Encyclopedia of Systems Biology - Home - Springer978-1-4419-9863...Werner Dubitzky † Olaf...

Encyclopedia of Systems Biology

Werner Dubitzky • Olaf WolkenhauerKwang-Hyun Cho • Hiroki YokotaEditors

Encyclopedia ofSystems Biology

With 830 Figures and 148 Tables

EditorsWerner DubitzkyBiomedical Sciences Research InstituteUniversity of UlsterColeraine, UK

Olaf WolkenhauerDepartment of Computer ScienceUniversity of RostockRostock, Germany

Kwang-Hyun ChoDepartment of Bio and Brain EngineeringKorea Advanced Institute of Science andTechnology (KAIST)Daejeon, Republic of Korea

Hiroki YokotaDepartment of Biomedical EngineeringRensselaer Polytechnic InstituteTroy, NY, USA

ISBN 978-1-4419-9862-0 ISBN 978-1-4419-9863-7 (eBook)ISBN 978-1-4419-9864-4 (Print and electronic bundle)DOI 10.1007/ 978-1-4419-9863-7Springer New York Heidelberg Dordrecht London

Library of Congress Control Number: 2013931182

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Preface

Systems biology refers to the quantitative analysis of the dynamic interactions among

multiple components of a biological system and aims to understand the behavior of

the system as a whole. Systems biology involves the development and application of

system-theoretic concepts for the study of complex biological systems through

iteration over mathematical modeling, computational simulation and biological

experimentation. Systems biology could be viewed as a new concept and tool to

increase our understanding of biological systems, to develop more directed experi-

ments, and to allow accurate predictions.

Systems biology is among the most rapidly growing fields of scientific research

and technology development. Over the past ten to fifteen years, the research activities

in this field have been increasing exponentially. This is evidenced by the number of

published papers as well as the growing number of conferences, journals, research

institutions and centers, and academic events on the topic of systems biology. While

research, development and applications in this field are becoming more widespread,

one major challenge is the lack of a single reference resource providing up-to-date

overviews and definitions of the major concepts and subjects across the various sub-

areas of systems biology. The Encyclopedia of Systems Biology is addressing this

lack and provides a unified information resource. It has been conceived as

a comprehensive reference work covering all aspects of systems biology, including

the investigation of living matter through a tight coupling of biological experimen-

tation, mathematical modeling and computational analysis and simulation. The main

aim of the Encyclopedia is to provide a complete reference of established knowledge

in systems biology – a ‘one-stop shop’ for someone seeking information on key

concepts in this field. As a result, the Encyclopedia comprises a broad range of topics

relevant in the context of systems biology.

The audience targeted by the Encyclopedia includes researchers, developers,

teachers, students and practitioners who are studying or working in the field of

systems biology. Keeping in mind the varying needs of the potential readership, we

have structured and presented the content in a way that is accessible to readers from

a wide range of backgrounds. In contrast to encyclopedic online resources, which

often rely on the general public to author their content, a key consideration in the

development of the Encyclopedia of Systems Biology was to have subject matter

experts define the concepts and subjects of systems biology. We believe that there is

no other treatment of this subject in terms of depth and authority of the field.

Ultimately, systems biology represents a trans-disciplinary scientific paradigm, in

which researchers from diverse backgrounds work jointly using a shared conceptual

framework and combined disciplinary-specific approaches to address complex life

science R&D problems. Thus, the Encyclopedia of Systems Biology derives its

v

raison d’etre from a modern trans-disciplinary perspective on how to think about and

explore complex biological phenomena. We believe that this new publication will

help to define themeaning and scope of systems biology, and to extend the impact that

systems biology will have on future developments in the life sciences.

Acknowledgments

It has taken several years of hard work by many people to bring this Encyclopedia to

life. We would like to give our sincere thanks to the members of the Editorial Board,

the contributing authors and the reviewers. Without their expertise, dedication and

continuous efforts this comprehensive reference work would not exist.

We wish to thank Joseph Burns (Senior Editor), Sandra Fabiani (Executive Editor)

and Melanie Tucker (Editor) who proposed the project to us and provided invaluable

counsel in shaping and developing this reference work. We wish to express our

profound gratitude to Sylvia Blago and Simone Giesler from Springer for their

outstanding editorial efforts in producing this exciting Encyclopedia.

March 2013 Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho,

Hiroki Yokota

Editors-in-Chief

Coleraine / Rostock / Daejeon / Indianapolis

vi Preface

Editors-in-Chief

Werner Dubitzky Biomedical Sciences Research Institute, University of Ulster,

Coleraine, UK

Olaf Wolkenhauer Department of Computer Science, University of Rostock,

Rostock, Germany

Kwang-Hyun Cho Department of Bio and Brain Engineering, Korea Advanced

Institute of Science and Technology (KAIST), Daejeon, Republic of Korea

Hiroki Yokota Department of Biomedical Engineering, Rensselaer Polytechnic

Institute, Troy, NY, USA

vii

About the Editors

ProfessorWerner Dubitzky currently occupies the Chair of Bioinformatics at the at

the University of Ulster, Coleraine, UK. In 1991, he received an MSc in electrical

engineering from the University of Applied Sciences, Augsburg, Germany, and in

1997 a Ph.D. in computer science from the University of Ulster at Jordanstown, UK.

His main research areas include bioinformatics and computational systems biology,

artificial intelligence, data mining and management, multi-scale modelling and

simulation, and large-scale computing technology.

I was always fascinated by the diversity and complexity in the life sciences. Lookingat the intricate inner workings of only a single cell, one wonders if humans will

ever fully understand its complicated ways. It is clear to me that a comprehensive

understanding of complex life phenomena requires a discipline-crossing approach.To make such an approach efficient, we require a shared trans-disciplinary conceptual

framework. I am excited to be involved in the development of the Encyclopedia of

Systems Biology, as I see it as an important contribution in the construction of sucha framework.

ix

Professor Olaf Wolkenhauer received first degrees in control engineering from the

University of Applied Sciences in Hamburg, Germany and the University of

Portsmouth, U.K. in 1994 and his Ph.D. from UMIST in Manchester in 1997). Before

moving to theUniversity ofRostock,where he occupies theChair in SystemsBiology&

Bioinformatics, he a research lectureship at the Control Systems Centre in Manchester,

a joint senior lectureship between the Department of Biomolecular Sciences and the

Department of Electrical Engineering and Electronics, at UMIST. Since October 2004

he is an Adjunct Professor in the Department of Electrical Engineering and Computer

Science at CaseWestern Reserve University, Cleveland, USA an became 2005 a fellow

of the Stellenbosch Institute for Advanced Study (STIAS). Olaf Wolkenhauer’s

research interest is mathematical modelling and data analysis, focussing on nonlinear

dynamical systems in molecular and cell biology. Further, detailed information can be

obtained from his webpage at www.sbi.uni-rostock.de.

Systems biology should not be considered a discipline but an approach to under-

stand complex biological systems. Nonlinear spatio-temporal phenomena, crossingmultiple levels of structural and functional organization are the reason why mathe-

matical modelling and simulation can play an important role. The fact that so manydifferent topics come together in systems biology is a challenge but also an additional

motivation to advance our understanding of living systems.

x About the Editors

http://www.sbi.uni-rostock.de/

Professor Kwang-Hyun Cho received B.S., M.S., and Ph.D. degrees in electrical

engineering from the Korea Advanced Institute of Science and Technology (KAIST)

in 1993 (summa cum laude), 1995, and 1998, respectively. He was an Associate

Professor at the College of Medicine, Seoul National University, Korea until 2007

and is currently the Chair Professor in the Department of Bio and Brain Engineering

at the KAIST and a director of the Laboratory for Systems Biology and Bio-Inspired

Engineering (http://sbie.kaist.ac.kr). He was the recipient of the IEEE/IEEK Joint

Award for Young IT Engineer, the Young Scientist Award from the President of

Korea, and the Walton Fellow Award from Science Foundation of Ireland. He has

been working on systems biology with biomedical applications, network evolution,

and bio-inspired engineering. His innovative contribution to systems biology and

bio-inspired engineering research by combining an engineering approach with

biochemical experimentation has led to over 126 high-profile international

journal publications. He is currently the Editor-in-Chief of IET Systems Biology

(IET, London, U.K.).

As a systems scientist, I was intrigued by the complex and puzzling dynamics of

living systems. In particular, their self-organizing behaviors and emergent propertiesled me to think about the fundamental difference of living systems compared to

non-living systems from a systems science point of view. Systems biology is the way

of approaching answers to such questions and I hope the Encyclopedia of SystemsBiology to be a useful travel guide for that expedition.

About the Editors xi

http://sbie.kaist.ac.kr/

Dr Hiroki Yokota is a Professor of Biomedical Engineering at the Purdue School of

Engineering and Technology, at Indiana University Purdue University Indianapolis

(IUPUI), U.S.A. He is also a Director of Biomechanics and Biomaterials Research

Centre at IUPUI. He received a PhD in astronautics from the University of Tokyo

(Japan) in 1983, and a PhD in molecular, cellular and developmental biology from

Indiana University (U.S.A.) in 1993. He is a fellow of American Institute for Medical

and Biological Engineering since 2009. Currently, his main research interests are

skeletal biology, molecular and cellular mechanics, and applications of control

theories in metabolic processes.

Unlike a construction crane’s arm, our long bones are constantly remodeled by

a series of destruction events followed by rebuilding. This simplified comparison

through my research of skeletal systems highlights two independent systems designprinciples in the crane and bone. My sincere hope is that the Encyclopaedia of

Systems Biology will assist our understanding of adaptive biological systems and

stimulate useful applications of their design principles.

xii About the Editors

Section Editors

Applications in Drug Discovery

Nagasuma Chandra Bioinformatics Centre and SERC, Indian Institute of Science,

Malleshwaram, Bangalore, India

Artificial Intelligence and Machine Learning

Daniel Berrar Tokyo Institute of Technology, Interdisciplinary Graduate School of

Science and Engineering, Nagatsuta, Midori-ku, Yokohama, Japan

Werner Dubitzky University of Ulster, Coleraine, UK

Aritificial Life

Jan T. Kim University of East Anglia, School of Computing Sciences, Norwich, UK

Cancer

Carlos Sonnenschein Department of Anatomy and Cellular Biology, Tufts Univer-

sity School of Medicine, Boston, MA, USA

Ana Soto Department of Anatomy and Cellular Biology, Tufts University School of

Medicine, Boston, MA, USA

Cell Cycle

Attila Csikasz-Nagy CoSBi, The Microsoft Research, Centre for Computational

and Systems Biology, University of Trento, Povo (Trento), Italy

Computational MicroRNA Biology

Ulf Schmitz Department of Systems Biology and Bioinformatics, University of

Rostock, Rostock, Germany

Julio Vera Group of Systems Biology for Cancer and Aging, Department of

Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

Gene Regulatory Networks: Modeling, Reconstruction and Analysis

Luonan Chen Department of Electrical Engineering and Electronics, Osaka Sangyo

University, Daito, Osaka, Japan

xiii

Large-Scale and High-Performance Computing

Mario Cannataro School of Informatics and Biomedical Engineering, University

“Magna Græcia” of Catanzaro, Viale Europa (Localita Germaneto), Catanzaro, Italy

Mathematical Theory and Methods

Daniel A. Beard Department of Physiology, Biotechnology and Bioengineering

Center, Medical College of Wisconsin, Milwaukee, WI, USA

Helen Byrne Centre for Mathematical Medicine and Biology, School of Mathemat-

ical Sciences, University of Nottingham, Nottingham, UK

Metabolic Networks

Osbaldo Resendis-Antonio Systems Biology Group, Instituto Nacional de

Medicina Genomica, (INMEGEN), Tlalpan, Mexico City, DF, Mexico

Model Databases

Jacky Snoep Department of Biochemistry, University of Stellenbosch, Matieland,

South Africa

Philosophical and Foundational Issues

Ulrich Krohs Department of Philosophy, University of Hamburg, Hamburg,

Germany

Quantitative Experiment Design

Ann E. Rundell Biomedical Engineering, Purdue University, West Lafayette,

IN, USA

Resources

EduardoMendoza Department of Computer Science, University of the Philippines,

Diliman, Quezon City, Philippines

Single Cell Experiments

Feng-Chun Yang Herman B Wells Center for Pediatric Research, Indiana Univer-

sity School of Medicine, Indianapolis, IN, USA

Standards, Exchange Formats, Guidelines and Ontologies

Chris Taylor EMBL, The European Bioinformatics Institute Wellcome Trust

Genome Campus, Hinxton, Cambridgeshire, UK

Statistical Theory and Methods

Eugene Kolker Biomedical and Health Informatics Division, Medical Education

and Biomedical Informatics Department, School of Medicine, Seattle, WA, USA

xiv Section Editors

Structural Network Analysis

Nitin Bhardwaj Molecular Biophysics and Biochemistry, Yale University, New

Haven, CT, USA

Systems Approaches to Translational Biomedical Research: Focus

on Diagnostic and Prognostic Applications

Francisco Azuaje Laboratory of Cardiovascular Research, CRP-Sante,

Luxembourg

Systems Immunology

Sudipto Saha Centenary Campus, Bose Institute, Kolkata, West Bengal, India

Text Mining

J€org Hakenberg Department of Computer Science and Department of Biomedical

Informatics, Arizona State University, Tempe, AZ, USA

Toponomics

Walter Schubert Molecular Pattern Recognition Research Group, Medical Faculty,

Otto-von-Guericke-University Magdeburg, Magdeburg, Germany

Transcriptional Regulation

Masami Horikoshi Institute of Molecular and Cellular Biosciences, University of

Tokyo, Bunkyo-ku, Tokyo, Japan

Translational Control and Systems Biology

Katsura Asano Division of Biology, Kansas State University, Manhattan, KS, USA

Section Editors xv

Contributors

Adele A. Abrahamsen Center for Research in Language, University of California,

San Diego, La Jolla, CA, USA

Pragyan Acharya Department of Biochemistry, Indian Institute of Science, Ban-

galore, Karnataka, India

Naruhiko Adachi Structure-guided Drug Development Project, JBIC Research

Institute, Japan Biological Informatics Consortium, Tokyo, Japan

Christoph Adami Department of Microbiology and Molecular Genetics, Michigan

State University, East Lansing, MI, USA

Giuseppe Agapito Department of Experimental Medicine and Clinic, University

Magna Graecia of Catanzaro, Catanzaro, Italy

Shipra Agrawal BioCOS Life Sciences Pvt. Limited, Institute of Bioinformatics

and Applied Biotechnology, Bangalore, Karnataka, India

Baltazar D. Aguda Mathematical Biosciences Institute, Ohio State University,

Columbus, OH, USA

Jesus Aguilar-Ruiz School of Engineering, Pablo de Olavide University, Escuela

Politecnica Superior, Seville, Spain

Mario Albrecht Computational Biology and Applied Algorithmics, Max Planck

Institute for Informatics, Saarbr€ucken, Germany

Annette A. Alcasabas BioSyntha Technology, Welwyn Garden City, UK

Roberta Alfieri Institute for Biomedical Technologies – CNR (Consiglio Nazionale

delle Ricerche), Segrate, Milan, Italy

Valencia Alfonso Structural Biology and BioComputing Programme, Spanish

National Cancer Research Centre (CNIO), Madrid, Spain

Syed Toufeeq Ali-Ahmed Department of BioMedical Informatics, Vanderbilt

University, Nashville, TN, USA

Frank Allg€ower Institute for Systems Theory and Automatic Control, University of

Stuttgart, Stuttgart, Germany

Ronnie Alves Instituto de Informatica, Universidade Federal do Rio Grande do Sul,

Porto Alegre, Brazil

xvii

Flavio Amara Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita

di Milano, Milan, Italy

Francesco Amato Department of Clinical and Experimental Medicine, Magna

Graecia University of Catanzaro, Catanzaro, Italy

Sophia Ananiadou National Centre for Text Mining, School of Computer Science,

University of Manchester, Manchester, UK

Hanne Andersen Department of Physics and Astronomy, Centre for Science

Studies, Aarhus University, Aarhus, Denmark

James Anderson Department of Engineering Science, University of Oxford,

Oxford, UK

Hifzur Rahman Ansari Bioinformatics Centre, Institute of Microbial Technology,

Chandigarh, Chandigarh, India

Erick Antezana Department of Biology, Systems Biology Group, Norwegian

University of Science and Technology, Trondheim, Norway

Dagoberto Armenta-Medina Departamento de Ingenierıa Celular y Biocatalisis,

Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca,

Morelos, Mexico

Katsura Asano Molecular, Cellular, and Developmental Biology Program,

Division of Biology, Kansas State University, Manhattan, KS, USA

Diana Ascencio Laboratorio Nacional de Genomica para la Biodiversidad,

CINVESTAV-IPN, Irapuato, Guanajuato, Mexico

Teresa K. Attwood Faculty of Life Sciences and School of Computer Science,


Claudio Avignone-Rossa Department of Microbial and Cellular Sciences,

Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK

M.Madan Babu MRC Laboratory of Molecular Biology, University of Cambridge,

Cambridge, UK

Walter de Back Centre for High Performance Computing (ZIH), Technical

University Dresden, Dresden, Germany

David A. Bader School of Computational Science and Engineering, College of

Computing, Georgia Institute of Technology, Atlanta, GA, USA

J€urg B€ahler Department of Genetics, Evolution and Environment and UCL Cancer

Institute, University College London, London, UK

Jose Ignacio Agulleiro Baldo Supercomputing-Algorithms Group, University of

Almerıa, Almerıa, Spain

Eva Balsa-Canto Ministerio de Economıa y Competitividad, Bioprocess Engineer-

ing Group, IIM-CSIC, Vigo, Spain

Julio R. Banga Ministerio de Economıa y Competitividad, Bioprocess Engineering

Group, IIM-CSIC, Vigo, Spain

xviii Contributors

Mary Helen Barcellos-Hoff Department of Radiation Oncology and Cell Biology,

New York University School of Medicine, New York, NY, USA

Andre Bardow Institute of Technical Thermodynamics, RWTH Aachen

University, Aachen, Germany

Neil Andrew D. Bascos Protein Structure and Immunology Laboratory, National

Institute of Molecular Biology and Biotechnology, University of the Philippines,

Quezon City, Philippines

Riza Theresa Batista-Navarro National Centre for Text Mining, Manchester

Interdisciplinary Biocentre, Manchester, UK

William A. Baumgartner Jr University of Colorado Denver, Aurora, CO, USA

Sean Bechhofer School of Computer Science, University of Manchester,

Manchester, UK

William Bechtel Department of Philosophy and Center for Chronobiology, Univer-

sity of California, San Diego, La Jolla, San Diego, CA, USA

Elena Beisswanger Jena University Language and Information Engineering

(JULIE) Laboratory, Friedrich-Schiller-University Jena, Jena, Germany

Xavier Belles Institut de Biologia Evolutiva, CSIC-UPF (Universitat Pompoi

Fabra), Barcelona, Spain

Bertrand Bellier Immunology-Immunopathology-Immunotherapy, UPMCUniver-

sity Paris 06, UMR7211, CNRS, UMR7211, INSERM, U959, Paris, France

Daniel Berrar Interdisciplinary Graduate School of Science and Engineering,

Tokyo Institute of Technology, Midori-ku, Yokohama, Japan

Dany Beste Division of Microbial Sciences, Faculty of Health and Medical

Sciences, University of Surrey, Guildford, Surrey, UK

Fabrizio Bezzo CAPE-Laboratory, Dipartimento di Ingegneria Industriale, Univer-

sity of Padova, Padova, Italy

Upinder S. Bhalla Neurobiology, National Center for Biological Sciences, Tata

Institute of Fundamental Research, Bangalore, India

M. M. Srinivas Bharath Department of Neurochemistry, National Institute of

Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India

P. Jayadeva Bhat School of Bioscience and Engineering, Indian Institute of

Technology, Mumbai, India

Animesh Bhattacharya Department of Dermatology, Venereology and

Allergology, University of Leipzig, Leipzig, Germany

Leonardo Bich Department of Logic and Philosophy of Science, IAS-Research

Center for Life, Mind, and Society, University of the Basque Country, UPV/EHU,

Donostia-San Sebastian, Spain

Jose Roman Bilbao-Castro Supercomputing-Algorithms Group, University of

Almerıa, Almerıa, Spain

Contributors xix

Zhao Bing Department of Biochemistry, University of Western Ontario, London,

ON, Canada

Emanuele G. Biondi CR1-CNRS-Laboratory of Biochemistry and Integrated

Structural Biology, Institut de Recherche Interdisciplinaire - IRI CNRS USR3078,

Villeneuve d’Ascq, France

Jesus Bisbal Departament de Tecnologies de la Informacio i les Comunicacions,

Universitat Pompeu Fabra, Barcelona, Spain

Hagen Blankenburg Computational Biology and Applied Algorithmics, Max

Planck Institute for Informatics, Saarbr€ucken, Germany

Rainer Blasczyk Hannover Medical School, Institute for Transfusion Medicine,

Hannover, Germany

Hendrik Blockeel Department of Computer Science, Katholieke Universiteit

Leuven, Heverlee, Belgium

Leiden Institute of Advanced Computer Science, Universiteit Leiden, Leiden, The

Netherlands

Olivier Bodenreider Lister Hill National Center for Biomedical Communications,

US National Library of Medicine, Bethesda, MD, USA

Davide Bolchini School of Informatics, Indiana University, Indianapolis, IN, USA

Daniel R. Boutz Institute for Cellular and Molecular Biology, University of Texas,

Austin, TX, USA

Vani Brahmachari Dr. B. R. Ambedkar Center for Biomedical Research,

University of Delhi, Delhi, India

Ryan R. Brinkman Terry Fox Laboratory, BC Cancer Agency, BC Cancer

Research Centre, Vancouver, BC, Canada

Department of Medical Genetics, University of British Columbia, Vancouver, BC,

Canada

Randall D. Britten Auckland Bioengineering Institute, University of Auckland,

Auckland, New Zealand

Alistair J. P. Brown Institute of Medical Sciences, University of Aberdeen,

Aberdeen, UK

Gerhard Buck-Sorlin Institut de Recherche en Horticulture et Semences, UMR

1345 (INRA/Agrocampus-ouest/Universite d’Angers) Agrocampus Ouest, Angers,

France

Scott M. Bugenhagen Computational Bioengineering Group, Biotechnology and

Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA

Marc Bullock Cancer Research UK Centre, University of Southampton

Cancer Sciences Division, Southampton University Hospital NHS Trust, Southamp-

ton, UK

RichardM. Burian Department of Philosophy, Virginia Tech, Blacksburg, VA, USA

xx Contributors

Michael E. Bushell Department of Microbial and Cellular Sciences, University of

Surrey, Guildford, Surrey, UK

Gregery T. Buzzard Department of Mathematics, Purdue University, West

Lafayette, IN, USA

Laurence Calzone Institut Curie – INSERMU900 –Mines ParisTech, Paris, France

Anyela Camargo Institute of Biological, Environmental and Rural Sciences,

Aberystwyth University, Aberystwyth, Ceredigion, UK

Mario Cannataro Department of Medical and Surgical Sciences, UniversityMagna

Graecia of Catanzaro, Catanzaro, Italy

Virginio Cantoni Department of Computer Engineering and Systems Science,

University of Pavia, Pavia, Italy

Computational Biology, KTH Royal Institute of Technology, Stockholm, Sweden

Martin Carrier Department of Philosophy, Bielefeld University, Bielefeld, Germany

Eugenio Cesario ICAR-CNR (Istituto di Calcolo e Reti ad Alte Prestazioni), Rende,

CS, Italy

Guilhem Chalancon MRC Laboratory of Molecular Biology, University of

Cambridge, Cambridge, UK

Alan Champneys Department of Engineering Mathematics, University of Bristol,

Bristol, UK

Mark R. Chance Center for Proteomics and Bioinformatics and Department of

Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH,

USA

Nagasuma Chandra Department of Biochemistry, Indian Institute of Science,

Bangalore, India

Rupanjali Chaudhuri G.N. Ramachandran Knowledge Centre for Genome Infor-

matics, Institute of Genomics and Integrative Biology, Delhi, India

Vijayalakshmi Chelliah EMBL European Bioinformatics Institute, Hinxton,

Cambridgeshire, UK

Katherine C. Chen Department of Biological Sciences, Virginia Polytechnic

Institute and State University, Blacksburg, VA, USA

James J. Chen U.S. Food and Drug Administration, National Center for Toxico-

logical Research (HFT-20), Jefferson, AR, USA

Li-Hsunan Chen Department of Chemical Engineering, National Chung Cheng

University, Chiayi, Taiwan

Xi Chen Advanced Modeling and Applied Computing Laboratory, Department of

Mathematics, University of Hong Kong, Hong Kong, China

Wai-Ki Ching Advanced Modeling and Applied Computing Laboratory, Depart-

ment of Mathematics, University of Hong Kong, Hong Kong, China

Contributors xxi

Miew Keen Choong Centre for Health Informatics, Australian Institute for Health

Innovation, University of New South Wales, Sydney, NSW, Australia

I-Chun Chou The Wallace H. Coulter Department of Biomedical Engineering,

Georgia Institute of Technology and Emory University, Atlanta, GA, USA

Yunfei Chu Artie McFerrin Department of Chemical Engineering, Texas A&M

University, College Station, TX, USA

Andrea Ciliberto IFOM – The FIRC Institute of Molecular Oncology, Milan, Italy

Jean Clairambault Equipe-Projet BANG, INRIA Paris-Rocquencourt BP 105,

Le Chesnay, Paris, France

Amanda Clare Department of Computer Science, Aberystwyth University,

Aberystwyth, UK

Tim Clark Department of Neurology, Massachusetts General Hospital and Harvard

Medical School, Boston, MA, USA

Richard H. Clayton Department of Computer Science, University of Sheffield,

Sheffield, UK

Gilles Clermont Center for Inflammation and Regenerative Modeling, University

of Pittsburgh, Pittsburgh, PA, USA

George M. Coghill Institute for Complex System and Mathematical Biology,

University of Aberdeen, Aberdeen, UK

Kevin Bretonnel Cohen Center for Computational Pharmacology, University of

Colorado, Aurora, CO, USA

Matteo Comin Department Information Engineering, University of Padova,

Padova, Italy

David Cook AstraZeneca, Translational Patient Safety and Enabling Science,

Macclesfield, Chester, UK

Carlo Cosentino Department of Clinical and Experimental Medicine, Magna

Graecia University of Catanzaro, Catanzaro, Italy

Richard G. Cote European Molecular Biology Laboratory, European Bioinformat-

ics Institute (EBI), Hinxton, Cambridge, UK

Carl F. Craver Philosophy and Philosophy-Neuroscience-Psychology Program,

Philosophy Department, Washington University in Saint Louis, St. Louis, MO, USA

Attila Csikasz-Nagy The Microsoft Research - University of Trento Centre for

Computational and Systems Biology, Trento, Italy

Lalit Darunte Department of Chemical Engineering, Indian Institute of Techno-

logy, Mumbai, India

Ranjan K. Dash Department of Physiology, Biotechnology and Bioengineering


Jonathan F. Davies Fondazione Bruno Kessler, Trento, Italy

xxii Contributors

Barbara J. Davis Section of Pathology, Tufts Cummings School of Veterinary

Medicine Biomedical Sciences, North Grafton, MA, USA

Thomas S. Deisboeck Harvard-MIT (HST) Athinoula A. Martinos Center for

Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA

David S. DeLuca Cancer Genome Analysis Group, The Broad Institute, Cambridge,

MA, USA

Alexander DeLuna Laboratorio Nacional de Genomica para la Biodiversidad,

CINVESTAV-IPN, Irapuato, Guanajuato, Mexico

Andreas Deutsch Center for Information Services and High Performance Compu-

ting (ZIH), Technical University Dresden, Dresden, Germany

Rohan Dhiman Center for Pulmonary and Infectious Disease Control, University of

Texas Health Science Center at Tyler, Tyler, TX, USA

Akos Dobay Institute of Evolutionary Biology and Environmental Studies (IEU),

University of Zurich, Zurich, Switzerland

Maria Pamela Dobay Department of Physics, Ludwig-Maximilians University,

Munich, Germany

Andreas Doncic Department of Biology, Stanford University School of Medicine,

Stanford, CA, USA

Brecht M. R. Donckels Department of Mathematical Modelling, Statistics and

Bioinformatics, Ghent University, Ghent, Belgium

Piercarlo Dondi Department of Computer Engineering and Systems Science,


Francis J. Doyle III Department of Chemical Engineering, Institute for

Collaborative Biotechnologies, University of California, Santa Barbara, CA, USA

Andreas Dr€ager Center for Bioinformatics, University of Tuebingen, Tuebingen,

Germany

Dirk Drasdo Institute National de Recherche en Informatique et en Automatique,

Paris–Rocquencourt, France

Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Andreas Dress University of Bielefeld, Bielefeld, Germany

Key Laboratory for Computational Biology (PICB), Shanghai Institutes

for Biological Sciences (SIBS), Chinese Academy of Science and Max Planck

Society (CAS–MPG) Partner Institute, Shanghai, China

Science Center at “infinity3 GmbH”, Bielefeld, Germany

Franco du Preez SysMO-DB team, Manchester Centre for Integrative Systems

Biology, University of Manchester, Manchester, UK

Werner Dubitzky Biomedical Sciences Research Institute, University of Ulster,

Coleraine, UK

Contributors xxiii

Włodzisław Duch Department of Informatics, Nicolaus Copernicus University,

Torun, Poland

School of Computer Engineering, Nanyang Technological University, Singapore,

Singapore

Franco duPreez SysMO-DB team, University of Manchester, Manchester Centre

for Integrative Systems Biology, Manchester, UK

Harsh Dweep Medical Research Center, Medical Faculty Mannheim, University of

Heidelberg, Mannheim, Germany

Gaurav Dwivedi The Wallace H. Coulter Department of Biomedical Engineering,


Oliver Ebenh€oh Institute for Complex Systems and Mathematical Biology,

University of Aberdeen, Kings College, Old Aberdeen, Aberdeen, UK

Karen Eilbeck Department of Biomedical Informatics, University of Utah, Salt

Lake City, UT, USA

Department of Human Genetics, Eccles Institute of Human Genetics, University of

Utah, Salt Lake City, UT, USA

Yasser EL-Manzalawy Center for Computational Intelligence, Learning, and Dis-

covery, Computer Science, Iowa State University, Ames, IA, USA

Heiko Enderling Center of Cancer Systems Biology, St. Elizabeth’s Medical Cen-

ter - CBR 115D, Tufts University School of Medicine, Boston, MA, USA

David Epstein Mathematics Institute, University of Warwick, Warwick, UK

Arantza Etxeberria Department of Logic and Philosophy of Science, IAS-

Research Center for Life, Mind, and Society, University of the Basque Country,

UPV/EHU, Donostia - San Sebastian, Spain

Anthony Faiola School of Informatics, Indiana University, Indianapolis, IN, USA

Dana Faratian Centre for Molecular Pathology, Institute of Cancer Research,

Surrey, UK

Malcolm Farrow School of Mathematics & Statistics, Newcastle University,

Newcastle upon Tyne, UK

Adrien Faure Graduate School of Science and Engineering, Yamaguchi Univesity,

Yamaguchi, Japan

Nnenna A. Finn The Wallace H. Coulter Department of Biomedical Engineering,


Darren R. Flower School of Life and Health Sciences, Aston University, Birming-

ham, UK

Thomas Fober Philipps-Universit€at Marburg, Marburg, Germany

Luıs L. Fonseca Department of Biomedical Engineering, Georgia Institute of

Technology and Emory University, Atlanta, GA, USA

xxiv Contributors

Christian V. Forst Department of Clinical Sciences, Southwestern Medical Center,

University of Texas, Dallas, TX, USA

Erika De Francesco Exeura, Rende (CS), Italy

Sherry Freiesleben Department of Systems Biology and Bioinformatics, Institute

of Computer Science, University of Rostock, Rostock, Germany

Peter Frick Vanderbilt University, Nashville, TN, USA

Tamaki Fujimori HumanMetabolomeTechnologies Inc., Tsuruoka,Yamagata, Japan

Johannes F€urnkranz Technical University of Darmstadt, Darmstadt, Germany

Alessandro Gaggia Department of Computer Engineering and Systems Science,


Ester M. Garzon Department of Computer Architecture and Electronics, Univer-

sity of Almerıa, Almerıa, Spain

Riccardo Gatti Department of Computer Engineering and Systems Science,


Hao Ge School of Mathematical Sciences and Centre for Computational Systems

Biology, Fudan University, Shanghai, China

Martin Gerner Faculty of Life Sciences, University of Manchester, Manchester, UK

Andrew D. Gewitz Institute for Computational and Mathematical Engineering and

School of Medicine, Stanford University, Stanford, CA, USA

Anne Gieseler Molecular Pattern Recognition Research (MPRR) Group, Otto-von-

Guericke-University Magdeburg Medical Faculty, Magdeburg, Germany

Veronique Giudicelli Laboratoire d’ImmunoGenetique Moleculaire, Institut de

Genetique Humaine UPR 1142, Universite Montpellier 2, Montpellier, France

CaroleGoble School ofComputer Science,University ofManchester,Manchester, UK

Andres Fernando Gonzalez Barrios Department of Chemical Engineering,

Universidad de los Andes, Bogota, Colombia

Orland Gonzalez Institute for Bioinformatics, Ludwig-Maximilians-University

Munich, Munich, Germany

Sara Green Department of Physics and Astronomy, Centre for Science Studies,

Aarhus University, Aarhus, Denmark

Norbert Gretz Medical Research Center, Medical Faculty Mannheim, University

of Heidelberg, Mannheim, Germany

Manish Grover Department of Biochemistry, Indian Institute of Science, Banga-

lore, Karnataka, India

Daniel V. Guebel Department of Systems Biology and Bioinformatics, Institute of

Computer Sciences, University of Rostock, Rostock, Germany

Concettina Guerra Department Information Engineering, University of Padova,

Padova, Italy

Contributors xxv

Shailendra K. Gupta Indian Institute of Toxicology Research (CSIR), Lucknow,

India

Pietro Hiram Guzzi Department of Experimental Medicine and Clinic, University

Magna Gratia of Catanzaro, Catanzaro, Italy

Gordon L. Hager Laboratory of Receptor Biology and Gene Expression, National

Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Juergen Hahn Artie McFerrin Department of Chemical Engineering, Texas A&M

University, College Station, TX, USA

Udo Hahn Jena University Language and Information Engineering (JULIE) Labo-

ratory, Friedrich-Schiller-University Jena, Jena, Germany

J€org Hakenberg Department of Computer Science and Department of Biomedical

Informatics, Arizona State University, Tempe, AZ, USA

Marta Halina Department of Philosophy and Science Studies Program, University

of California, San Diego, San Diego, La Jolla, CA, USA

David Harrison School of Medicine, University of St Andrews, St Andrews,

Scotland, UK

G. V. HarshaRani Neurobiology, National Center for Biological Sciences, Tata

Institute of Fundamental Research, Bangalore, India

Jan Hasenauer Institute for Systems Theory and Automatic Control, University of

Stuttgart, Stuttgart, Germany

Haralambos Hatzikirou Department of Pathology, School of Medicine, University

of New Mexico, Albuquerque, NM, USA

Michael Hauhs Ecological Modeling, University of Bayreuth, Bayreuth, Germany

Winston Haynes Seattle Children’s Research Institute, Seattle, WA, USA

Yongzheng He Department of Pediatrics, Indiana University School of Medicine,

Indianapolis, IN, USA

Michael Hecker Department of Neurology, Institute of Immunology, University of


Jan G. Hengstler Leibniz Research Center for Working Environment and Human

Factors, Dortmund, Germany

Alexander Herbig Center for Bioinformatics T€ubingen, Faculty of Science,

University of T€ubingen, T€ubingen, Germany

Georgina Hernandez-Montes Departamento de Medicina Molecular y

Bioprocesos, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos,

Mexico

Roger Higdon Seattle Children’s Research Institute, Seattle, WA, USA

Reyk Hillert Molecular Pattern Recognition Research (MPRR) Group, Otto-von-

Guericke-University, Magdeburg, Germany

xxvi Contributors

Stefan Hoehme Interdisciplinary Center for Bioinformatics, University of Leipzig,

Leipzig, Germany

Carson Holt Department of Human Genetics, University of Utah, Salt Lake City,

UT, USA

Vasant Honavar Center for Computational Intelligence, Learning, and Discovery,

Computer Science, Iowa State University, Ames, IA, USA

Christian I. Hong Department of Molecular and Cellular Physiology, University of

Cincinnati College of Medicine, Cincinnati, OH, USA

Seok-Hee Hong School of IT, University of Sydney, Sydney, NSW, Australia

Katsuhisa Horimoto Computational Biology Research Center, National Institute of

Advanced Industrial and Science and Technology, Koto-ku, Tokyo, Japan

Anna Horvath Department of Applied Biotechnology and Food Science, Budapest

University of Technology and Economics, Budapest, Hungary

Peter Horvatovich Department of Pharmacy, Analytical Biochemistry Research

Group, University of Groningen, Groningen, The Netherlands

C. Vyvyan Howard Centre for Molecular Biosciences, University of Ulster,

Coleraine, UK

Yufei Huang Picower Institute for Learning and Memory, Massachusetts Institute

of Technology, Cambridge, MA, USA

Greehey Children’s Cancer Research Institute, University of Texas at Texas Health

Science Center at San Antonio, San Antonio, TX, USA

Department of Epidemiology and Biostatistics, University of Texas at Texas Health

Science Center at San Antonio, San Antonio, TX, USA

Fuyan Hu Institute of Systems Biology, Shanghai University, Shanghai, China

Michael Hucka Computing and Mathematical Sciences, California Institute of

Technology, Pasadena, CA, USA

Eyke H€ullermeier Philipps-Universit€at Marburg, Marburg, Germany

Andreas H€uttemann Department of Philosophy, University of Cologne, Cologne,

Germany

Philippe Huneman Institut d’Histoire et de Philosophie (IHPST), des Sciences et

des Techniques, Universite Paris 1 Pantheon-Sorbonne, Paris, France

Ying Hung Department of Statistics and Biostatistics, Rutgers University,

Piscataway, NJ, USA

C. Anthony Hunt Department of Bioengineering and Therapeutic Sciences,

University of California, San Francisco, CA, USA

Akira Ishihama Department of Frontier Bioscience, Hosei University, Tokyo,

Japan

Contributors xxvii

Koichi Ito Graduate School of Frontier Sciences, University of Tokyo, Chiba,

Tokyo, Japan

Ravi Iyengar Department of Pharmacology and Systems Therapeutics, Mount Sinai

School of Medicine, New York, NY, USA

James W. Jacobberger Case Comprehensive Cancer Center, Case Western

Reserve University, Cleveland, OH, USA

Shruti Jain Dr. B. R. Ambedkar Center for Biomedical Research, University of

Delhi, Delhi, India

Lars Juhl Jensen Novo Nordisk Foundation Center for Protein Research,

University of Copenhagen, Copenhagen, Denmark

Paul A. Jensen Department of Biomedical Engineering, University of Virginia,

Charlottesville, VA, USA

Euna Jeong Institute of Medical Science, University of Tokyo, Tokyo, Japan

Di Jia Department of Surgery/Harvard Medical School, Vascular Biology Program/

Children’s Hospital Boston, Boston, MA, USA

Guangxu Jin Systems Medicine and Bioengineering, Bioengineering and Bioinfor-

matics Program, The Methodist Hospital Research Institute, Weill Medical College,

Cornell University, Houston, TX, USA

Andrew R. Jones Institute of Integrative Biology, University of Liverpool,

Liverpool, UK

Bj€orn Junker Systems Biology and Bioinformatic, Leibniz Institute of Plant Gene-

tics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany

Nick Juty EMBL-European Bioinformatics Institute, Wellcome Trust Genome

Campus, Hinxton, Cambridgeshire, UK

Lars Kaderali Institute for Medical Informatics and Biometry Technical

University, Dresden, Germany

Marie I. Kaiser Department of Philosophy, University of Cologne, Cologne,

Germany

Aleksi Kallio CSC, IT Center for Science Ltd, Espoo, Finland

Orsolya Kapuy Department of Biochemistry, Oxford Centre for Integrative Sys-

tems Biology, University of Oxford, Oxford, UK

Mahendra Kavdia Department of Biomedical Engineering, Wayne State

University, Detroit, MI, USA

Gota Kawai Department of Life and Environmental Sciences, Chiba Institute of

Technology, Narashino, Chiba, Japan

Junya Kawauchi Department of Biochemical Genetics, Medical Research Institute,

Tokyo Medical and Dental University, Tokyo, Japan

Sarah M. Keating EMBL -European Bioinformatics Institute, Wellcome Trust


xxviii Contributors

C. Maria Keet KRDB Research Centre, Free University of Bozen-Bolzano,

Bolzano, Italy

Douglas Bruce Kell School of Chemistry and Manchester Interdisciplinary

Biocentre, University of Manchester, Manchester, UK

Evelyn Fox Keller Massachusetts Institute of Technology (MIT), Cambridge,

MA, USA

Melissa L. Kemp The Wallace H. Coulter Department of Biomedical Engineering,


Stefan Kempa Integrative Metabolomics and Proteomics, BIMSB (Berlin Institute

for Medical Systems Biology), Berlin, Germany

Noel Kennedy School of Biomedical Sciences, University of Ulster, Coleraine, UK

Carsten Kettner Beilstein-Institut zur F€orderung der Chemischen Wissenschaften,

Frankfurt am Main, Germany

Melissa Key Center for Computational Diagnostics, Indianapolis, IN, USA

Michael Khan Department of Biological Science, Biomedical Research Institute,

University of Warwick, Coventry, UK

JavedMohammedKhan Department of Chemistry and Biomolecular Sciences and

ARC Center of Excellence in Bioinformatics, Macquarie University, Sydney, NSW,

Australia

Narsis Aftab Kiani ViroQuant Research Group Modeling, BioQuant, University of

Heidelberg, Heidelberg, Germany

AndrzejM. Kierzek Division ofMicrobial Sciences, Faculty of Health andMedical


Jan T. Kim School of Computing Sciences, University of East Anglia, Norwich,

Norfolk, UK

Jin-Dong Kim Database Center for Life Science, Tokyo, Japan

Angelika Kimmig Departement Computerwetenschappen, Katholieke Universiteit

Leuven, Heverlee, Belgium

John R. King School of Mathematical Sciences, University of Nottingham,

Nottingham, UK

Alexandros Kiparissides Biological Systems Engineering Laboratory, Department

of Chemical Engineering, Centre for Process Systems Engineering, Imperial College,

London, UK

Max Kistler IHPST, Universite Paris 1 Pantheon-Sorbonne, Paris, France

Shigetaka Kitajima Department of Biochemical Genetics, Medical Research

Institute, Tokyo Medical and Dental University, Tokyo, Japan

David Klatzmann Immunology-Immunopathology-Immunotherapy, UPMC Uni-

versity Paris 06, UMR7211, CNRS, UMR7211, INSERM, U959, Paris, France

Contributors xxix

Edda Klipp Theoretical Biophysics, Humboldt-Universit€at zu Berlin, Berlin,

Germany

Dirk Koczan Department of Neurology, Institute of Immunology, University of


Tetsuro Kokubo Department of Supramolecular Biology, Graduate School of

Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan

Michal Kolar Institute of Molecular Genetics, Academy of Sciences of the Czech

Republic, Prague, Czech Republic

Eugene Kolker Bioinformatics and High–throughput Analysis Laboratory, Seattle

Children’s Research Institute, Seattle, WA, USA

Departments of Biomedical Informatics and Medical Education and Pediatrics,

University of Washington, Seattle, WA, USA

Arun S. Konagurthu Clayton School of Information Technology, Monash

University, Clayton, VIC, Australia

K. K. Koutroumpas Automatic Control Laboratory, ETH Zurich, Zurich,

Switzerland

Martin Krallinger Structural Biology and BioComputing Programme, Spanish


Clemens Kreutz Institute for Physics, Freiburger Center for Data Analysis

and Modeling (FDM), University of Freiburg, Freiburg, Germany

Ulrich Krohs Department of Philosophy, University ofM€unster, M€unster, Germany

Andreas Krusche Molecular Pattern Recognition Research (MPRR) Group,

Otto-von-Guericke-University, Magdeburg, Germany

Kai Kruse MRC Laboratory of Molecular Biology, University of Cambridge,

Cambridge, UK

Martin Kuiper Department of Biology, Systems Biology Group, Norwegian


Sanjeev Kumar BioCOS Life Sciences Private Limited, Bangalore, Karnataka, India

Manfred Kunz Department of Dermatology, Venereology and Allergology,

University of Leipzig, Leipzig, Germany

Hitoshi Kurumizaka Graduate School of Advanced Science and Engineering,

Waseda University, Tokyo, Japan

Xin Lai Department of Systems Biology and Bioinformatics, Institute of Computer

Science, University of Rostock, Rostock, Germany

Camille Laibe EMBL-European Bioinformatics Institute, Wellcome Trust Genome

Campus, Hinxton, Cambridgeshire, UK

Tai Ning Lam Department of Bioengineering and Therapeutic Sciences, University

of California, San Francisco, CA, USA

xxx Contributors

Tze Hau Lam Department of Microbiology, Yong Loo Lin School of Medicine,

National University of Singapore, Singapore, Singapore

Christoph H. Lampert IST Austria, Klosterneuburg, Austria

Qizong Lao Laboratory of Receptor Biology and Gene Expression, National Cancer

Institute, National Institutes of Health, Bethesda, MD, USA

Sneh Lata Cold Spring Harbor Laboratory, Genome Research Center, Woodbury,

NY, USA

Reinhard Laubenbacher Virginia Bioinformatics Institute, Virginia Tech,

Blacksburg, VA, USA

Sang Yup Lee Department of Chemical and Biomolecular Engineering and

Department of Bio and Brain Engineering, Korea Advanced Institute of Science

and Technology (KAIST), Daejeon, Korea

Tae Lee School of Biology and School of Physics, Georgia Institute of Technology,

Atlanta, GA, USA

Yun Lee The Wallace H. Coulter Department of Biomedical Engineering, Georgia

Institute of Technology and Emory University, Atlanta, GA, USA

Marie-Paule Lefranc Laboratoire d’ImmunoGenetique Moleculaire, Institut de

Genetique Humaine UPR 1142, Universite Montpellier 2, Montpellier, France

Jinzhi Lei Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University of

Beijing, Beijing, China

Florian Leitner Structural Biology and BioComputing Programme, Spanish


Sabina Leonelli ESRC Centre for Genomics in Society, University of Exeter,

Exeter, Devon, UK

Ulf Leser Institute for Computer Science, Humboldt-Universit€at zu Berlin, Berlin,

Germany

Arthur M. Lesk Department of Biochemistry and Molecular Biology, and Huck

Institutes of Genomics, Proteomics, and Bioinformatics, Pennsylvania State Univer-

sity, University Park, PA, USA

Wentian Li The Robert S. Boas Center for Genomics and Human Genetics,

Feinstein Institute for Medical Research, Manhasset, NY, USA

Yan Li Department of Pediatrics, Indiana University School of Medicine, Indiana-

polis, IN, USA

Zhenping Li School of Information, Beijing Wuzi University, Beijing, China

Wolfram Liebermeister Institut f€ur Biochemie, Charite - Universit€atsmedizin

Berlin, Berlin, Germany

Frank Lin Centre for Health Informatics, Australian Institute for Health Innovation,

University of New South Wales, Sydney, NSW, Australia

Ke-Qin Liu Institute of Systems Biology, Shanghai University, Shanghai, China

Contributors xxxi

Xiaojun Liu Internal Medicine, The Second Hospital of Hebei Medical University,

Shijiazhuang, Hebei, China

Xiaoping Liu Institute of Systems Biology, Shanghai University, Shanghai, China

Zhi-Ping Liu Key Laboratory of Systems Biology, Shanghai Institutes for Biolo-

gical Sciences, Chinese Academy of Sciences, Shanghai, China

Catherine M. Lloyd Auckland Bioengineering Institute, University of Auckland,


Luca Lombardi Department of Computer Engineering and Systems Science,


Isaac F. Lopez-Moyado Center for Genomic Sciences-UNAM, Universidad

Nacional Autonoma de Mexico, Cuernavaca (Morelos), Mexico

Jingky Lozano-K€uhne Department of Public Health, University of Oxford,

Oxford, UK

Long Jason Lu Division of Biomedical Informatics, Cincinnati Children’s Hospital

Research Foundation, Cincinnati, OH, USA

John Lygeros Automatic Control Laboratory, ETH Zurich, Zurich, Switzerland

Zoi Lygerou School of Medicine, Laboratory of General Biology, University of

Patras, Patras, Greece

Shuangge Ma Yale School of Public Health, Yale University, New Haven, CT, USA

Hong-Wu Ma School of Informatics, University of Edinburgh, Edinburgh, UK

Lars Malmstr€om Institute of Molecular Systems Biology IMSB, ETH Zurich,

Zurich, Switzerland

Marcos Malumbres Spanish National Cancer Research Centre (CNIO), Madrid,

Spain

Sebastian Mana-Capelli Department of Molecular Genetics and Microbiology,

University of Massachusetts, Worcester, MA, USA

Athanasios Mantalaris Biological Systems Engineering Laboratory, Department


London, UK

Samuel Marguerat Department of Genetics, Evolution and Environment and UCL

Cancer Institute, University College London, London, UK

Alberto Marin-Sanguino Faculty of Mechanical Engineering, Specialty

Division for Systems Biotechnology, Technical University Munich, Garching,

Germany

Jose Antonio Martınez Department of Computer Architecture and Electronics,

University of Almerıa, Almerıa, Spain

Elio Mattia Centre for Systems Chemistry, Stratingh Institute for Chemistry,

Rijksuniversiteit Groningen, Groningen, The Netherlands

xxxii Contributors

Dannel McCollum Department of Molecular Genetics and Microbiology,

University of Massachusetts, Worcester, MA, USA

Johnjoe McFadden Division of Microbial Sciences, Faculty of Health and Medical


Barry McMullin The Rince Institute, Dublin City University, Dublin, Ireland

HendrikMehlhorn Leibniz Institute of PlantGenetics andCropPlantResearch (IPK),

Gatersleben, Stadt Seeland, Germany

Francisco Melo Pontificia Universidad Catolica de Chile, Santiago, Chile

Millennium Institute on Immunology and Immunotherapy, Santiago, Chile

Nuno D. Mendes Knowledge Discovery and Bioinformatics (KDBIO) Group,

INESC–ID, Lisbon, Portugal

Network Modelling Group, Instituto Gulbenkian de Ciencia (IGC), Oeiras,

Portugal

EduardoMendoza Department of Computer Science, University of the Philippines

Diliman, Quezon City, Philippines

Donna L. Mendrick Division of Systems Biology, National Center for

Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA

Jia Meng Picower Institute for Learning and Memory, Massachusetts Institute of

Technology, Cambridge, MA, USA

Carsten Mente Center for Information Services and High Performance

Computing (ZIH), Technical University Dresden, Dresden, Germany

Ivan Merelli Institute for Biomedical Technologies – CNR (Consiglio Nazionale


Marco Mernberger Philipps-Universit€at Marburg, Marburg, Germany

Luciano Milanesi Institute for Biomedical Technologies – CNR (Consiglio

Nazionale delle Ricerche), Segrate, Milan, Italy

Andrew K. Miller Auckland Bioengineering Institute, University of Auckland,


Alex Mirnezami Cancer Sciences, Faculty of Medicine, University of

Southampton, Southampton, UK

Cancer Research UK Centre, Cancer Sciences Division, School of Medicine,

Southampton General Hospital, Southampton, UK

Vladimir Mironov Department of Biology, Systems Biology Group, Norwegian


Satoru Miyano Institute of Medical Science, University of Tokyo, Tokyo, Japan

Raul Montanez Institut de Biologia Evolutiva CSIC-UPF (Universitat Pompoi

Fabra), Barcelona, Spain

Contributors xxxiii

Emily A. Moon Functional Genomics Laboratory, Department of Psychiatry and

Human Behavior, University of California, Irvine, CA, USA

Ion Moraru R.D. Berlin Center for Cell Analysis and Modeling, University of

Connecticut Health Center, Farmington, CT, USA

Alvaro Moreno Department of Logic and Philosophy of Science, University of the

Basque Country, San Sebastian, Spain

Rafael Moreno-Sanchez Department of Biochemistry, National Institute for

Cardiology “Ignacio Chavez”, Mexico City, Mexico

Sergio Moreno Instituto de Biologıa Molecular y Celular del Cancer, CSIC/

Universidad de Salamanca, Salamanca, Spain

Hisao Moriya Okayama University Research Core for Interdisciplinary Sciences,

Kita-ku, Okayama, Japan

Ettore Mosca Institute for Biomedical Technologies – CNR (Consiglio Nazionale


Marsha A. Moses Department of Surgery/Harvard Medical School, Vascular

Biology Program/Children’s Hospital Boston, Boston, MA, USA

Lenny Moss Department of Sociology and Philosophy, University of Exeter,

Exeter, Devon, UK

Matteo Mossio IAS-Research Philosophy of Biology Group, Department of

Logic and Philosophy of Science, University of the Basque Country (UPV/EHU),

Donostia – San Sebastian, Spain

Sumanta Mukherjee Bioinformatics Centre, Indian Institute of Science,

Bangalore, Karnataka, India

Ivan Mura The Microsoft Research - University of Trento Centre for Computa-

tional and Systems Biology, Trento, Italy

Katsuhiko S. Murakami Department of Biochemistry and Molecular Biology,

Pennsylvania State University, University Park, PA, USA

Yota Murakami Department of Chemistry, Hokkaido University, Sapporo, Japan

Mark A. Musen Stanford Center for Biomedical Informatics Research, Stanford

University, Stanford, CA, USA

Marco Muzi-Falconi Dipartimento di Scienze Biomolecolari e Biotecnologie,

Universita di Milano, Milan, Italy

Rajeswara Babu Mythri Department of Neurochemistry, National Institute of

Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India

Jose C. Nacher Department of Information Science, Faculty of Science, Toho

University, Funabashi, Chiba, Japan

Haroon Naeem Institute for Bioinformatics, Ludwig-Maximilians-University

Munich, Munich, Germany

Masao Nagasaki Institute of Medical Science, University of Tokyo, Tokyo, Japan

xxxiv Contributors

Grzegorz Nalepa Department of Pediatrics, Section of Pediatric Hematology-

Oncology, Riley Hospital for Children, Indiana University School of Medicine,

Indianapolis, IN, USA

Nobukazu Nameki Gunma University, Kiryu, Japan

Jeyakumar Natarajan Data Mining and Text Mining Laboratory, Department of

Bioinformatics, Bharathiar University, Coimbatore, India

Tim W. Nattkemper Biodata Mining Group, Faculty of Technology, Bielefeld

University, Bielefeld, Germany

Chrystopher L. Nehaniv Royal Society/Wolfson Bio Computation

Research Laboratory, School of Computer Science, University of Hertfordshire,

Hatfield, UK

Patrick Nelson CCMB 2017 Palmer Commons, University of Michigan, Ann

Arbor, MI, USA

Goran Nenadic Manchester Interdisciplinary Biocentre, University of Manchester,

Manchester, UK

David P. Nickerson Auckland Bioengineering Institute, University of Auckland,


Poul M. Nielsen Department of Engineering Science, University of Auckland,


Kay Nieselt Center for Bioinformatics T€ubingen, Faculty of Science, University of

T€ubingen, T€ubingen, Germany

Siegfried Nijssen Katholieke Universiteit, Leuven, Belgium

Svetoslav Nikolov Institute of Mechanics and Biomechanics-BAS, Bulgarian

Academy of Science, Sofia, Bulgaria

Chris J. Norbury Sir William Dunn School of Pathology, University of Oxford,

Oxford, UK

Bela Novak Department of Biochemistry, Oxford Centre for Integrative Systems

Biology, University of Oxford, Oxford, UK

Nicolas le Novere EMBL-European Bioinformatics Institute, Wellcome Trust


Geoff Nunns Auckland Bioengineering Institute, University of Auckland,


Michael F. Ochs Department of Oncology, Johns Hopkins University, Baltimore,

MD, USA

Maureen A. O’Malley Department of Philosophy, University of Sydney, Sydney,

NSW, Australia

Sandra Orchard EMBL Outstation, European Bioinformatics Institute, Hinxton,

Cambridge, UK

Gerard J. Ostheimer Department of Agriculture, Washington, DC, USA

Contributors xxxv

Casey L. Overby Medical Education and Biomedical Informatics, University of

Washington School of Medicine, Seattle, WA, USA

Brigitte Katrin Paap Department of Neurology, Institute of Immunology, Univer-

sity of Rostock, Rostock, Germany

Graham Packham Cancer Research UK Centre, University of Southampton

Cancer Sciences Division, Southampton University Hospital NHS Trust,

Southampton, UK

Niall Palfreyman Biotechnology and Bioinformatics, Weihenstephan-Triesdorf

University of Applied Science, Freising, Germany

Alida Palmisano Department of Biological Sciences and Department of Computer

Science, Department of Biological Sciences Virginia Tech, Virginia Polytechnic

Institute and State University, Blacksburg, VA, USA

Luigi Palopoli Dipartimento di Elettronica, Informatica e Sistemistica Universita

della Calabria, Rende, Italy

Paolo De Paoli Centro di Riferimento Oncologico (CRO) – IRCCS, Aviano, PN, Italy

Antonis Papachristodoulou Department of Engineering Science, University of

Oxford, Oxford, UK

Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK

Jason A. Papin Department of Biomedical Engineering, University of Virginia,


Sunwon Park Department of Chemical and Biomolecular Engineering, Korea

Advanced Institute of Science and Technology (KAIST), Daejeon, Korea

Chaitali Paul G.N. Ramachandran Knowledge Centre for Genome Informatics,

Institute of Genomics and Integrative Biology, Delhi, India

Shayn M. Peirce Department of Biomedical Engineering, University of Virginia,


Luiz O. F. Penalva Department of Cellular and Structural Biology, Greehey

Children’s Cancer Research Institute, University of Texas Health Science Center,

San Antonio, TX, USA

Livia Perez-Hidalgo Instituto de Biologıa Molecular y Celular del Cancer, CSIC/

Universidad de Salamanca, Salamanca, Spain

Ernesto Perez-Rueda Departamento de Ingenierıa Celular y Biocatalisis, Instituto

de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, More-

los, Mexico

Nikolai Petrovsky Department of Endocrinology, Flinders Medical Centre/Flinders

University, Adelaide, Australia

Steve R. Pettifer Faculty of Life Sciences and School of Computer Science,


Andres Mauricio Pinzon Velasco Department of Systems Engineering,

Universidad Jorge Tadeo Lozano, Bogota, Colombia

xxxvi Contributors

Efstratios Pistikopoulos Biological Systems Engineering Laboratory, Department


London, UK

Conrad Plake Biotechnology Center (BIOTEC), Technische Universit€at Dresden,

Dresden, Germany

Hannes Planatscher Natural and Medical Sciences Institute at the University of

Tuebingen, Reutlingen, Germany

Paolo Plevani Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita

di Milano, Milan, Italy

Daniel Polani Adaptive Systems Research Group, School of Computer Science,

University of Hertfordshire, Hatfield, UK

Joseph R. Pomerening Department of Biology, Indiana University, Bloomington,

IN, USA

Ranjan K. Pradhan Department of Physiology, Biotechnology and Bioengineering


Karyala Prashanthi Bioinformatics Centre, Indian Institute of Science, Bangalore,

Karnataka, India

Corrado Priami Microsoft Research-University of Trento Centre for Computa-

tional and Systems Biology and DISI, University of Trento, Povo, Trento, Italy

Ela Pustulka-Hunt GS SystemsX, ETH Zurich, Zurich, Switzerland

SampoPyysalo Department ofComputer Science, University of Tokyo, Tokyo, Japan

Zhen Qi The Wallace H. Coulter Department of Biomedical Engineering, Georgia

Institute of Technology and Emory University, Atlanta, GA, USA

Hong Qian Department of Applied Mathematics, University of Washington,

Seattle, WA, USA

Yu-Qing Qiu Department of Chemical Pathology, The Chinese University of Hong

Kong, Hong Kong, China

Novi Quadrianto SML-NICTA and RSISE-ANU, Canberra, ACT, Australia

Andreas Quandt Institute of Molecular Systems Biology IMSB, ETH Zurich,

Zurich, Switzerland

Vito Quaranta The Vanderbilt-Ingram Cancer Center, Nashville, TN, USA

Anna Racz-Monus Department of Applied Biotechnology and Food Science,

Budapest University of Technology and Economics, Budapest, Hungary

Gajendra Raghava Bioinformatics Centre, Institute of Microbial Technology,

Chandigarh, Chandigarh, India

Kalpana Raja Data Mining and Text Mining Laboratory, Department of Bioinfor-

matics, Bharathiar University, Coimbatore, India

Contributors xxxvii

Meghna Rajvanshi Department of Chemical Engineering, Indian Institute of

Technology Bombay, Powai, Mumbai, Maharashtra, India

Jorge Mario Gomez Ramirez Department of Chemical Engineering, Universidad

de los Andes, Bogota, Colombia

Jan Ramon Declarative Languages and Artificial Intelligence Group, Katholieke

Universiteit Leuven, Leuven, Belgium

Shoba Ranganathan Department of Chemistry and Biomolecular Sciences and

ARC Center of Excellence in Bioinformatics, Macquarie University, Sydney,

NSW, Australia

Department of Biochemistry, Yong Loo Lin School of Medicine, National University

of Singapore, Singapore

Rajni Rani Molecular Immunogenetics Group, National Institute of Immunology,

New Delhi, Delhi, India

M. R. Satyanarayana Rao Chromatin Biology Laboratory, Molecular Biology and

Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Banga-

lore, Karnataka, India

Andreas Raue Institute for Physics, University of Freiburg, Freiburg, Germany

Dietrich Rebholz-Schuhmann European Bioinformatics Institute, Hinxton, UK

Ee chee Ren Laboratory of Immunogenetics and Viral Host-Pathogen Genomics,

Singapore Immunology Network, Department of Microbiology, Yong Loo Lin

School of Medicine, National University of Singapore, Singapore, Singapore

Xianwen Ren Key Laboratory of Systems Biology of Pathogens, Ministry of

Health, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and

Peking Union Medical College, Beijing, China

Osbaldo Resendis-Antonio Center for Genomics Sciences-UNAM, Universidad

Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico

Silvia Restrepo Department of Biological Sciences, Universidad de los Andes,

Bogota, Colombia

Steven D. Rhodes School of Medicine, Indiana University, Indianapolis, IN, USA

Robert C. Richardson Department of Philosophy, University of Cincinnati,

Cincinnati, OH, USA

Gregory Riddick Neuro-Oncology Branch, National Cancer Institute, Bethesda,

MD, USA

Andrea Rocco Division of Microbial Sciences, Faculty of Health and Medical


Carlos Rodrıguez-Caso Complex Systems Laboratory, University Pompeu Fabra,

Barcelona, Spain

Domingo Rodrıguez-Baena School of Engineering, Pablo de Olavide University,

Escuela Politecnica Superior, Seville, Spain

xxxviii Contributors

Maria Rodriguez-Fernandez Department of Chemical Engineering, Institute for

Collaborative Biotechnologies, University of California, Santa Barbara, CA, USA

M. Carmen Romano Institute for Complex Systems and Mathematical Biology,

University of Aberdeen, Aberdeen, UK

Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK

Simona E. Rombo Istituto di Calcolo e Reti ad Alte Prestazioni, Consiglio

Nazionale delle Ricerche, Rende (CS), Italy

Dipartimento di Elettronica, Informatica e Sistemistica, Universita della Calabria,

Rende, Italy

Ricardo Cruz-Herrera del Rosario Genome Institute of Singapore, Singapore,

Singapore

Sigrid Rouam Universite Paris-Sud, Villejuif, France

Jianhua Ruan Department of Computer Science, University of Texas at San

Antonio, San Antonio, TX, USA

Fabian Rudolf Department of Biosystems Science and Engineering, ETH Zurich,

Basel, Switzerland

Oliver Ruebenacker Center for Cell Analysis and Modeling, University of Con-

necticut Health Center, Farmington, CT, USA

Kepa Ruiz-Mirazo Department Logic and Philosophy of Science, University of the

Basque Country, Donostia – San Sebastian, Spain

Biophysics Unit (CSIC–UPV/EHU), University of the Basque Country, Leioa, Spain

Ann E. Rundell Biomedical Engineering, PurdueUniversity,West Lafayette, IN, USA

Mika O. Ruonala NeuroToponomics Group, Center for Membrane Proteomics

Campus Riedberg, Goethe University of Frankfurt, Frankfurt, Germany

Emma Saavedra Department of Biochemistry, National Institute for Cardiology

“Ignacio Chavez”, Mexico City, Mexico

Sudipto Saha School of Medicine, Center for Proteomics and Bioinformatics, Case

Western Reserve University, Cleveland, OH, USA

Kazuki Saito Graduate School of Frontier Sciences, University of Tokyo, Chiba,

Tokyo, Japan

Shigeru Saito Infocom Corporation, Tokyo, Japan

Taiichi Sakamoto Chiba Institute of Technology, Narashino, Japan

Kishore R. Sakharkar Infectious Diseases Cluster, Universiti Sains Malaysia,

Pulau Pinang, Malaysia

Meena K. Sakharkar Graduate School of Life and Environmental Science,

University of Tsukuba, Tsukuba, Ibaraki, Japan

Alberto Sanguino Specialty Division for Systems Biotechnology, Technical

University of Munich, Garching, Germany

Contributors xxxix

Giuliana Di Santo Dipartimento di Elettronica, Informatica e Sistemistica

Universita della Calabria, Rende, Italy

Akinori Sarai Department of Bioscience and Bioinformatics, Kyushu Institute of

Technology (KIT), Iizuka, Japan

Kazunori Sasaki HumanMetabolome Technologies Inc., Tsuruoka, Yamagata, Japan

Masamitsu Sato Department of Biophysics and Biochemistry, Graduate School of

Science, University of Tokyo, Bunkyo–ku, Tokyo, Japan

PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan

Emre Sayan Cancer Research UK Centre, University of Southampton Cancer

Sciences Division, Southampton University Hospital NHS Trust, Southampton, UK

Jutta Schickore Department of History and Philosophy of Science, Indiana Uni-

versity, Bloomington, IN, USA

Tamar Schlick Department of Chemistry and Courant Institute of Mathematical

Sciences, New York University, New York, NY, USA

Oliver Schmidt School of Biomedical Sciences, University of Ulster, Coleraine, UK

Bernhard Schmierer Department of Biochemistry, Oxford Centre for Integrative

Systems Biology (OCISB), University of Oxford, Oxford, UK

Ulf Schmitz Department of Systems Biology and Bioinformatics, Institute of Com-

puter Science, University of Rostock, Rostock, Germany

Christian Sch€onbach Department of Bioscience and Bioinformatics, Kyushu Insti-

tute of Technology, Iizuka, Fukuoka, Japan

Falk Schreiber Leibniz Institute of Plant Genetics and Crop Plant Research (IPK),

OT Gatersleben, Stadt Seeland, Germany

Martin Luther University Halle–Wittenberg, Halle, Germany

Walter Schubert Molecular Pattern Recognition Research (MPRR) Group,

Otto–von–Guericke University Magdeburg, Magdeburg, Germany

Chinese Academy of Science and Max Planck Society (CAS–MPG) Partner Institute

for Computational Biology (PICB), Shanghai, China

Human Toponome Project, ToposNomos Ltd, Munich, Germany

Jean-Marc Schwartz Manchester Institute of Biotechnology, Faculty of Life

Sciences, University of Manchester, Manchester, UK

Masayuki Seki Graduate School of Pharmaceutical Sciences, Tohoku University,

Sendai, Miyagi, Japan

Rituparna Sen G.N. Ramachandran Knowledge Centre for Genome Informatics,


Toshiya Senda Biomedicinal Information Research Centre (BIRC), National Insti-

tute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

xl Contributors

Ab Rauf Shah G.N. Ramachandran Knowledge Centre for Genome Informatics,


Jagesh Shah Department of Systems Biology, Harvard Medical School and Renal

Division, Brigham and Women’s Hospital, Boston, MA, USA

Deepak Sharma Translational Health Science and Technology Institute, Gurgaon,

India

Nobuo Shimamoto Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan

Richard Simon Division of Cancer Treatment and Diagnosis, National Cancer

Institute, Rockville, Maryland, USA

Harpreet Singh Computational Biology Service Unit, Cornell University, Ithaca,

NY, USA

Biomedical Informatics Centre, Indian Council of Medical Research, New Delhi,

India

Adrien Six Immunology-Immunopathology-Immunotherapy, UPMC University

Paris 06, UMR7211, CNRS, UMR7211, INSERM, U959, Paris, France

Jan M. Skotheim Department of Biology, Stanford University School of Medicine,

Stanford, CA, USA

Brian D. Sleeman School of Mathematics, University of Leeds, Leeds, UK

Andrew D. Smith Molecular and Computational Biology Section, Division of

Biological Sciences, University of Southern California, Los Angeles, CA, USA

Jacky L. Snoep Department of Biochemistry, Stellenbosch University, Matieland,

South Africa

Manchester Institute for Biotechnology, University of Manchester, Manchester, UK

Molecular Cell Physiology, Vrije Universiteit Amsterdam, Amsterdam, The

Netherlands

Tatsuhiko Someya University of Tsukuba, Tsukuba, Japan

Pramod R. Somvanshi Department of Chemical Engineering, Indian Institute of

Technology Bombay, Powai, Mumbai, Maharashtra, India

Carlos Sonnenschein Department of Anatomy and Cellular Biology, Tufts Univer-

sity School of Medicine, Boston, MA, USA

Ana M. Soto Department of Anatomy and Cellular Biology, Tufts University

School of Medicine, Boston, MA, USA

Sandro J. de Souza Ludwig Institute for Cancer Research, Sao Paolo, Brazil

Irena Spasic School of Computer Science and Informatics, Cardiff University,

Cardiff, UK

Josef Spidlen Terry Fox Laboratory, BC Cancer Agency, BC Cancer Research

Centre, Vancouver, BC, Canada

Contributors xli

Rahul Sreekumar Cancer Research UK Centre, University of Southampton Cancer

Sciences Division, Southampton University Hospital NHS Trust, Southampton, UK

Ramachandran Srinivasan G.N. Ramachandran Knowledge Centre for Genome

Informatics, Institute of Genomics and Integrative Biology, Delhi, India

Gesa Staats Centre for Molecular Biosciences, University of Ulster, Coleraine, UK

Larissa Stanberry Bioinformatics and High-throughput Analysis Laboratory,

Seattle Children’s Research Institute, Seattle, WA, USA

Ian Stansfield Institute ofMedical Sciences, University of Aberdeen, Aberdeen, UK

J€orn Starruß Centre for High Performance Computing (ZIH), Technical University

Dresden, Dresden, Germany

Karl Staser Departments of Pediatrics and Biochemistry, Indiana University School

of Medicine, Indianapolis, IN, USA

Christiana Staudinger Department of Molecular Systems Biology, University of

Vienna, Vienna, Austria

Joerg Stelling Department of Biosystems Science and Engineering, ETH Zurich,

Basel, Switzerland

Achim Stephan Institute of Cognitive Science, University of Osnabr€uck,Osnabr€uck, Germany

Susan Stepney Department of Computer Science, University of York, York, UK

Carsten Sticht Medical Research Center, Medical FacultyMannheim, University of

Heidelberg, Mannheim, Germany

Beatriz Stransky Universidade Federal do ABC, Santo Andre, Brazil

Suresh Subramani Data Mining and Text Mining Laboratory, Department of

Bioinformatics, Bharathiar University, Coimbatore, India

Chenglei Sun Institute of Systems Biology, Shanghai University, Shanghai,

Shanghai, China

Xiaojuan Sun Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua

University of Beijing, Beijing, China

Myong-Hee Sung Laboratory of Receptor Biology and Gene Expression, National

Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Avadhesha Surolia Molecular Biophysics Unit, Indian Institute of Science,

Bangalore, India

Akos Sveiczer Department of Applied Biotechnology and Food Science, Budapest

University of Technology and Economics, Budapest, Hungary

Martin Swain Institute of Biological, Environmental, and Rural Sciences,

Aberystwyth University, Aberystwyth, Ceredigion, UK

Hideaki Tagami Graduate School of Natural Sciences, Nagoya City University,

Nagoya, Aichi, Japan

xlii Contributors

Kan Tanaka Chemical Resources Laboratory, Tokyo Institute of Technology,

Yokohama, Kanagawa, Japan

Jijun Tang Department of Computer Science and Engineering, University of South

Carolina, Columbia, SC, USA

Luis Tari Pharma Early Development Informatics, Hoffmann-La Roche Inc.,

Nutley, NJ, USA

Utpal Tatu Department of Biochemistry, Indian Institute of Science, Bangalore,

Karnataka, India

Giorgio Terracina Dipartimento diMatematica, Universita della Calabria, Rende, Italy

Madhan Thamilarasan Department of Neurology, Institute of Immunology,

University of Rostock, Rostock, Germany

Denis Thieffry IBENS - UMR ENS - CNRS 8197 - INSERM 1024, Paris,

France

Veronique Thomas-Vaslin Immunology-Immunopathology-Immunotherapy,

UPMC University Paris 06, UMR7211, CNRS, UMR7211, INSERM, U959, Paris,

France

Paul Thompson School of Biomedical Sciences, University of Ulster, Coleraine, UK

Jens Timmer Institute for Physics, University of Freiburg, Freiburg, Germany

BIOSS Centre for Biological Signalling Studies and Freiburg Institute for Advanced

Studies (FRIAS), Freiburg, Germany

Department of Clinical and Experimental Medicine, Link€oping University,

Link€oping, Sweden

Jared Toettcher University of California, San Francisco, CA, USA

Joo Chuan Tong Data Mining Department, Institute for Infocomm Research,

Singapore, Singapore

Department of Biochemistry, Yong Loo Lin School of Medicine, National University

of Singapore, Singapore

Weida Tong Division of Systems Biology, National Center for Toxicological

Research, US Food and Drug Administration, Jefferson, AR, USA

Nestor V. Torres Department of Biochemistry and Molecular Biology, University

of La Laguna, San Cristobal de La Laguna, Islas Canarias, Tenerife, Spain

Giuseppe Tradigo Department of Experimental and Clinical Medicine, University

Magna Græcia of Catanzaro, Catanzaro, Italy

Baltasar Trancon y Widemann Ecological Modelling, University of Bayreuth,

Bayreuth, Germany

Guy Tsafnat Centre for Health Informatics, Australian Institute for Health

Innovation, University of New South Wales, Sydney, NSW, Australia

Krasimira Tsaneva-Atanasova Department of Engineering Mathematics,

University of Bristol, Bristol, UK

Contributors xliii

Nam-Kiu Tsing Advanced Modeling and Applied Computing Laboratory,

Department of Mathematics, University of Hong Kong, Hong Kong, China

Jarno Tuimala Finnish Red Cross Blood Service, Helsinki, Finland

Tamas Turanyi Institute of Chemistry, E€otv€osUniversity (ELTE), Budapest, Hungary

John J. Tyson Department of Biological Sciences, Virginia Polytechnic Institute

and State University, Blacksburg, VA, USA

Darren Tyson Vanderbilt University, Nashville, TN, USA

Jon Umerez IAS-Research Philosophy of Biology Group, Department of Logic and

Philosophy of Science, University of the Basque Country (UPV/EHU), Donostia –

San Sebastian, Spain

Leos Shivaya Valasek Laboratory of Regulation of Gene Expression, Institute of

Microbiology AVCR, Prague, Czech Republic

Shireen Vali Cell Works Group Inc., Bangalore, India

Justin N. Vaughn Department of Biochemistry, Cellular, and Molecular Biology,

University of Tennessee, Knoxville, USA

Marquis P. Vawter Functional Genomics Laboratory, Department of Psychiatry

and Human Behavior, University of California, Irvine, CA, USA

Fransisco Vazquez Department of Computer Architecture and Electronics, Univer-

sity of Almerıa, Almerıa, Spain

Kann Vearasilp Department of Systems Biology and Bioinformatics, Institute of

Computer Science, University of Rostock, Rostock, Germany

Nubia Velasco Department of Industrial Engineering, Universidad de los Andes,

Bogota, Colombia

Pierangelo Veltri Department of Medical and Surgical Sciences, University Magna

Græcia of Catanzaro, Catanzaro, Italy

Kareenhalli V. Venkatesh Department of Chemical Engineering, Indian Institute

of Technology Bombay, Powai, Mumbai, Maharashtra, India

Celine Vens Department of Computer Science, Katholieke Universiteit Leuven,

Leuven, Belgium

Julio Vera Department of Systems Biology and Bioinformatics, Institute of

Computer Science, University of Rostock, Rostock, Germany

Rajni Verma G.N. Ramachandran Knowledge Centre for Genome Informatics,


Karin Verspoor Victoria Research Laboratory, National ICT Australia, University

of Melbourne, Melbourne, VIC, Australia

Center for Computational Pharmacology, University of Colorado, Aurora, CO, USA

Basilio Vescio Department of Clinical and Experimental Medicine, Magne Graecia

University of Catanzaro, Catanzaro, Italy

xliv Contributors

Kalyan C. Vinnakota Computational Bioengineering Group, Biotechnology and

Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA

P. K. Vinod Department of Biochemistry, Oxford Centre for Integrative Systems

Biology, University of Oxford, Oxford, UK

Rosella Visintin IEO, European Institute of Oncology, Milan, Italy

Olga Vitek Department of Statistics, Department of Computer Science, Purdue

University, West Lafayette, IN, USA

Juan Antonio Vizcaıno EMBL Outstation, European Bioinformatics Institute

(EBI), European Molecular Biology Laboratory Wellcome Trust Genome Campus,

Hinxton, Cambridge, UK

Dat T. Vo Department of Cellular and Structural Biology, Greehey Children’s Cancer

Research Institute, University of Texas Health Science Center, San Antonio, TX, USA

Eberhard O. Voit TheWallace H. Coulter Department of Biomedical Engineering,


Albrecht G. von Arnim Department of Biochemistry, Cellular, and Molecular

Biology and Graduate Program in Genome Science and Technology, University of

Tennessee, Knoxville, USA

Anja Voss-B€ohme Center for Information Services and High Performance Com-

puting (ZIH), Technical University Dresden, Dresden, Germany

Christine Waddington MOAC/University of Warwick, Coventry, UK

Andreas Wagner Institute of Evolutionary Biology and Environmental Studies,

University of Zurich, Zurich, Switzerland

Steffen Waldherr Institute for Systems Theory and Automatic Control, University

of Stuttgart, Stuttgart, Germany

Feng-Sheng Wang Department of Chemical Engineering, National Chung Cheng

University, Chiayi, Taiwan

Haiying Wang School of Computing and Mathematics, Computer Science

Research Institute, University of Ulster, Jordanstown, UK

Jiguang Wang Beijing Institute of Genomics, Chinese Academy of Sciences,

Beijing, Beijing, China

Lin Wang School of Computer Science and Information Engineering, Tianjin

University of Science and Technology, Tianjin, China

Rui-Sheng Wang Department of Physics, Pennsylvania State University, Univer-

sity Park, PA, USA

Ruiqi Wang Institute of Systems Biology, Shanghai University, Shanghai, China

Yong Wang Academy of Mathematics and Systems Sciences, Chinese Academy of

Sciences, Beijing, China

Zhihui Wang Harvard-MIT (HST) Athinoula A. Martinos Center for Biomedical

Imaging, Massachusetts General Hospital, Charlestown, MA, USA

Contributors xlv

Lin Wanglin School of Computer Science and Information Engineering, Tianjin

University of Science and Technology, Tianjin, China

Eric Werner Department of Physiology, Anatomy and Genetics, University of

Oxford, Oxford, UK

Department of Computer Science, University of Oxford, Oxford, UK

Oxford Advanced Research Foundation, Fort Myers, FL, USA

Stefanie Wienkoop Department of Molecular Systems Biology, University of

Vienna, Vienna, Austria

Peter Wilkinson Vaccine and Gene Therapy Institute, Port St. Lucie, FL, USA

Jana Wolf Mathematical Modelling of Cellular Processes, MDC Max Delbr€uck

Center for Molecular Medicine, Berlin, Germany

Katy Wolstencroft School of Computer Science, University of Manchester,

Manchester, UK

Arno Wouters Department of Philosophy, Erasmus University Rotterdam,

Rotterdam, The Netherlands

Xiaohua Wu Department of Pediatrics, Herman B Wells Center for Pediatric

Research, Indiana University School of Medicine, Indianapolis, IN, USA

Kejia Xu Institute of Systems Biology, Shanghai University, Shanghai, China

Yuki Yamaguchi Tokyo Institute of Technology, Graduate School of Bioscience

and Biotechnology, Yokohama, Japan

Feng-Chun Yang Departments of Pediatrics, Herman B Wells Center for Pediatric

Research, School of Medicine, Indiana University, Indianapolis, IN, USA

Guang Yao Department of Molecular and Cellular Biology, University of Arizona,

Tucson, AZ, USA

Weiwei Yin Department of Biomedical Engineering, Georgia Institute of Technol-

ogy and Emory University, Atlanta, GA, USA

Elizabeth Yohannes Center for Proteomics and Bioinformatics, School of

Medicine, Case Western Reserve University, Cleveland, OH, USA

Lingchong You Biomedical Engineering Department, DukeUniversity, Durham, NC,

USA

Tao You Computational Biology, Innovative Medicines, AstraZeneca,

Macclesfield, Cheshire, UK

Tommy Yu Auckland Bioengineering Institute, University of Auckland, Auckland,

New Zealand

Choamun Yun Department of Chemical and Biomolecular Engineering, Korea


Hongseok Yun Department of Chemical and Biomolecular Engineering, Korea


xlvi Contributors

Judit Zamborszky The Microsoft Research - University of Trento Centre for

Computational and Systems Biology, CoSBi, Trento, Italy

An-Ping Zeng Institute of Bioprocess and Biosystems, Technical University

Hamburg-Harburg, Hamburg, Germany

Yi Zeng Department of Pediatrics, University of Arizona, Tucson, AZ, USA

Marie Lisandra Zepeda-Mendoza Center for Genomics Sciences-UNAM,

Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico

Uwe Klaus Zettl Department of Neurology, Institute of Immunology, University of


Junhua Zhang Academy of Mathematics and Systems Science, Chinese Academy

of Sciences, Beijing, China

Key Laboratory of Random Complex Structures and Data Science, Chinese Academy


National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy


Minlu Zhang Department of Computer Science, University of Cincinnati,

Cincinnati, OH, USA

Shihua Zhang National Center for Mathematics and Interdisciplinary Sciences,

Academy of Mathematics and Systems Science, Chinese Academy of Sciences,

Beijing, China

Shu-Qin Zhang School of Mathematical Sciences, Fudan University, Shanghai,

China

Xiujun Zhang Institute of System Biology, Shanghai University, Shanghai, China

Yan Zhang Key Laboratory of Systems Biology, Shanghai Institutes for Biological

Sciences, Chinese Academy of Sciences, Shanghai, China

Zhong-Yuan Zhang School of Statistics, Central University of Finance and Eco-

nomics, Beijing, China

Shan Zhao Department of Pharmacology and Systems Therapeutics, Mount Sinai

School of Medicine, New York, NY, USA

Xing-Ming Zhao Institute of System Biology, Shanghai University, Shanghai,

China

Yingdong Zhao Division of Cancer Treatment and Diagnosis, National Cancer

Institute, Rockville, Maryland, USA

Huiru Zheng School of Computing and Mathematics, Computer Science Research

Institute, University of Ulster, Jordanstown, UK

Tianshou Zhou School of Mathematics and Computational Sciences, Sun Yet-Sen

University, Guangzhou, Guangdong, China

Contributors xlvii

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