VOLUME 1 - Contents
1) PREBIOTIC CHEMISTRY ON THE PRIMITIVE EARTH
Stanley L. Miller and H. James Cleaves
2) PREBIOTIC EVOLUTION AND THE ORIGIN OF LIFE: IS A SYSTEM-
LEVEL UNDERSTANDING FEASIBLE?
Antonio Lazcano
3) SHOTGUN FRAGMENT ASSEMBLY
Granger Sutton and Ian Dew
4) GENE FINDING
John Besemer and Mark Borodovsky
5) LOCAL SEQUENCE SIMILARITIES
Temple F. Smith
6) COMPLETE PROKARYOTIC GENOMES: READING AND
COMPREHENSION
Michael Y. Galperin and Eugene V. Koonin
7) PROTEIN STRUCTURE PREDICTION
Jeffrey Skolnick and Yang Zhang
8) DNA-PROTEIN INTERACTIONS
Gary D. Stormo
9) SOME COMPUTATIONAL PROBLEMS ASSOCIATED WITH
HORIZONTAL GENE TRANSFER
Michael Syvanen
10) NONCODING RNA AND RNA REGULATORY NETWORKS IN THE
SYSTEMS BIOLOGY OF ANIMALS
John S. Mattick
Library of Congress Subject Headings for this publication:
Computational biology.
Genomics.
Bioinformatics.
Genomics.
Computational Biology.
Models, Genetic.
Systems Biology.
Volume II
Contents
1. Mass Spectrometry in Systems Biology 3 , Cristian I. Ruse & John R. Yates III
2. Mathematical Modeling and Optimization Methods for De Novo Protein Design 42 , C. A. Floudas & H. K. Fung
3. Molecular Simulation and Systems Biology 67 , William C. Swope, Jed W. Pitera, & Robert S. Germain
4. Global Gene Expression Assays: Quantitative Noise Analysis 103 , G. A. Held, Gustavo Stolovitzky, & Yuhai Tu
5. Mapping the Genotype-Phenotype Relationship in Cellular Signaling Networks: Building Bridges Over the Unknown 137 , Jason A. Papin, Erwin P. Gianchandani, & Shankar Subramaniam
6. Integrating Innate Immunity into a Global "Systems" Context: The Complement Paradigm Shift 169 , Dimitrios Mastellos & John D. Lambris
7. Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications 193 , Sang Yup Lee, Dong-Yup Lee, Tae Yong Kim, Byung Hun Kim, & Sang Jun Lee
8. Genome-Scale Models of Metabolic and Regulatory Networks 232 , Markus J. Herrgard & Bernhard O. Palsson
9. Biophysical Models of the Cardiovascular System 265 , Raimond L. Winslow, Joseph. L. Greenstein, & Patrick A. Helm
10. Embryonic Stem Cells as a Module for Systems Biology 297 , Andrew M. Thomson, Paul Robson, Huck Hui Ng, Hasan H. Otu, & Bing Lim
Index 319