Handbook of Research on Systems Biology Applications in Medicine

1.	Pathway Biology Approach to Medicine
	Pages 1-10
	Peter Ghazal (University of Edinburgh Medical School, Scotland, and Centre for Systems Biology at Edinburgh, Scotland)

2.	Systems and Control Theory for Medical Systems Biology
	Pages 11-26
	Peter Wellstead (The Hamilton Institute, National University of Maynooth, Ireland) Sree Sreenath (Case Systems Biology Initiative, Case Western Reserve University, USA) Kwang-Hyun Cho (Korea Advanced Institute of Science and Technology (KAIST), Kor)

3.	Mathematical Description of Time Delays in Pathways Cross Talk
	Pages 27-73
	S. Nikolov (Institute of Mechanics and Biomechanics, Bulgaria)

4.	Deterministic Modeling in Medicine
	Pages 74-96
	Elisabeth Maschke-Dutz (Max Planck Institute for Molecular Genetics, Germany)

5.	Synthetic Biology as a Proof of Systems Biology
	Pages 97-115
	Andrew Kuznetsov (Freiburg University, Germany)

6.	Computational Models for the Analysis of Modern Biological Data
	Pages 117-125
	Tuan Pham (James Cook University, Australia)

7.	Computer Aided Knowledge Discovery in Biomedicine
	Pages 126-141
	Vanathi Gopalakrishnan (University of Pittsburgh, USA)

8.	Function and Homology of Proteins Similar in Sequence
	Pages 143-166
	Thomas Meinel (Max Planck Institute for Molecular Genetics, Germany)

9.	Computational Methods for the Prediction of GPCRs Coupling Selectivity
	Pages 167-181
	Nikolaos Sgourakis (Rensselaer Polytechnic Institute, USA) Pantelis Bagos (University of Central Greece, and University of Athens, Greece) Stavros Hamodrakas (University of Athens, Greece)

10.	Bacterial ß-Barrel Outer Membrane Proteins
	Pages 182-207
	Pantelis Bagos (University of Central Greece, and University of Athens, Greece) Stavros Hamodrakas (University of Athens, Greece)

11.	Clustering Methods for Gene-Expression Data
	Pages 209-220
	L.K. Flack (University of Queensland, Australia)

12.	Uncovering Fine Structure in Gene Expression Profile by Maximum Entropy Modeling of cDNA Microarray Images and Kernel Density Methods
	Pages 221-238
	George Sakellaropoulos (University of Patras, Greece) Antonis Daskalakis (University of Patras, Greece) George Nikiforidis (University of Patras, Greece) Christos Argyropoulos (University of Pittsburgh Medical Center, USA)

13.	Gene Expression Profiling with the BeadArrayTM Platform
	Pages 239-250
	Wasco Wruck (Max Planck Institute for Molecular Genetics, Germany)

14.	The Affymetrix GeneChip® Microarray Platform
	Pages 251-261
	Djork-Arné Clevert (Charité Universitaetsmedizin Berlin, Germany and Johannes Kepler University Linz, Austria) Axel Rasche (Max-Planck-Institute for Molecular Genetics, Germany)

15.	Alternative Isoform Detection Using Exon Arrays
	Pages 262-277
	Jacek Majewski (McGill University and Genome Québec Innovation Centre, Canada)

16.	Gene Expression in Microbial Systems for Growth and Metabolism
	Pages 278-290
	Prerak Desai (Utah State University, USA)

17.	Alternative Splicing and Disease
	Pages 291-310
	Heike Stier (Charité Universitaetsmedizin Berlin, Germany)

18.	Mathematical Modeling of the Aging Process
	Pages 312-330
	Axel Kowald (Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Germany)

19.	The Sebaceous Gland
	Pages 331-337
	Evgenia Makrantonaki (Dessau Medical Center, Germany and Charité Universitaetsmedizin Berlin, Germany)

20.	Systems Biology Applied to Cancer Research
	Pages 339-353
	R. Seigneuric (GROW Research Institute, University of Maastricht, The Netherlands) N.A.W. van Riel (Eindhoven University of Technology, The Netherlands) M.H.W. Starmans (GROW Research Institute, University of Maastricht, The Netherlands) A. van Erk (University)

21.	Systems Biology Strategies in Studies of Energy Homeostasis In Vivo
	Pages 354-360
	Matej Orešic (VTT Technical Research Centre of Finland, Finland) Antonio Vidal-Puig (Institute of Metabolic Science, Addenbrooke’s Hospital, UK)

22.	Approaching Type 2 Diabetes Mellitus by Systems Biology
	Pages 361-376
	Axel Rasche (Max-Planck-Institute for Molecular Genetics, Germany)

23.	Systems Biology and Infectious Diseases
	Pages 377-402
	Alia Benkahla (Institut Pasteur de Tunis, Tunisia) Lamia Guizani-Tabbane (Institut Pasteur de Tunis, Tunisia) Ines Abdeljaoued-Tej (ESSAI-UR Algorithmes et Structures, Tunisia) Slimane Miled (Institut Pasteur de Tunis, Tunisia and ENIT-LAMSIN, Tunisia) Koussay Dellagi (Institut Pasteur de Tu)

24.	Systems Biology of Human-Pathogenic Fungi
	Pages 403-421
	Daniela Albrecht (Leibniz Institute for Natural Product Research and Infection Biology -Hans-Knoell-Institute (HKI), Germany) Reinhard Guthke (Leibniz Institute for Natural Product Research and Infection Biology -Hans-Knoell-Institute)

25.	Development of Specific Gamma Secretase Inhibitors
	Pages 423-437
	Jessica Ahmed (Charité Universitaetsmedizin Berlin, Germany)

26.	In Machina Systems for the Rational De Novo Peptide Design
	Pages 438-457
	Paul Wrede (Charité Universitaetsmedizin Berlin, Germany)

27.	Applications of Metabolic Flux Balancing in Medicine
	Pages 458-474
	Ferda Mavituna (The University of Manchester, UK) Raul Munoz-Hernandez (The University of Manchester, UK) Ana de Carvalho Lima Lobato (Federal University of Rio Grande do Norte, Brazil, and Potiguar University, Brazil)

28.	Multi-Level Data Integration and Data Mining in Systems Biology
	Pages 476-496
	Roberta Alfieri (CNR - Institute for Biomedical Technologies, Italy and CILEA, Italy) Luciano Milanesi (CNR - Institute for Biomedical Technologies, Italy)

29.	Methods for Reverse Engineering of Gene Regulatory Networks
	Pages 497-515
	Hendrik Hache (Max Planck Institute for Molecular Genetics, Germany)

30.	Data Integration for Regulatory Gene Module Discovery
	Pages 516-529
	Alok Mishra (Imperial College London, UK)

31.	Discrete Networks as a Suitable Approach for the Analysis of Genetic Regulation
	Pages 530-540
	Elizabeth Santiago-Cortés (Universidad Nacional Autónoma de México, Mexico)

32.	Investigating the Collective Behavior of Neural Networks
	Pages 541-555
	A. Maffezzoli (Politecnico di Milano, Italy)

33.	The System for Population Kinetics
	Pages 556-571
	Paolo Vicini (University of Washington, USA)

34.	Photosynthesis
	Pages 573-587
	Julia Adolphs (Freie Universität Berlin, Germany)

35.	Photodynamic Therapy
	Pages 588-642
	Michael Hamblin (Massachusetts General Hospital - Boston, USA)

36.	Modeling of Porphyrin Metabolism with PyBioS
	Pages 643-654
	Andriani Daskalaki (Max Planck Institute for Molecular Genetics, Germany)

37.	Interference Microscopy for Cellular Studies
	Pages 656-672
	Alexey Brazhe (Technical University of Denmark, Denmark and Moscow State University, Russia) Nadezda Brazhe (Technical University of Denmark, Denmark and Moscow State University, Russia) Alexey Pavlov (Saratov State University, Russia) Georgy Maksimov (Moscow Sta)

38.	Fluorescence Imaging of Mitochondrial Long-Term Depolarization in Cancer Cells Exposed to Heat-Stress
	Pages 673-692
	Cathrin Dressler (Laser- und Medizin-Technologie GmbH, Berlin, Germany) Olaf Minet (Charité Universitaetsmedizin Berlin, Germany) Urszula Zabarylo (Charité Universitaetsmedizin Berlin, Germany) Jürgen Beuthan (Charité Universitaetsmedizin Berlin, Germany)

39.	Protein Interactions and Diseases
	Pages 694-713
	Athina Theodosiou (Biomedical Research Foundation of the Academy of Athens, Greece) Charalampos Moschopoulos (Biomedical Research Foundation of the Academy of Athens, Greece) Marc Baumann (Biomedicum, Helsinki University, Finland) Sophia Kossida (Biomedical Research Foundati)

40.	The Breadth and Depth of BioMedical Molecular Networks
	Pages 714-729
	Bernard de Bono (European Bioinformatics Institute, UK and University of Malta, Malta)

41.	Entropy and Thermodynamics in Biomolecular Simulation
	Pages 731-758
	Jorge Numata (Freie Universität Berlin, Germany)

42.	Model Development and Decomposition in Physiology
	Pages 759-797
	Isabel Reinecke (Zuse Institute Berlin, Germany) Peter Deuflhard (Zuse Institute Berlin, Germany)

43.	A Pandemic Avian Influenza Mathematical Model
	Pages 798-808
	Mohamed Derouich (Faculté des sciences Oujda-Morocco, Morocco)

44.	Dengue Fever
	Pages 809-824
	Mohamed Derouich (Faculté des sciences Oujda-Morocco, Morocco)

45.	Automated Image Analysis Approaches in Histopathology
	Pages 826-849
	Ross Foley (University College Dublin (UCD), Ireland)