Systems Medicine

480 Pages·2016·12.375 MB·English

by  Ulf Schmitz, Olaf Wolkenhauer (eds.)

Methods in
Molecular Biology 1386
Ulf Schmitz
Olaf Wolkenhauer Editors
Systems
Medicine
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
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Systems Medicine
Edited by
Ulf Schmitz
Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
Olaf Wolkenhauer
Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
Editors
Ulf Schmitz Olaf Wolkenhauer
Department of Systems Biology & Bioinformatics Department of Systems Biology & Bioinformatics
University of Rostock University of Rostock
Rostock, Germany Rostock , Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3282-5 ISBN 978-1-4939-3283-2 (eBook)
DOI 10.1007/978-1-4939-3283-2
Library of Congress Control Number: 2015956342
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Prefa ce
It is now more than a decade ago since systems biology was celebrated as a new promising
approach that can predict the behavior of cellular systems through mathematical modeling
and simulation. It was the hope of many that, once systems biology helped deciphering
mechanisms underlying disease emergence and progression, it is only a short path toward
the design of novel, more successful therapeutic approaches.
Although technological advancements allow the generation of ever more detailed snap-
shots of life across multiple levels of temporal and spatial scales, and despite a wealth of new
insights on how life is organized, it is a long way before we are able to translate this improved
understanding to achieve a sustainable impact on clinical practice.
To guide this path, there is a need to survey the diverse approaches, the multitude of
methodologies, and the myriad of tools that should and will be integrated into customized
protocols and workfl ows for the reliable prognoses of disease outbreak and course, for the
identifi cation of therapeutic targets, the development of targeted therapies for individual
patients, and for monitoring therapy success and patient well-being.
This book presents trends, initiatives, and recent developments in this emerging fi eld
called systems medicine, which has the goal of fi nding solutions to the challenges described
above. We are glad that leading experts have contributed to this fi rst book on systems medi-
cine and provided their insights into the state of the art in the fi eld.
Structure of the Book
This book is structured in four parts. The fi rst part, “A Road Map Toward Systems Medicine,”
consists of six chapters that outline the fi eld of systems medicine by defi ning the terminology
and describing how established computational methods from bioinformatics and systems
biology can be taken forward to an integrative systems medicine approach. One chapter
describes the necessity for redefi ning training curricula for medical and computational stu-
dents, and in two chapters the impact is discussed that a systems medicine approach possibly
has on handling diseases and patients and on the pharmaceutical industry.
The second part of the book, “Opinions and Perspectives,” provides an outlook on the role
that systems medicine may or should play in various medical fi elds like oncology, neurology, the
study of lung diseases, immune-related diseases and therapies, and infectious diseases.
In Part III case studies are presented that demonstrate different facets of the systems
medicine approach in action to study, e.g., the human metabolism, chronic obstructive
pulmonary disease, transcriptomics, and regenerative stem cell medicine. These chapters
nicely illustrate the interdisciplinary combination of computational methods with wet lab
experiments.
The fourth part of the book, “Tools and Methodologies,” contains four chapters that
introduce tools, resources, and methodologies from bioinformatics and systems biology
and shows how to apply these in a systems medicine project.
Rostock, Germany U lf S chmitz
O laf Wolkenhauer
v

Acknowledgements
We thank all authors for fi nding the time in their busy schedules and making the effort
contributing to this book with their highly engaging chapters.
vii

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x i
PART I A ROAD MAP TOWARD SYSTEMS MEDICINE
1 Systems Medicine: Sketching the Landscape . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Marc K irschner
2 Taking Bioinformatics to Systems Medicine. . . . . . . . . . . . . . . . . . . . . . . . . . . 1 7
Antoine H. C. v an Kampen and Perry D. Moerland
3 S ystems Medicine: The Future of Medical Genomics, Healthcare,
and Wellness. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Mansoor Saqi , J ohann Pellet , Irina Roznovat , A lexander Mazein ,
Stéphane Ballereau , B ertrand D e Meulder , and Charles Auffray
4 N ext-Generation Pathology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1
Peter D . C aie and David J . H arrison
5 T raining in Systems Approaches for the Next Generation
of Life Scientists and Medical Doctors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Damjana Rozman , J ure Acimovic , and Bernd S chmeck
6 S ystems Medicine in Pharmaceutical Research and Development. . . . . . . . . . . 8 7
Lars K uepfer and Andreas A . Schuppert
PART II OPINIONS AND PERSEPECTIVES
7 Systems Medicine and Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 07
Ruth Bowness
8 Systems Medicine for Lung Diseases: Phenotypes and Precision Medicine
in Cancer, Infection, and Allergy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Bernd Schmeck , W ilhelm Bertrams , Xin L ai , and Julio Vera
9 Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics
and Informatics to Become Quantitative and Predictive. . . . . . . . . . . . . . . . . . 135
Martin Eberhardt , X in L ai , N amrata T omar , S hailendra G upta ,
Bernd Schmeck , A lexander S teinkasserer , G erold S chuler , and Julio Vera
10 S ystems Medicine in Oncology: Signaling Network Modeling
and New-Generation Decision-Support Systems . . . . . . . . . . . . . . . . . . . . . . . 181
Silvio P arodi , Giuseppe Riccardi , N icoletta C astagnino , L orenzo T ortolina ,
M assimo Maffei , Gabriele Z oppoli , A lessio N encioni , A lberto Ballestrero ,
and Franco P atrone
11 Neurological Diseases from a Systems Medicine Point of View . . . . . . . . . . . . 2 21
Marek Ostaszewski , Alexander S kupin , and R udi B alling
ix