Advances in Bioinformatics and Its Applications

by He, Matthew

• ISBN13: 9789812561480
• ISBN10: 981256148X
• Edition: 1st
• Format: Hardcover
• Copyright: 2005-06-01
• Publisher: World Scientific Pub Co Inc

Summary

This unique volume presents major developments and trends in bioinformatics and its applications, Comprising high-quality scientific research papers and state-of-the-art survey articles, the book has been divided into three main sections: Sequences, Structures, and Functions; Pathways, Biological Networks, and System Biology; and Microarray Data, Medical Informatics, and Applications. These results of these investigations help the practicing biologist in many ways: in identifying unknown connections, in narrowing down possibilities fora search, in suggesting new hypotheses, designing new experiments validating existing models or proposing new ones. It is an essential source of reference for researchers and graduate students in bioinformatics, computer science, mathematics, statistics, and biological sciences based on selected papers from the "The International Conference on Bioinformatics and Its Application" (ICBA), held December 16-19 2004 in Fort Lauderdale, Florida, USA.

Table of Contents

1. Microarray Analysis and Regulatory Networks
Microarray Normalization using Proportional Abundance	3	(10)
S. A. Eschrich
C. A. Beam
Emerging Pattern Based Subspace Clustering of Microarray Gene Expression Data using Mixture Models	13	(12)
Y. B. Kim
J. H. Oh
J. Gao
Thermodynamic Feasibility of Metabolic Networks	25	(12)
R. Nigam
S. Liang
Computational Reconstruction of the Carbon Fixation Pathway in Synechococcus sp. WH8102	37	(10)
P. Dam
Z. Su
V. Olman
Y. Xu
Modular Neural Networks and their Application in Exon Prediction	47	(15)
Y. Pan
C. W. Sensen
Gene Definition in Different Databases and its Implication in Microarray Data Interpretation	62	(9)
P. Wang
M. Dai
R. Thompson
S. J. Watson
F. Meng
Exploring Important Issues in the Implementation of Gene Set Enrichment Analysis	71	(10)
Y. Wang
S. J. Watson
F. Meng
Querying A Database of Regulatory Elements	81	(14)
C. Yang
E. Zeng
K. Mathee
G. Narasimhan
2. Machine Learning and Statistical Analyses
Computational Epidemiology: Bayesian Disease Surveillance	95	(12)
K. Abbas
A. R. Mikler
A. Ramezani
S. Menezes
Non-Equilibrium Fluctuations in a Stochastic Planktonic Model: Periodicity of Phytoplankton Bloom	107	(12)
R. Bhattacharyya
B. Mukhopadhyay
Fuzzy Decoding in Profile Hidden Markov Models for Protein Family Identification	119	(13)
N. P. Bidargaddi
M. Chetty
J. Kamruzzaman
Screening Potential Allele-Frequency Disequilibrium in Data from Affymetrix Gene Expression Arrays	132	(8)
M. Dai
Y. Wang
E. Sliwerska
M. Burmeister
S. J. Watson
H. Akil
F. Meng
The Application of Self Organizing Maps for the Analyses of DNA Sequences	140	(11)
H. Dozono
S. Hara
H. Tokushima
Y. Noguchi
Gaussian Kernel Width Generation for Support Vector Clustering	151	(12)
S.-H. Lee
K. Daniels
Serum Proteomic Pattern Analysis for Early Cancer Detection	163	(10)
Y. Liu
A Linear Solution for Haplotype Perfect Phylogeny Problem (Extended Abstract)	173	(12)
Y. Liu
C.-Q. Zhang
In Silico Biology: Haplotype Inference, Linkage Disequilibrium Analysis, and Microarray-Based Gene Selection Techniques	185	(12)
T. Niu
The Role of Feature Redundancy in Tumor Classification	197	(12)
C. H. Ooi
M. Chetty
I. Gondal
Clustering of Eukaryotic Orthologs based on Sequence and Domain Similiarities using the Markov Graph-Flow Algorithm	209	(12)
H. Ozer
J. Chen
F. Zhang
B. Yuan
Rapid Drug Target Identification in Microbial Genomes--An in silico Approach with Special Reference to Salmonella Species	221	(8)
K. R. Sakharkar
C. Verma
M. K. Sakharkar
V. T. K. Chow
A Collimator Neural Network Model for the Classification of Genetic Data	229	(11)
M. S. B. Sehgal
I. Gondal
L. Dooley
Training Set Design for Pattern Discovery with Applications to Protein Motif Detection	240	(12)
Y. Sun
Z. Deng
G. Narasimhan
K. Mathee
Gene Selection by Weighted Fisher Criterion for Multiclass Prediction	252	(12)
J. Xuan
Y. Dong
J. Khan
R. Clarke
E. Hoffman
Y. Wang
Sequential Bifurcation Approach to Learning Protein Functional Classes	264	(12)
M. Q. Yang
O. K. Ersoy
J. Y. Yang
Identification of Contaminants in MALDI-TOF Proteomics Spectra via Data Mining	276	(9)
C.-Y. Yen
K. J. Cios
M. W. Duncan
Analysis of the Effects of Recombinant Human Erythropoietin (EPO) on Murine Bone Marrow Populations using Mixture Modeling Techniques	285	(12)
G. Zheng
R. Capocasale
B. Amegadzie
P. Bugelski
J. Lu
Discovery of Local Protein Sequence Motifs using Improved K-Means Clustering Technique	297	(10)
W. Zhong
G. Altun
R. Harrison
P. C. Tai
Y. Pan
3. Biomolecular Sequence and Structure Analysis
Predicting and Characterizing Metal-Binding Sites using Support Vector Machines	307	(12)
L. Bobadilla
F. Nino
G. Narasimhan
MTMM---A Matlab Toolbox for Macromolecular Modeling	319	(10)
F. Cui
T. Bibi
Z. Wu
Stabbing Balls and Simplifying Proteins	329	(12)
O. Daescu
J. Luo
Step-Wise Mutations of mRNA Sequences Lead to Progressive Changes in Calculated Folding Free Energies	341	(10)
D. Digby
W. Seffens
Aligning Sequences with Non-Affine Gap Penalty: Plains Algorithm, A Practical Implementation, and Its Biological Applications in Comparative Genomics	351	(12)
O. Gill
Y. Zhou
B. Mishra
Using the Length Constraints of Helix to Evaluate Protein Secondary Structure Prediction for Helix	363	(10)
J. He
Y. Lu
An Algorithm for Finding Similarities in Protein Active Sites	373	(7)
K. Kupas
A. Ultsch
G. Klebe
Parallel Tempering in Rosetta Practice	380	(10)
Y. Li
C. E. M. Strauss
A. Gorin
An Application of Association Rule Mining to HLA-A*0201 Epitope Prediction	390	(12)
T. Milledge
G. Zheng
G. Narasimhan
A Two-Way Searching Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry	402	(12)
J. H. Oh
Y. B. Kim
J. Gao
An Algorithm for Determining Glycan Structures from MS/MS Spectra	414	(12)
B. Shan
K. Zhang
B. Ma
C. Zhang
G. Lajoie
Counting and Enumeration of Self-Assembly Pathways for Symmetric Macromolecular Structures	426	(11)
M. Sitharam
M. Bona
Improving Multiple Whole Genomes Alignment by Considering Rearrangement	437	(10)
J. Yang
J. S. Deogun
A Filtering Approach to Splice Site Predictions in Human Genes	447	(12)
K. Yoon
S. Kwek
The Construction of Structural Templates for the Modeling of Conserved Protein Domains	459	(14)
F. Zhang
J. Chen
Z. Liu
B. Yuan
4. Symmetry in Sequences
Applications of Hyper Genetic Code to Bioinformatics	473	(9)
M. A. Jimenez-Montano
A Dodecahedron-Based Model of Spatial Representation of the Canonical Set of Amino Acids	482	(12)
V. A. Karasev
V. V. Luchinin
V. E. Stefanov
Molecular Mappings: Group Theory, Coding Theory, and the Emergence of Replication	494	(8)
D. A. MacDonaill
Symmetry and Information in the Genetic Code	502	(10)
T. Negadi
The Rules of Degeneracy and Segregations in Genetic Codes--The Chronocyclic Conception and Parallels with Mendel's Laws	512	(21)
S. V. Petoukhov
Symbolic Coding of Amino Acid and Nucleotide Properties	533	(11)
N. Stambuk
P. Konjevoda
N. Gotovac
Analyzing Patterns of Tripeptides using Statistical Approach and Neural Network Paradigms	544	(10)
R. Szabo
M. He
E. Burnham
J. Jurani
Molecular Versus Atomic Information Logic behind the Genetic Coding Contents Constrained by Two Evolutionary Axes and the Fibonacci-Lucas Sequence	554	(11)
C. M. Yang
5. Signal Processing, Image Processing and Visualization
Use of EEG Recordings as Valid Measures of Kinesthetic and Visual Imagery Ability	565	(11)
J. G. Cremades
M. Tito
M. Adjouadi
A. Barreto
The Merits of the Third Dimension for Visual Analysis of Multiple Anatomy Ontologies	576	(12)
A.-S. Dadzie
A. Burger
Localization of Brain Activation through Integration of Optical Topography and Magnetic Resonance Imaging	588	(12)
M. Mourad
M. Adjouadi
I. Yaylali
A Distributed Multimedia Database Visualization Within an Immersive Environment for Bioinformatics	600	(13)
P.-E. Gros
N. Ferey
J. Herisson
R. Gherbi
Author Index	613