Abstract: Technological advances of computer science and data
analysis are helping to provide continuously huge volumes of
biological data, which are available on the web. Such advances
involve and require powerful techniques for data integration to
extract pertinent knowledge and information for a specific question.
Biomedical exploration of these big data often requires the use
of complex queries across multiple autonomous, heterogeneous
and distributed data sources. Semantic integration is an active
area of research in several disciplines, such as databases,
information-integration, and ontology. We provide a survey of some
approaches and techniques for integrating biological data, we focus
on those developed in the ontology community.
Abstract: This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate
crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still
lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.
Abstract: For the past one decade, biclustering has become popular data mining technique not only in the field of biological data analysis but also in other applications like text mining, market data analysis with high-dimensional two-way datasets. Biclustering clusters both rows and columns of a dataset simultaneously, as opposed to traditional clustering which clusters either rows or columns of a dataset. It retrieves subgroups of objects that are similar in one subgroup of variables and different in the remaining variables. Firefly Algorithm (FA) is a recently-proposed metaheuristic inspired by the collective behavior of fireflies. This paper provides a preliminary assessment of discrete version of FA (DFA) while coping with the task of mining coherent and large volume bicluster from web usage dataset. The experiments were conducted on two web usage datasets from public dataset repository whereby the performance of FA was compared with that exhibited by other population-based metaheuristic called binary Particle Swarm Optimization (PSO). The results achieved demonstrate the usefulness of DFA while tackling the biclustering problem.
Abstract: Cluster analysis divides data into groups that are
meaningful, useful, or both. Analysis of biological data is creating a
new generation of epidemiologic, prognostic, diagnostic and
treatment modalities. Clustering of protein sequences is one of the
current research topics in the field of computer science. Linear
relation is valuable in rule discovery for a given data, such as if value
X goes up 1, value Y will go down 3", etc. The classical linear
regression models the linear relation of two sequences perfectly.
However, if we need to cluster a large repository of protein sequences
into groups where sequences have strong linear relationship with
each other, it is prohibitively expensive to compare sequences one by
one. In this paper, we propose a new technique named General
Regression Model Technique Clustering Algorithm (GRMTCA) to
benignly handle the problem of linear sequences clustering. GRMT
gives a measure, GR*, to tell the degree of linearity of multiple
sequences without having to compare each pair of them.
Abstract: We have developed a computer program consisting of
6 subtests assessing the children hand dexterity applicable in the
rehabilitation medicine. We have carried out a normative study on a
representative sample of 285 children aged from 7 to 15 (mean age
11.3) and we have proposed clinical standards for three age groups
(7-9, 9-11, 12-15 years). We have shown statistical significance of
differences among the corresponding mean values of the task time
completion. We have also found a strong correlation between the task
time completion and the age of the subjects, as well as we have
performed the test-retest reliability checks in the sample of 84
children, giving the high values of the Pearson coefficients for the
dominant and non-dominant hand in the range 0.740.97 and
0.620.93, respectively.
A new MATLAB-based programming tool aiming at analysis of
cardiologic RR intervals and blood pressure descriptors, is worked
out, too. For each set of data, ten different parameters are extracted: 2
in time domain, 4 in frequency domain and 4 in Poincaré plot
analysis. In addition twelve different parameters of baroreflex
sensitivity are calculated. All these data sets can be visualized in time
domain together with their power spectra and Poincaré plots. If
available, the respiratory oscillation curves can be also plotted for
comparison. Another application processes biological data obtained
from BLAST analysis.
Abstract: Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.
Abstract: Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.
Abstract: Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.
Abstract: Nowadays scientific data is inevitably digital and
stored in a wide variety of formats in heterogeneous systems.
Scientists need to access an integrated view of remote or local
heterogeneous data sources with advanced data accessing, analyzing,
and visualization tools. This research suggests the use of Service
Oriented Architecture (SOA) to integrate biological data from
different data sources. This work shows SOA will solve the problems
that facing integration process and if the biologist scientists can
access the biological data in easier way. There are several methods to
implement SOA but web service is the most popular method. The
Microsoft .Net Framework used to implement proposed architecture.
Abstract: The scientific achievements coming from molecular
biology depend greatly on the capability of computational
applications to analyze the laboratorial results. A comprehensive
analysis of an experiment requires typically the simultaneous study
of the obtained dataset with data that is available in several distinct
public databases. Nevertheless, developing a centralized access to
these distributed databases rises up a set of challenges such as: what
is the best integration strategy, how to solve nomenclature clashes,
how to solve database overlapping data and how to deal with huge
datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main
advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported
databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be
publicly downloaded or remotely access through SOAP web services.
Abstract: Approximate tandem repeats in a genomic sequence are
two or more contiguous, similar copies of a pattern of nucleotides.
They are used in DNA mapping, studying molecular evolution
mechanisms, forensic analysis and research in diagnosis of inherited
diseases. All their functions are still investigated and not well
defined, but increasing biological databases together with tools for
identification of these repeats may lead to discovery of their specific
role or correlation with particular features. This paper presents a new
approach for finding approximate tandem repeats in a given sequence,
where the similarity between consecutive repeats is measured using
the Hamming distance. It is an enhancement of a method for finding
exact tandem repeats in DNA sequences based on the Burrows-
Wheeler transform.
Abstract: Availability of high dimensional biological datasets such as from gene expression, proteomic, and metabolic experiments can be leveraged for the diagnosis and prognosis of diseases. Many classification methods in this area have been studied to predict disease states and separate between predefined classes such as patients with a special disease versus healthy controls. However, most of the existing research only focuses on a specific dataset. There is a lack of generic comparison between classifiers, which might provide a guideline for biologists or bioinformaticians to select the proper algorithm for new datasets. In this study, we compare the performance of popular classifiers, which are Support Vector Machine (SVM), Logistic Regression, k-Nearest Neighbor (k-NN), Naive Bayes, Decision Tree, and Random Forest based on mock datasets. We mimic common biological scenarios simulating various proportions of real discriminating biomarkers and different effect sizes thereof. The result shows that SVM performs quite stable and reaches a higher AUC compared to other methods. This may be explained due to the ability of SVM to minimize the probability of error. Moreover, Decision Tree with its good applicability for diagnosis and prognosis shows good performance in our experimental setup. Logistic Regression and Random Forest, however, strongly depend on the ratio of discriminators and perform better when having a higher number of discriminators.