New Frontiers of Network Analysis in Systems Biology

1. Front Matter

   Pages i-x

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2. Gene Expression Profiling and Regulatory Networks in Single Cells

   • Fumio Arai, Kentaro Hosokawa, Yoshiko Matsumoto, Hirofumi Toyama, Toshio Suda

   Pages 1-13

3. Cell Fate Regulatory Networks

   • Sonya J. Ridden, Ben D. MacArthur

   Pages 15-29

4. Noise in Regulatory Networks

   • Srinandan Dasmahapatra

   Pages 31-58

5. Generalised Modelling in Systems Biology

   • Thilo Gross

   Pages 59-75

6. Relative Quantification Mass Spectrometry Using iTRAQ Isobaric Tags

   • Richard D. Unwin, Emma Carrick, Anthony D. Whetton

   Pages 77-95

7. Deciphering Protein Complexes and Protein Interaction Networks for Stem Cell Pluripotency

   • Jianlong Wang

   Pages 97-118

8. Omics Era in Stem Cell Research: Data Integration of Multi-regulatory Layers

   • Ana Sevilla, Benjamin Trinite, Ihor R. Lemischka

   Pages 119-137

9. High Throughput Affinity Purification and Mass Spectrometry to Determine Protein Complex Interactions

   • Anna Malovannaya, Rainer B. Lanz, Bert W. O’Malley, Jun Qin

   Pages 139-159

10. Network Pharmacology to Aid the Drug Discovery Process

    • Ruth Dannenfelser, Huilei Xu, Catherine Raimond, Avi Ma’ayan

    Pages 161-172

11. What Can Networks Do for You?

    • Bernhard M. Schuldt, Franz-Josef Müller, Andreas A. Schuppert

    Pages 173-194

12. Back Matter

    Pages 195-199

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The rapidly developing field of systems biology is influencing many aspects of biological research and is expected to transform biomedicine. Some emerging offshoots and specialized branches in systems biology are receiving particular attention and are becoming highly active areas of research. This collection of invited reviews describes some of the latest cutting-edge experimental and computational advances in these emerging sub-fields of systems biology. In particular, this collection focuses on the study of mammalian embryonic stem cells; new technologies involving mass-spectrometry proteomics; single cell measurements; methods for modeling complex stochastic systems; network-based classification algorithms; and the revolutionary emerging field of systems pharmacology.

• Gene Set Enrichment Analysis
• Networks Analysis
• Proteomics and Phosphoproteomics
• Systems Biology
• Proteomics
• gene expression

• Pharmacology & Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, New York, USA

  Avi Ma'ayan

• Institute For Life Sciences, Southampton University, Southampton, United Kingdom

  Ben D. MacArthur

Avi Ma’ayan, Ph.D., is an Assistant Professor in the Department of Pharmacology and Systems Therapeutics at Mount Sinai School of Medicine, New York, NY, USA. His interests are in applying graph theory, machine learning, dimensionality reduction, dynamical modeling, and visualization methods for integrating “omics” datasets collected from mammalian sources to better understand biological regulation on a global scale.

Ben D. MacArthur, Ph.D., is a Lecturer in Mathematics at the Life Science Interface in the Schools of Mathematics and Medicine at the University of Southampton, UK. His interests are in applying mathematical methods to problems in cell and molecular biology including modeling of cell fate, analysis of the structure and function of biological regulatory networks, and high throughput data analysis and bioinformatics.

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