Feny? D. (Ed.) Computational Biology
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Computational Biology
Edited by
David Fenyö
The Rockefeller University, New York, NY, USA
Editor
David Fenyö
The Rockefeller University
New York, NY
USA
fenyo@rockefeller.edu
ISSN 1064-3745 e-ISSN 1940-6029
ISBN 978-1-60761-841-6 e-ISBN 978-1-60761-842-3
DOI 10.1007/978-1-60761-842-3
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2010934634
© Springer Science+Business Media, LLC 2010
All rights reserved. This work may not be translated or copied in whole or in part without the written permission of
the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013,
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v
Preface
Computational biology is an interdisciplinary field that applies mathematical, statistical,
and computer science methods to answer biological questions. The importance of compu-
tational biology has increased with the introduction of high-throughput techniques such
as automatic DNA sequencing, comprehensive expression analysis with microarrays, and
proteome analysis with modern mass spectrometry. Computational methods are not only
critical for the effective analysis of the large amount of data from these experiments but
also important to fully utilize this wealth of information to provide more realistic models
of biological systems. The ultimate goal of modeling complex systems like an entire cell
might be far in the future, but computational methods are essential in building the foun-
dation that will allow this goal to be reached. The primary purpose of this book is to pres-
ent a broad survey of computational biology methods by focusing on their applications,
including primary sequence analysis, protein structure elucidation, transcriptomics and
proteomics data analysis, and exploration of protein interaction networks.
New York, NY David Fenyö
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vii
Contents
Preface ................................................................. v
Contributors ............................................................. ix
1 Sequencing and Genome Assembly Using Next-Generation Technologies....... 1
Niranjan Nagarajan and Mihai Pop
2 RNA Structure Prediction........................................... 19
István Miklós
3 Normalization of Gene-Expression Microarray Data ....................... 37
Stefano Calza and Yudi Pawitan
4 Prediction of Transmembrane Topology and Signal Peptide
Given a Protein’s Amino Acid Sequence ................................ 53
Lukas Käll
5 Protein Structure Modeling ......................................... 63
Lars Malmström and David R. Goodlett
6 Template-Based Protein Structure Modeling............................. 73
Andras Fiser
7 Automated Protein NMR Structure Determination in Solution............... 95
Wolfram Gronwald and Hans Robert Kalbitzer
8 Computational Tools in Protein Crystallography.......................... 129
Deepti Jain and Valerie Lamour
9 3-D Structures of Macromolecules Using Single-Particle Analysis in EMAN ..... 157
Steven J. Ludtke
10 Computational Design of Chimeric Protein Libraries
for Directed Evolution ............................................. 175
Jonathan J. Silberg, Peter Q. Nguyen, and Taylor Stevenson
11 Mass Spectrometric Protein Identification Using the Global
Proteome Machine ................................................ 189
David Fenyö, Jan Eriksson, and Ronald Beavis
12 Unbiased Detection of Posttranslational Modifications Using
Mass Spectrometry ................................................ 203
Maria Fälth Savitski and Mikhail M. Savitski
13 Protein Quantitation Using Mass Spectrometry .......................... 211
Guoan Zhang, Beatrix M. Ueberheide, Sofia Waldemarson,
Sunnie Myung, Kelly Molloy, Jan Eriksson, Brian T. Chait,
Thomas A. Neubert, and David Fenyö
14 Modeling Experimental Design for Proteomics ........................... 223
Jan Eriksson and David Fenyö
viii Contents
15 A Functional Proteomic Study of the Trypanosoma brucei Nuclear
Pore Complex: An Informatic Strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Jeffrey A. DeGrasse and Damien Devos
16 Inference of Signal Transduction Networks from Double Causal Evidence ...... 239
Réka Albert, Bhaskar DasGupta, and Eduardo Sontag
17 Reverse Engineering Gene Regulatory Networks Related to Quorum Sensing
in the Plant Pathogen Pectobacterium atrosepticum ........................ 253
Kuang Lin, Dirk Husmeier, Frank Dondelinger, Claus D. Mayer, Hui Liu,
Leighton Prichard, George P.C. Salmond, Ian K. Toth, and Paul R.J. Birch
18 Parameter Inference and Model Selection in Signaling Pathway Models ........ 283
Tina Toni and Michael P. H. Stumpf
19 Genetic Algorithms and Their Application to In Silico Evolution
of Genetic Regulatory Networks...................................... 297
Johannes F. Knabe, Katja Wegner, Chrystopher L. Nehaniv,
and Maria J. Schilstra
Index ................................................................... 323
ix
Contributors
Ré k a al b e R t
•
Department of Physics, Penn State University,
University Park, PA, USA
R
o n a l d be a v i s
•
The Biomedical Research Centre, University of British Columbia,
Vancouver, BC, Canada
P
a u l R. J. bi R c h
•
Scottish Crop Research Institute, Dundee, UK
s
t e f a n o ca l z a
•
Department of Medical Epidemiology and Biostatistics,
Karolinska Institute, Stockholm, Sweden
b
R i a n t. ch a i t
•
The Rockefeller University, New York, NY, USA
b
h a s k a R da s Gu P t a
•
Department of Computer Science, University of Illinois
at Chicago, Chicago, IL, USA
J
e f f R e y a. deGR a s s e
•
U.S. Food and Drug Administration, College Park, MD, USA
d
a m i e n de v o s
•
Structural Bioinformatics, European Molecular Biology Laboratory,
Heidelberg, Germany
f
R a n k do n d e l i n G e R
•
Biomathematics & Statistics Scotland and School
of Informatics, University of Edinburgh, Edinburgh, UK
J
a n eR i k s s o n
•
Department of Chemistry, Swedish University of Agricultural Sciences,
Uppsala, Sweden
m
a R i a fä l t h sa v i t s k i
•
Unit Cancer Genome Research, Division of Molecular
Genetics, Heidelberg, Germany
d
a v i d fe n y ö
•
The Rockefeller University, New York, NY, USA
a
n d R a s fi s e R
•
Department of Systems and Computational Biology & Department
for Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
d
a v i d R. Go o d l e t t
•
Department of Medicinal Chemistry,
University of Washington, Seattle, Washington, USA
W
o l f R a m GR o n W a l d
•
Institute for Biophysics and Physical Biochemistry,
University of Regensburg, Regensburg, Germany
d
i R k hu s m e i e R
•
Biomathematics and Statistics Scotland, Edinburgh & Aberdeen, UK
d
e e P t i Ja i n
•
National Centre for Biological Sciences, Bangalore, India
h
a n s Ro b e R t ka l b i t z e R
•
Institute for Biophysics and Physical Biochemistry,
University of Regensburg, Regensburg, Germany
l
u k a s kä l l
•
Department of Biochemistry and Biophysics,
Center for Biomembrane Research and Stockholm Bioinformatics Center,
Stockholm University, Stockholm, Sweden
J
o h a n n e s f. kn a b e
•
Biological and Neural Computation Laboratory
and Adaptive Systems Research Group, STRI, University of Hertfordshire,
Hatfield, Hertfordshire, UK
v
a l e R i e la m o u R
•
Institute of Genetics and Molecular and Cellular Biology,
Illkirch, France
k
u a n G li n
•
Biomathematics and Statistics Scotland, Edinburgh & Aberdeen, UK
h
u i li u
•
Scottish Crop Research Institute, Dundee, UK
s
t e v e n J. lu d t k e
•
Department of Biochemistry and Molecular Biology,
Baylor College of Medicine, Houston, TX, USA
x Contributors
la R s ma l m s t R ö m
•
Institute for Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
c
l a u s d. ma y e R
•
Biomathematics and Statistics Scotland, Edinburgh & Aberdeen, UK
i
s t v á n mi k l ó s
•
Rényi Institute, Hungarian Academy of Sciences, Budapest,
Hungary
k
e l l y mo l l o y
•
The Rockefeller University, New York, NY, USA
s
u n n i e my u n G
•
The Rockefeller University, New York, NY, USA
n
i R a n J a n na G a R a J a n
•
Center for Bioinformatics and Computational Biology,
Institute for Advanced Computer Studies and Department of Computer Science,
University of Maryland, College Park, MD, USA
c
h R y s t o P h e R l. ne h a n i v
•
Biological and Neural Computation Laboratory
and Adaptive Systems Research Group, STRI, University of Hertfordshire,
Hatfield, Hertfordshire, UK
t
h o m a s a. ne u b e R t
•
Kimmel Center for Biology and Medicine at the Skirball
Institute and Department of Pharmacology, New York University School
of Medicine, New York, NY, USA
P
e t e R Q. nG u y e n
•
Department of Biochemistry and Cell Biology,
Rice University, Houston, TX, USA
y
u d i Pa W i t a n
•
Department of Medical Epidemiology and Biostatistics,
Karolinska Institute, Stockholm, Sweden
m
i h a i Po P
•
Center for Bioinformatics and Computational Biology,
Institute for Advanced Computer Studies and Department of Computer Science,
University of Maryland, College Park, MD, USA
l
e i G h t o n PR i t c h a R d
•
Scottish Crop Research Institute, Dundee, UK
G
e o R G e P. c. sa l m o n d
•
Department of Biochemistry, University of Cambridge,
Cambridge, UK
m
i k h a i l m. sa v i t s k i
•
Cellzome AG, Heidelberg, Germany
m
a R i a J. sc h i l s t R a
•
Biological and Neural Computation Laboratory,
University of Hertfordshire, Hatfield, Hertfordshire, UK
J
o n a t h a n J. si l b e R G
•
Cellzome AG, Heidelberg, Germany
e
d u a R d o so n t a G
•
Department of Mathematics, Rutgers University,
New Brunswick, NJ, USA
t
a y l o R st e v e n s o n
•
Department of Biochemistry and Cell Biology,
Rice University, Houston, TX, USA
m
i c h a e l P. h. st u m P f
•
Division of Molecular Biosciences, Centre for Bioinformatics,
Imperial College London, London, UK
t
i n a to n i
•
Division of Molecular Biosciences, Centre for Bioinformatics,
Imperial College London, London, UK
i
a n k. to t h
•
Scottish Crop Research Institute, Dundee, UK
b
e a t R i x m. ue b e R h e i d e
•
The Rockefeller University, New York, NY, USA
s
o f i a Wa l d e m a R s o n
•
Kimmel Center for Biology and Medicine at the Skirball
Institute and Department of Pharmacology, New York University School
of Medicine, New York, NY, USA