Systems Biology
Description
Each chapter represents a valuable introduction to one specific branch of systems biology, while also including the current state of the art and pointers to future directions. Following different methods for the integrative analysis of omics data, the book goes on to describe techniques that allow for the direct quantification of carbon fluxes in large metabolic networks, including the use of 13C labelled substrates and genome-scale metabolic models. The latter is explained on the basis of the model organism Escherichia coli as well as the human metabolism. Subsequently, the authors deal with the application of such techniques to human health and cell factory engineering, with a focus on recent progress in building genome-scale models and regulatory networks. They highlight the importance of such information for specific biological processes, including the ageing of cells, the immune system and organogenesis. The book concludes with a summary of recent advances in genome editing, which have allowed for precise genetic modifications, even with the dynamic control of gene expression.
This is part of the Advances Biotechnology series, covering all pertinent aspects of the field with each volume prepared by eminent scientists who are experts on the topic in question.
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Persons
Stefan Hohmann is Head of the Department of Biology and Biological Engineering at Chalmers University (Sweden). He studied biology and microbiology at the Technische Universität Darmstadt (Germany), where he received his PhD in 1987 and became professor in 1993. He held positions as visiting professor at the Katholieke Universiteit Leuven (Belgium) and the University of the Orange Free State (South Africa), before joining the University of Gothenburg in 1999 as professor, a position he hold until his change to Chalmers University in 2015. Stefan Hohmann serves as chairman of several committees and is the Swedish representative at the European Molecular Biology Laboratory (EMBL) Research Council.
Sang Yup Lee is Distinguished Professor at the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST). He is currently the Director of the Center for Systems and Synthetic Biotechnology, Director of the BioProcess Engineering Research Center, and Director of the Bioinformatics Research Center. He received numerous awards, including the National Order of Merit, the Merck Metabolic Engineering Award and the Elmer Gaden Award. Lee is the Editor-in-Chief of the Biotechnology Journal and Associate Editor and board member of numerous other journals. Lee is currently serving as a member of Presidential Advisory Committee on Science and Technology (Korea).
Professor Gregory Stephanopoulos is the W. H. Dow Professor of Chemical Engineering at the Massachusetts Institute of Technology (MIT, USA) and Director of the MIT Metabolic Engineering Laboratory. He is also Instructor of Bioengineering at Harvard Medical School (since 1997). He has been recognized by numerous awards from the American Institute of Chemical Engineers (AIChE) (Wilhelm, Walker and Founders awards), American Chemical Society (ACS), Society of industrial Microbiology (SIM), BIO (Washington Carver Award), the John Fritz Medal of the American Association of Engineering Societies, and others. In 2003 he was elected member of the National Academy of Engineering (USA) and in 2014 President of AIChE.
Content
2. 13C Flux Analysis in Biotechnology and Medicine
3. Metabolic Modeling for Design of Cell Factories
4. Genome-Scale Metabolic Modeling and in silico Strain Design of Escherichia coli
5. Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Reconstruction
6. Computational Modeling of Microbial Communities
7. Drug Targeting of the Human Microbiome
8. Towards Genome-Scale Models of Signal Transduction Networks
9. Systems Biology of Ageing
10. Modeling the Dynamics of the Immune Response
11. Dynamics of Signal Transduction in Single Cells Quantified by Microscopy
12. Image-Based in silico Models of Organogenesis
13. Progress Towards Quantitative Design Principles of Multicellular Systems
14. Precision Genome Editing for Systems Biology - A Temporal Perspective
List of Contributors
Elena Abad
Universitat Pompeu Fabra
Departament de Ciències Experimentals i de la Salut
Barcelona Biomedical Research Park
Dr. Aiguader 88
08003 Barcelona
Spain
and
IDIBAPS-Hospital Clínic
Center for Neuroimmunology
Barcelona
Spain
Johannes Borgqvist
Chalmers University of Technology and the University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
Siu H. J. Chan
The Pennsylvania State University
Department of Chemical Engineering
112 Fenske Laboratory
University Park, PA 16802
USA
Matthew W. Chang
National University of Singapore
Yong Loo Lin School of Medicine, Department of Biochemistry
8 Medical Drive
Singapore 117597
Singapore
and
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
Yi Ern Cheah
Vanderbilt University
Department of Chemical and Biomolecular Engineering
Nashville, TN 37235
USA
Marija Cvijovic
Chalmers University of Technology and University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
Riccardo Dainese
Chalmers University of Technology and the University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
and
École Polytechnique Fédérale de Lausanne (EPFL)
Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences
Lausanne
Switzerland
Bonnie V. Dougherty
University of Virginia
Department of Biomedical Engineering
415 Lane Road
Charlottesville, VA 22908
USA
Jee L. Foo
National University of Singapore
Yong Loo Lin School of Medicine, Department of Biochemistry
8 Medical Drive
Singapore 117597
Singapore
and
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
Jordi García-Ojalvo
Universitat Pompeu Fabra
Departament de Ciències Experimentals i de la Salut
Barcelona Biomedical Research Park
Dr. Aiguader 88
08003 Barcelona
Spain
Lada Georgieva
ETH Zurich
Department of Biosystems, Science and Engineering (D-BSSE), Swiss Institute of Bioinformatics (SIB)
Mattenstraße 26
4058 Basel
Switzerland
Harold F. Gómez
ETH Zurich
Department of Biosystems, Science and Engineering (D-BSSE), Swiss Institute of Bioinformatics (SIB)
Mattenstraße 26
4058 Basel
Switzerland
Diego R. Gomez-Alvarez
Chalmers University of Technology and University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
Sanjan T. P. Gupta
University of Wisconsin-Madison
Department of Chemical and Biological Engineering
3639 Engineering Hall
1415 Engineering Drive
Madison, WI 53706
USA
and
University of Wisconsin-Madison
Great Lakes Bioenergy Research Center
Madison, WI
USA
Clinton M. Hasenour
Vanderbilt University
Department of Chemical and Biomolecular Engineering
Nashville, TN 37235
USA
Dagmar Iber
ETH Zurich
Department of Biosystems, Science and Engineering (D-BSSE), Swiss Institute of Bioinformatics (SIB)
Mattenstraße 26
4058 Basel
Switzerland
Edda Klipp
Humboldt-Universität zu Berlin
Institute of Biology
Invalidenstr. 42
10115 Berlin
Germany
Marcus Krantz
Humboldt-Universität zu Berlin
Institute of Biology
Invalidenstr. 42
10115 Berlin
Germany
Erik Kristiansson
Chalmers University of Technology/University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
Prashant Kumar
University of Wisconsin-Madison
Department of Chemical and Biological Engineering
3639 Engineering Hall
1415 Engineering Drive
Madison, WI 53706
USA
Meiyappan Lakshmanan
Agency for Science, Technology and Research (A*STAR)
Bioprocessing Technology Institute
20 Biopolis Way, #06-01, Centros
Singapore 138668
Singapore
Dong-Yup Lee
Agency for Science, Technology and Research (A*STAR)
Bioprocessing Technology Institute
20 Biopolis Way, #06-01, Centros
Singapore 138668
Singapore
and
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
and
National University of Singapore
Department of Chemical and Biomolecular Engineering
4 Engineering Drive 4
Singapore 117585
Singapore
Na-Rae Lee
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
Rune Linding
University of Copenhagen (UCPH)
Biotech Research and Innovation Centre (BRIC)
Ole Maaløes Vej 5, 4
2200 Copenhagen
Denmark
Hua Ling
National University of Singapore
Yong Loo Lin School of Medicine, Department of Biochemistry
8 Medical Drive
Singapore 117597
Singapore
and
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
Timo Lubitz
Humboldt-Universität zu Berlin
Institute of Biology
Invalidenstr. 42
10115 Berlin
Germany
Min Ma
University of Lausanne
Department of Fundamental Microbiology
Biophore building
1015 Lausanne
Switzerland
Costas D. Maranas
The Pennsylvania State University
Department of Chemical Engineering
112 Fenske Laboratory
University Park, PA 16802
USA
Odysse Michos
ETH Zurich
Department of Biosystems, Science and Engineering (D-BSSE), Swiss Institute of Bioinformatics (SIB)
Mattenstraße 26
4058 Basel
Switzerland
Nadim Mira
University of Lausanne
Department of Fundamental Microbiology
Biophore building
1015 Lausanne
Switzerland
Thomas J. Moutinho Jr.
University of Virginia
Department of Biomedical Engineering
415 Lane Road
Charlottesville, VA 22908
USA
Ulrike Münzner
Humboldt-Universität zu Berlin
Institute of Biology
Invalidenstr. 42
10115 Berlin
Germany
Eduardo P. Olimpio
Delft University of Technology
Department of Bionanoscience, Kavli Institute of Nanoscience
Lorentzweg 1, Building 22
2628 CJ Delft
The Netherlands
Tobias Österlund
Chalmers University of Technology/University of Gothenburg
Department of Mathematical Sciences
Chalmers tvärgata 3
412 96 Gothenburg
Sweden
Jason Papin
University of Virginia
Department of Biomedical Engineering
415 Lane Road
Charlottesville, VA 22908
USA
Serge Pelet
University of Lausanne
Department of Fundamental Microbiology
Biophore building
1015 Lausanne
Switzerland
Jennifer L. Reed
University of Wisconsin-Madison
Department of Chemical and Biological Engineering
3639 Engineering Hall
1415 Engineering Drive
Madison, WI 53706
USA
and
University of Wisconsin-Madison
Great Lakes Bioenergy Research Center
Madison, WI
USA
Gourvendu Saxena
National University of Singapore
NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
and
National University of Singapore
Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Life Sciences Institute
28 Medical Drive
Singapore 117456
Singapore
and
National University of Singapore
Faculty of Science, Department of Biological...
