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With the explosion of protein sequences generated in the Post-Genomic Age, it is urgent to develop an automated method to predict protein quaternary structure. To explore this problem, we adopted an approach based on a sequence encoding descriptor by fusing PseAA (Pseudo Amino Acid) and DC (Dipeptide Composition) representing a protein sample. Here, a completely different approach, manifold learning...
The Human Protein Atlas (HPA) is a repository of location patterns of about 11000 proteins within tissues and cell lines. In this work we summarize some of our current work on analyzing immunohistochemical images of proteins within 7 distinct tissues. Firstly, we present our efforts to analyze spatial point patterns of protein staining and determine protein subcellular location from image-derived...
A growing number of screening applications require the automated monitoring of cell populations enabled by cell segmentation and tracking algorithms in a high-throughput, high-content environment. Building upon the tracks generated by such algorithms, we derive biologically relevant features and demonstrate a range of biological studies made possible by such quantitative measures. In the first, we...
MicroRNAs are one type of noncoding RNA that regulate their target mRNAs before mRNAs are translated into proteins. Although it has been demonstrated that the regulation is through partial binding of the seed region of a miRNA and its targets, the mechanism of this process is not fully discovered. Some biological experiments have shown that even perfect base pairing in the seed region does not always...
Previous studies about protein-DNA interaction focused on the bound structure of DNA-binding proteins and provided good but not practical results. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and use structural alignment to develop an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of...
Protein features are often complex, and they are challenging to classify. In identifying the most discriminatory features in protein sequences, we propose a new feature-selection strategy by integrating the multivariate filter and Particle Swarm Optimisation (PSO) algorithms. Experimental results, based on the number of reducts and classification accuracy, were analysed in both the filter and wrapper...
The progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computational models of protein-protein interactions. However, distinguishing between the physiological and non-physiological interactions remains a challenging problem. In this work, two related problems of interface classification have been addressed. The first problem...
An important aspect in understanding and classifying protein-protein interactions (PPI) is to analyze their interfaces in order to distinguish between transient and obligate complexes. We propose a classification approach to discriminate between these two types of complexes. Our approach has two important aspects. First, we have used desolvation energies - amino acid and atom type - of the residues...
Golgi membrane proteins contribute protein glycosylation, which is one of post-translational modification. It plays an important role in the cellular processes such as cell-cell adhesion, signal transfer, and subcellular localization. In this regard, the development of a computational method to discrimination of Golgi membrane proteins from the mammal genomes is desired. In this study, we succeeded...
New technological advances in large-scale protein-protein interaction (PPI) detection provide researchers a valuable source for elucidating the bimolecular mechanism in the cell. In this paper, we investigate the problem of protein complex detection from noisy protein interaction data, i.e., finding the subsets of proteins that are closely coupled via protein interactions. Many people try to solve...
This paper presents our empirical results by using 32 channel NIRS system to examine the changes in oxygenation in regions of prefrontal cortex. Four healthy subjects participated in the experiment by performing various cognitive tasks such as mathematical, imaginary and computer game. The concentration levels in oxyHb and deoxyHb varied depending on subject's mental workload as a result we could...
This work introduces a two-stage active contour-based scheme for the detection of protein spots in two-dimensional gel electrophoresis images. The proposed scheme is formulated as an expansion of the Chan-Vese model and is capable of distinguishing overlapping spots. Moreover, it remains unaffected in the presence of noise and the inhomogeneous background that characterize these images. The experimental...
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. Using the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. In this paper, the...
Glycosylation is one of the most important post-translation modifications steps in eukaryotic cell. In this paper, we propose a new approach based on independent component analysis (ICA) for prediction O-linked glycosylation site and pattern analysis. Principal component analysis (PCA) is first used to find significant uncorrelated components, and then ICA is used to extract independent components...
Kernel method has witnessed many successful applications in computational biology in recent years, and thus kernel design is a key step to define the similarity between two protein sequences. This paper aims at designing a kernel to derive more accurate similarity between two protein sequences by incorporating homology. Here a homologous sequence is viewed as one evolutionary instance of the target...
The purpose of this paper was to find some feature pattern which may be used in diagnosis of blood stasis syndrome (BSS, a unique concept of traditional Chinese medicine) with myocardial ischemia. After establishing an animal model of Chinese experimental miniature swine, 7 indicators in plasma, e.g. troponin T (cTNT), heat shock protein 27 (HSP27), cytochrome C (Cyt C), endothelin-1 (ET-1), calcitonin...
HER-2/neu, a protein often giving higher aggressiveness in breast cancers, has been shown that if the gene is expanded for some reason, the Her-2 protein produced by the cells will be over-expressed to enhance the cancer cells reproduced ability, the prognosis will be also relatively less, too. The HER-2 immunohistochemical stained provides a simple and reliable method for pathologist in clinical...
Cell polarity is involved in many biological functions such as development, wound healing and immune responses. In human neutrophils, polarization is characterized by the translocation of distinct sets of signaling molecules to opposite ends of the cell and the rapid rearrangement of cytoskeleton to initiate migration. While many image-based studies have described cellular morphology and the intensity...
Previous computational models generally exclude homology out of the training set to reduce potential predictive bias. This paper proposes a hierarchical kernel to incorporate homology for more accurate similarity definition between two protein sequences. Metaphorized as the scenario of multi-instance learning, a homologous sequence is viewed as one evolutionary instance of the target sequence and...
In this paper, we propose to use dual-tree complex and double density discrete wavelet transform for extracting mass spectrometry features. Two corresponding procedures are suggested for mass spectrometry classification. Several experiments are deployed on two types of MALDI-TOF mass spectra, including stable spectra and noisy spectra. The classification results show that our proposed procedures not...
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