0, an enhanced rule-based information extraction (IE) system for mining kinase, substrate, and phosphorylation site information from scientific literature. Consisting of natural language processing and IE modules, the s...

Sequence-based protein superfamily classification using computational intelligence techniques: a review.

International journal of data mining and bioinformatics
Protein superfamily classification deals with the problem of predicting the family membership of newly discovered amino acid sequence. Although many trivial alignment methods are already developed by previous researchers, but the present trend demand...