November 2024: Top 10

Cited Articles in
Bioinformatics &
Biosciences (IJBB)

International Journal on Bioinformatics&

Biosciences (IJBB)
ISSN:1839-9614

https://wireilla.com/ijbb/index.html
Reconstruction and Analysis of Cancerspecific Gene Regulatory Networks from Gene
Expression Profiles

Khalid Raza1* and Rajni Jaiswal2

1Department of Computer Science, Jamia Millia Islamia (Central University),

New Delhi-110025, India.

2Department of Computer Science, Jamia Hamdard, New Delhi-110062, India

ABSTRACT

The main goal of Systems Biology research is to reconstruct biological networks for its topological
analysis so that reconstructed networks can be used for the identification of various kinds of disease. The
availability of high-throughput data generated by microarray experiments fuelled researchers to use
whole-genome gene expression profiles to understand cancer and to reconstruct key cancer-specific gene
regulatory network. Now, the researchers are taking a keen interest in the development of algorithm for
the reconstruction of gene regulatory network from whole genome expression profiles. In this study, a
cancer-specific gene regulatory network (prostate cancer) has been constructed using a simple and novel
statistics based approach. First, significant genes differentially expressing them self in the disease
condition has been identified using a two-stage filtering approach t-test and fold-change measure. Next,
regulatory relationships between the identified genes has been computed using Pearson correlation
coefficient. The obtained results has been validated with the available databases and literatures. We
obtained a cancer-specific regulatory network of 29 genes with a total of 55 regulatory relations in which
some of the genes has been identified as hub genes that can act as drug target for the cancer diagnosis.

KEYWORDS
Gene regulatory network, microarray analysis, prostate cancer, differentially expressed genes

Source URL: https://wireilla.com/ijbb/vol3.html

Volume URL: https://wireilla.com/papers/ijbb/V3N2/3213ijbb03.pdf

Cited by:39
 Anti-Synchronizing Backstepping Control Design for Arneodo Chaotic System
Sundarapandian Vaidyanathan 1

1Research and Development Centre, Vel Tech Dr. RR & Dr. SR Technical University

Avadi, Chennai-600 062, Tamil Nadu, INDIA

ABSTRACT

In this paper, we derive new results for backstepping controller design for the anti-synchronization of
Arneodo chaotic system (1980). Backstepping control is a recursive procedure that combines the choice
of a Lyapunov function with the design of a feedback controller. In anti-synchronization of chaotic
systems, the states of the synchronized systems have the same absolute values, but opposite signs. First,
we derive an active backstepping controller for the anti-synchronization of identical Arneodo chaotic
systems. Next, we derive an adaptive backstepping controller for the anti-synchronization of identical
Arneodo chaotic system, when the system parameters are unknown. The anti-synchronization results for
Arneodo chaotic systems have been proved using Lyapunov stability theory. Numerical simulations have
been shown to illustrate the backstepping controllers derived in this paper for Arneodo chaotic system.

KEYWORDS
Backstepping Control; Chaos; Anti-Synchronization; Arneodo System

Source URL: https://wireilla.com/ijbb/vol3.html

Volume URL: https://wireilla.com/papers/ijbb/V3N1/3113ijbb03.pdf

Cited by:26
 Application of three graph Laplacian based semisupervised learning methods to
protein function prediction problem

Loc Tran

University of Minnesota

ABSTRACT

Protein function prediction is the important problem in modern biology. In this paper, the un-normalized,
symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods will
be applied to the integrated network combined from multiple networks to predict the functions of all yeast
proteins in these multiple networks. These multiple networks are network created from Pfam domain
structure, co-participation in a protein complex, protein-protein interaction network, genetic interaction
network, and network created from cell cycle gene expression measurements. Multiple networks are
combined with fixed weights instead of using convex optimization to determine the combination weights
due to high time complexity of convex optimization method. This simple combination method will not
affect the accuracy performance measures of the three semi-supervised learning methods. Experiment
results show that the un-normalized and symmetric normalized graph Laplacian based methods perform
slightly better than random walk graph Laplacian based method for integrated network. Moreover, the
accuracy performance measures of these three semi-supervised learning methods for integrated network
are much better than the best accuracy performance measures of these three methods for the individual
network.

KEYWORDS
semi-supervised learning, graph Laplacian, yeast, protein, function

Source URL: https://wireilla.com/ijbb/vol3.html

Volume URL: https://wireilla.com/papers/ijbb/V3N2/3213ijbb02.pdf

Cited by:24
 Gene Expression Mining for Predicting Survivability of Patients in Earlystages of
Lung Cancer

Shoon Lei Win, Zaw Zaw Htike, Faridah Yusof, Ibrahim A. Noorbatcha

Faculty of Engineering, IIUM, Kuala Lumpur, Malaysia

ABSTRACT

After numerous breakthroughs in medicine, microbiology, and pathology in the past century, lung cancer
still remains as a leading cause of cancer-related death even in the developed countries. Lung cancer
accounts roughly for 30% of all cancer-related deaths in the world. Diagnosis and treatments are still
based on traditional histopathology. It is of paramount importance to predict the survivability of patients
in early stages of lung cancer so that specific treatments can be sought. Nonetheless, histopathology has
been shown by previous studies to be inadequate in predicting lung cancer development and clinical
outcome. The microarray technology allows researchers to examine the expression of thousands of genes
simultaneously. This paper describes a state-of-the-art machine learning based approach called averaged
one-dependence estimators with subsumption resolution to tackle the problem of predicting whether a
patient in early stages of lung cancer will survive by mining DNA microarray gene expression data. To
lower the computational complexity, we employ an entropy-based gene selection approach to select
relevant genes that are directly responsible for lung cancer survivability prognosis. The proposed system
has achieved an average accuracy of 92.31% in predicting lung cancer survivability over 2 independent
datasets. The experimental results provide confirmation that gene expression mining can be used to
predict survivability of patients in early stages of lung cancer.

KEYWORDS
Lung cancer, survivability prediction; microarray gene expression

Source URL: https://wireilla.com/ijbb/vol4.html

Volume URL: https://wireilla.com/papers/ijbb/V4N2/4214ijbb01.pdf

Cited by:20

Adaptive Control and Synchronization of a Generalized Lotka-Volterra System

 Sundarapandian Vaidyanathan1

1Research and Development Centre, Vel Tech Dr. RR & Dr. SR Technical University

Avadi, Chennai-600 062, Tamil Nadu, INDIA

ABSTRACT

The Lotka-Volterra equations are a system of equations proposed to provide a simplified model of
twospecies predator-prey population dynamics. In this paper, we investigate the problem of adaptive
chaos control and synchronization of a generalized Lotka-Volterra system discovered by Samardzija and
Greller (1988). The Samardzija-Greller model is a two-predator, one-prey generalization of the Lotka-
Volterra system. First, adaptive control laws are designed to stabilize the generalized Lotka-Volterra
system to its unstable equilibrium point at the origin based on the adaptive control theory and Lyapunov
stability theory. Then adaptive control laws are derived to achieve global chaos synchronization of
identical generalized Lotka-Volterra systems with unknown parameters. Numerical simulations are shown
to validate and demonstrate the effectiveness of the proposed adaptive control and synchronization
schemes for the generalized Lotka-Volterra system.

KEYWORDS
Adaptive Control, Stabilization, Chaos Synchronization, Generalized Lotka-Volterra Chaotic System

Source URL: https://wireilla.com/ijbb/vol1.html

Volume URL: https://wireilla.com/papers/ijbb/V1N1/1011ijbb01.pdf

Cited by:14
 An Efficient PSO Optimized Integration Weight Estimation Using D-prime Statistics
for A Multibiometric System

S. M. Anzar1 and P. S. Sathidevi2

1Department of Electronics & Communication Engineering, National Institute of Technology,
Calicut, India, 673601
2Department of Electronics & Communication Engineering, National Institute of Technology,
Calicut, India, 673601

ABSTRACT

The efficiency of a multibiometric system can be improved by weighting the scores obtained from the
degraded modalities in an appropriate manner. In this paper, we propose an efficient PSO (Particle Swarm
Optimization) based integration weight optimization scheme using d-prime statistics to determine the
optimal weight factors for the complementary modalities, under different noise conditions. Instead of
treating the weight estimation process from an algebraic point of view, an attempt is made to consider the
same from the principles of linear programming techniques. The performance of the proposed method is
analysed in the context of fingerprint and voice biometrics using sum rule of fusion. The d-prime statistics
of fingerprint and voice modalities are measured and the integration weights are computed as the ratio of
these two statistics. The computed d-prime ratio is then optimized against the recognition accuracy. The
optimizing parameter is estimated in the training/validation phase using Leave-One-Out Cross Validation
(LOOCV) technique. Experimental studies show that the proposed method improves recognition rate
under normal operating conditions and reduces the FAR (False Acceptance Rate) considerably even at
extreme low SNR (Signal to Noise Ratio) conditions. The proposed biometric solution can be easily
integrated into any multibiometric system with score level fusion. Moreover, it finds extremely useful in
applications where there are less number of available training samples.

KEYWORDS
Multibiometric System, Integration Weight, d-prime Statistics, Particle Swarm Optimization, Robustness

Source URL: https://wireilla.com/ijbb/vol2.html

Volume URL: https://wireilla.com/papers/ijbb/V2N3/2312ijbb04.pdf

Cited by:12

Improvement of the Fingerprint Recognition Process

 Farah Dhib Tatar1 And Mohsen Machhout2
1Department of Electrical Engineering, National School of the Studies of Engineer of Tunis, Tunisia
2Faculty of Sciences of Monastir, Monastir, Tunisia

ABSTRACT

The increased development of IT tools and social communication networks has significantly increased the
need for people to be identified with reliable and secure tools hence the importance of using biometric
technology. Biometrics is an emerging field where technology improves our ability to identify a person.
The advantage of biometric identification is that each individual has its own physical characteristics that
cannot be changed, lost or stolen. The use of fingerprinting is today one of the most reliable technologies
on the market to authenticate an individual. This technology is simple to use and easy to implement. The
techniques of fingerprint recognition are numerous and diversified, they are generally based on generic
algorithms and tools for filtering images.

This article proposes a fingerprint recognition chain by highlighting improved processing tools to
facilitate data retrieval. The results are retrieved and validated using Matlab.

KEYWORDS
Fingerprint, Biometrics, Images Processing, Minutiae, Matlab

Source URL: https://wireilla.com/ijbb/vol7.html

Volume URL: https://wireilla.com/papers/ijbb/V7N2/7217ijbb01.pdf

Cited by:9
 A Survey on Recent Trends in Human-Computer Interaction

Srinivas Koppu1 , V. Madhu Viswanatham2 and Kamalakannan J1

1 School of Information Technology and Engineering, VIT University, Vellore, India
2School of computing Science and Engineering VIT University, Vellore, India

ABSTRACT

This paper identifies the different kinds of methods, which helps human to communicate with computer.
Traditionally the user interacting with computer via command line or GUI or common hand-held devices
such as mouse and keyboard which is not feasible for a handicapped or a blind or a mute people. In order
to interact with computer, the good interface required, the interface is sub part of human computer
Interaction (HCI). HCI not only software design, it also concentrates on design of hardware devices.
Describe the interaction between Brain and Computer based on EEG patterns. Brain generates EEG signal
Based upon that system has to act and it has to perform tasks like human in real world. Thus the research
work that is proposed would be to build a human to computer interaction through EEG signal. The system
that allow the user to interact directly brain to computer based EEG signal and no need to use any input
device to interact with any type of systems such are computer , TV’s. This way the computer system can
reduce the man work needed to feed information into the system by a large extent.

KEYWORDS
EEG signal, Brain Computer Interface (BCI), Human Computer Interaction (HCI), Speech Recognizer,
Neural Networks, Cognitive Science.

Source URL: https://wireilla.com/ijbb/vol2.html

Volume URL: https://wireilla.com/papers/ijbb/V2N3/2312ijbb02.pdf

Cited by:8

Analysis of Hepatitis C Virus using Data Mining Algorithm -Apriori, Decision Tree
 Ha YeongJeong and Tae Seon Yoon

Hankuk Academy of Foreign Studies, Yongin, Gyeonggi, Republic of Korea

ABSTRACT

Hepatitis C, which presents with symptoms such as acute fatigue and jaundice, is highly likely to become
chronic, and is the main cause of liver cancer, attracting much public attention. Moreover, the number of
infected people is increasing worldwide nowadays. However, we found that there are 6 different genotype
in hcv. In vaccine and medicine developing for viruses, analysis of them is most important. Therefore, we
decided to compare 6 genotype using Apriori algorithm and Decision tree algorithm. We tried to find out
some difference between genotype 1 and others by analyzing the genotype 1, since genotype 1 is most
common, and tried to find out the correlation between the genotype 1b and 2a with the highest number of
infections in Korea. With these algorithm, we were able to find several rules and differences between
them.

KEYWORDS
Hepatitis C virus, Apriori algorithm, Decision tree algorithm, virus, Bioinformatics

Source URL: https://wireilla.com/ijbb/vol7.html

Volume URL: https://wireilla.com/papers/ijbb/V7N3/7317ijbb01.pdf

Cited by:7