Table Of ContentSYSTEMS AND
COMPUTATIONAL BIOLOGY
– MOLECULAR AND
CELLULAR EXPERIMENTAL
SYSTEMS
Edited by Ning-Sun Yang
Systems and Computational Biology – Molecular and Cellular Experimental
Systems
Edited by Ning-Sun Yang
Published by InTech
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First published September, 2011
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Systems and Computational Biology – Molecular and Cellular Experimental Systems,
Edited by Ning-Sun Yang
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ISBN 978-953-307-280-7
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Contents
Preface IX
Part 1 Approaches for Studying
Genomes, Transcriptomes, and Proteomes 1
Chapter 1 Gene Expression Analysis Using RNA-Seq
from Organisms Lacking Substantial Genomic Resources 3
Yingjia Shen, Tzintzuni Garcia and Ronald B. Walter
Chapter 2 Linguistic Approaches for
Annotation, Visualization and Comparison
of Prokaryotic Genomes and Environmental Sequences 27
Oliver Bezuidt, Hamilton Ganesan, Phillip Labuschange,
Warren Emmett, Rian Pierneef and Oleg N. Reva
Chapter 3 On the Structural Characteristics of the Protein
Active Sites and Their Relation to Thermal Fluctuations 53
Shao-Wei Huang and Jenn-Kang Hwang
Chapter 4 Decomposition of Intramolecular
Interactions Between Amino-Acids in
Globular Proteins - A Consequence for Structural
Classes of Proteins and Methods of Their Classification 69
Boris Fackovec and Jiri Vondrasek
Chapter 5 The Prediction and Analysis of
Inter- and Intra-Species Protein-Protein Interaction 83
Theresa Tsun-Hui Tsao, Chen-Hsiung Chan,
Chi-Ying F. Huang and Sheng-An Lee
Chapter 6 Computational Prediction of
Post-Translational Modification Sites in Proteins 105
Yu Xue, Zexian Liu, Jun Cao and Jian Ren
Chapter 7 Protein Networks: Generation,
Structural Analysis and Exploitation 125
Enrico M. Bucci, Massimo Natale and Alice Poli
VI Contents
Part 2 Gene Regulation, Networking and
Signaling in and Between Genomes 147
Chapter 8 Prediction and Analysis of
Gene Regulatory Networks in Prokaryotic Genomes 149
Richard Münch, Johannes Klein and Dieter Jahn
Chapter 9 Mining Host-Pathogen Interactions 163
Dmitry Korkin, Thanh Thieu,
Sneha Joshi and Samantha Warren
Chapter 10 Prediction of Novel Pathway
Elements and Interactions Using Bayesian Networks 185
Andrew P. Hodges, Peter Woolf and Yongqun He ξ
Chapter 11 MicroRNA Identification
Based on Bioinformatics Approaches 205
Malik Yousef, Naim Najami and Walid Khaleifa
Chapter 12 Motif Discovery with
Compact Approaches - Design and Applications 217
Cinzia Pizzi
Part 3 Omics-Based Molecular and Cellular
Experimental Systems - Examples and Applications 235
Chapter 13 Data Mining Pubmed Using
Natural Language Processing to
Generate the β-Catenin Biological Association Network 237
Fengming Lan, Xiao Yue, Lei Han, Peiyu Pu and Chunsheng Kang
Chapter 14 In Silico Identification of
Plant-Derived Antimicrobial Peptides 249
Maria Clara Pestana-Calsa and Tercilio Calsa Jr.
Chapter 15 Mining Effector Proteins in Phytopathogenic Fungi 273
Li Cheng-yun and Yang Jing
Chapter 16 Immuno-Modulatory Effects of
Phytomedicines Evaluated Using Omics Approaches 289
Shu-Yi Yin and Ning-Sun Yang
Chapter 17 High Content and Throughput Drug Discovery 315
Quin Wills
Preface
Immediately after the first drafts of the human genome sequence were reported almost
a decade ago, the importance of genomics and functional genomics studies became
well recognized across the broad disciplines of biological sciences research. The
initiatives of Leroy Hood and other pioneers on developing systems biology
approaches for evaluating or addressing global and integrated biological activities,
mechanisms, and network systems have motivated many of us, as bioscientists, to re-
examine or revisit a whole spectrum of our previous experimental findings or
observations in a much broader, link-seeking and cross-talk context. Soon thereafter,
these lines of research efforts generated interesting, fancy and sometimes misleading
new names for the now well-accepted “omics” research areas, including functional
genomics, (functional) proteomics, metabolomics, transcriptomics, glycomics,
lipidomics, and cellomics. It may be interesting for us to try to relate these “omics”
approaches to one of the oldest omics studies that we all may be quite familiar with,
and that is “economics”, in a way that all “omics” indeed seemed to have meant to
address the mechanisms/activities/constituents in a global, inter-connected and
regulated way or manner.
The advancement of a spectrum of technological methodologies and assay systems for
various omics studies has been literally astonishing, including next-generation DNA
sequencing platforms, whole transcriptome microarrays, micro-RNA arrays, various
protein chips, polysaccharide or glycomics arrays, advanced LC-MS/MS, GC-MS/MS,
MALDI-TOF, 2D-NMR, FT-IR, and other systems for proteome and metabolome
research and investigations on related molecular signaling and networking
bioactivities. Even more excitingly and encouragingly, many outstanding researchers
previously trained as mathematicians, information or computation scientists have
courageously re-educated themselves and turned into a new generation of
bioinformatics scientists. The collective achievements and breakthroughs made by our
colleagues have created a number of wonderful database systems which are now
routinely and extensively used by not only young but also “old” researchers. It is very
difficult to miss the overwhelming feeling and excitement of this new era in systems
biology and computational biology research.
It is now estimated, with good supporting evidence by omics information, that there
are approximately 25,000 genes in the human genome, about 45,000 total proteins in
the human proteome, and around 3000 species of primary and between 3000 and 6000
X Preface
species of secondary metabolites, respectively, in the human body fluid/tissue
metabolome. These numbers and their relative levels to each other are now helping us
to construct a more comprehensive and realistic view of human biology systems.
Likewise, but maybe to a lesser extent, various baseline omics databases on mouse,
fruit fly, Arabidopsis plant, yeast, and E. coli systems are being built to serve as model
systems for molecular, cellular and systems biology studies; these efforts are projected
to result in very interesting and important research findings in the coming years.
Good findings in a new research area may not necessarily translate quickly into good
or high-impact benefits pertaining to socio-economic needs, as may be witnessed now
by many of us with regard to research and development in omics science/technology.
To some of us, the new genes, novel protein functions, unique metabolite profiles or
PCA clusters, and their signaling systems that we have so far revealed seemed to have
yielded less than what we have previously (only some 5 to 10 years ago) expected, in
terms of new targets or strategies for drug or therapeutics development in medical
sciences, or for improvement of crop plants in agricultural science. Nonetheless, some
useful new tools for diagnosis and personalized medicine have been developed as a
result of genomics research. Recent reviews on this subject have helped us more
realistically and still optimistically to address such issues in a socially responsible
academic exercise. Therefore, whereas some “microarray” or “bioinformatics”
scientists among us may have been criticized as doing “cataloging research”, the
majority of us believe that we are sincerely exploring new scientific and technological
systems to benefit human health, human food and animal feed production, and
environmental protections. Indeed, we are humbled by the complexity, extent and
beauty of cross-talks in various biological systems; on the other hand, we are
becoming more educated and are able to start addressing honestly and skillfully the
various important issues concerning translational medicine, global agriculture, and the
environment.
I am very honored to serve as the editor of these two volumes on Systems and
Computational Biology: (I) Molecular and Cellular Experimental Systems, and (II)
Bioinformatics and Computational Modeling. I believe that we have collectively
contributed a series of high-quality research or review articles in a timely fashion to
this emerging research field of our scientific community.
I sincerely hope that our colleagues and readers worldwide will help us in future
similar efforts, by providing us feedback in the form of critical comments,
interdisciplinary ideas and innovative suggestions on our book chapters, as a way to
pay our high respect to the biological genomes on planet earth.
Dr. Ning-Sun Yang
Agricultural Biotechnology Research Center, Academia Sinica
Taiwan, R.O.C
