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Systems Biology Properties of Reconstructed Networks - Bernhard o. Palsson

Contents


1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2 Basic Concepts in Systems Biology . . . . . . . . . . . . . . . . . . . . . . . . 12
PART I. RECONSTRUCTION OF BIOCHEMICAL NETWORKS
3 Metabolic Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4 Transcriptional Regulatory Networks . . . . . . . . . . . . . . . . . . . . . . . 54
5 Signaling Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
PART II. MATHEMATICAL REPRESENTATION OF RECONSTRUCTED NETWORKS
6 Basic Features of the Stoichiometric Matrix . . . . . . . . . . . . . . . . . . .89
7 Topological Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
8 Fundamental Subspaces of S . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
9 The (Right) Null Space of S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
10 The Left Null Space of S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
11 The Row and Column Spaces of S . . . . . . . . . . . . . . . . . . . . . . . . 170

PART III. CAPABILITIES OF RECONSTRUCTED NETWORKS
12 Dual Causality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
13 Properties of Solution Spaces . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
14 Sampling Solution Spaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
15 Finding Functional States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
16 Parametric Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
17 Epilogue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282


APPENDIX A. Nomenclature and Abbreviations 287
APPENDIX B. E. coli Core Metabolic Network 294

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