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P R O C E E d i N q s Of T h E 5 T k A s i A - P A C i f i c

BIOINFORMATICS
CONFERENCE
 SERIES ON ADVANCES IN BIOINFORMATICS
AND COMPUTATIONAL BIOLOGY

Series Editors: ISSN: 1751-6404

Ying XU (University of Georgia, U S A )
Limsoon WONG (National University of Singapore, Singapore)

Associate Editors:
Ruth Nussinov (NU,U S A ) See-Kiong Ng (Inst for Infocomm Res, Singapore)
Rolf Apweiler (EBI, UK) Kenta Nakai (Uniu of Tokyo, Japan)
Ed Wingender (BioBase, Germany) Mark Ragan (Uniu of Queensland, Australia)

VOl. 1: Proceedings of the 3rd Asia-Pacific Bioinformatics Conference

Eds: Yi-Ping Phoebe Chen and Limsoon Wong

VOl. 2: Information Processing and Living Systems

Eds: Vladimir B. Bajic and Tan Tin Wee

VOl. 3: Proceedings of the 4th Asia-Pacific Bioinformatics Conference

Eds: Tao Jiang, Ueng-Cheng Yang, Yi-Ping Phoebe Chen
and Lirnsoon Wong

VOl. 4: Computational Systems Bioinformatics

Eds: Peter Markstein and Ying Xu

VOl. 5: Proceedings of the 5th Asia-Pacific Bioinformatics Conference

Eds: David Sankoff,Lusheng Wang and Francis Chin
Series on Advances inBioinformatics and Computational Biology– Volume 5

PROCEEdings OF THE 5TH ASIA PACIFIC

BIOINFORMATICS
C O N fERENCE

H O N KONG
~ 15 - 17 JANUARY 2007

Editorsd

DAvid SANkoFF
UNIVERSITY O f O T T A W A , C A N A d A

LuskENq WAN^
CITY UNIVERSITY Of H O NI<ONq,
~ H O NK~O N ~

FRANCk CkiN
TkE UNiVERSiTY Of HONGK o N ~ ,H O NK~O N ~

Imperial College Press

Published by
Imperial College Press
57 Shelton Street
Covent Garden
London WC2H 9HE

Distributed by
World Scientific Publishing Co. Pte. Ltd.
5 Toh Tuck Link, Singapore 596224
USA ofice: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601
UK ofice: 57 Shelton Street, Covent Garden, London WC2H 9HE

British Library Cataloguing-in-PublicationData

A catalogue record for this book is available from the British Library,

PROCEEDINGS OF THE 5TH ASIA-PACIFIC BIOINFORMATICS CONFERENCE

Copyright 02007 by Imperial College Press
All rights reserved. This book, orparts thereof, may not be reproduced in any form or by any means, electronic or
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For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center,
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ISBN- 13 978- 1-86094-783-4

ISBN-10 1-86094-783-2

Printed in Singapore by B & JO Enterprise

 PREFACE

High-throughput sequencing and functional genomics technologies have given us

the human genome sequence as well as those of other experimentally, medically and
agriculturally important species, and have enabled large-scale genotyping and gene
expression profiling of human populations. Databases containing large numbers
of sequences, polymorphisms, structures and gene expression profiles of normal
and diseased tissues are rapidly being generated for human and model organisms.
Bioinformatics is thus rapidly growing in importance in the annotation of genomic
sequences, in the understanding of the interplay among and between genes and
proteins, in the analysis the genetic variability of species, in the identification of
pharmacological targets and in the inference of evolutionary origins, mechanisms
and relationships.
The Asia-Pacific Bioinformatics Conference series is an annual forum for ex-
ploring research, development, and novel applications of bioinformatics. It brings
together researchers, professionals, and industrial practitioners for interaction and
exchange of knowledge and ideas. The Fifth Asia-Pacific Bioinformatics Conference,
APBC2007, was held in Hong Kong 15-17 January, 2007.
A total of 104 papers were submitted to APBC 2007. These submissions came
from Bangladesh, China, Hong Kong, India, Japan, Korea, Malaysia, Singapore,
Taiwan, Thailand, Australia, New Zealand, Denmark, France, Germany, Hungary,
Italy, Israel, Portugal, UK, Canada, Mexico and USA. We assigned each paper to
at least three members of the programme committee. Although not all members of
the programme committee managed to review all the papers assigned to them, a
total of 317 reviews were received, so that there were about three reviews per paper
on average.
A total of 35 papers (33%) were accepted for presentation and publication in
the proceedings of APBC 2007. Based on the affiliation of the authors, 1.25 of the
accepted papers were from China, 1.46 were from Hong Kong, 3 were from Japan,
0.83 were from Korea, 1were from Singapore, 2.30 were from Australia, 2 were from
Denmark, 0.15 were from France, 4.5 were from Germany, 0.5 were from Italy, 1
were from Portugal, 1.66 were from UK, 4.57 were from Canada, 10.78 were from
USA.
In addition to the accepted papers, the scientific programme of APBC 2006 also
included three keynote talks, by Jennifer A. Marshall Graves, Joseph H. Nadeau
and Pave1 A. Pevzner, as well as tutorial and poster sessions. The presentations
were of very high quality. Almost a third focused on evolution and phylogeny,
largely a t the genome level, a similar number dealt with protein structure and pro-
teomics more generally, and a good proportion studied various aspects of pathways,

V
vi

networks, transcriptomics and microarray technology. A range of other topics in

bioinformatics and computational biology were also covered, ranging from motif
and gene recognition, through haplotypes and population genetics, to databases
and text mining. Much of this work featured techniques of sequence analysis, while
many of the papers included applications to biology and medicine.
We had a great time in Hong Kong, enhancing the interactions between many
researchers and practitioners, and reuniting the Asia-Pacific bioinformatics commu-
nity in the context of an international conference with worldwide participation.
Finally, we wish to express our gratitude to the authors of the submitted papers,
the members of the programme commitee and their subreferees, the members of the
organizing committee, Phoebe Chen and Limsoon Wong (our liaisons in the APBC
steering committee), the keynote speakers, our generous sponsors, and supporting
organizations for making APBC 2007 a great success.

David Sankoff
Lusheng Wang
Francis Chin

17 January 2007
APBC2007
ORGANIZATION

Conference Chair
Francis YL Chin, The University of Hong Kong, Hong Kong

Organizing Committee
Francis YL Chin (Chair), The University of Hong Kong
David Smith (Poster Session), The University of Hong Kong
H.F. Ting (Finance and Registration), The University of Hong Kong
Lusheng Wang (Publication), The City University of Hong Kong
Xiaowen Liu (Publication), The City University of Hong Kong
S.M. Yiu (Local Arrangement and Tutorial), The University of Hong Kong
Daniel Hung (Webmaster), The University of Hong Kong
Samson Sin (Webmaster), The University of Hong Kong

Steering Committee
Phoebe Chen (Chair), Deakin University, Australia
Sang Yup Lee, KAIST, Korea
Satoru Miyano, University of Tokyo, Japan
Mark Ragan, University of Queensland, Australia
Limsoon Wong, National University of Singapore

vii
 ...
Vlll

Program Committee
David Sankoff (Chair), The University of Ottawa
Lusheng Wang (Chair), The City University of Hong Kong
Tatsuya Akutsu, Kyoto University
Miguel Andrade, Ottawa Health Research Institute
Stephane Aris-Brosou, University of Ottawa
Joel Bader, Johns Hopkins University
Serafim Batzoglou, Stanford University
David Bryant, University of Auckland
Jeremy Buhler, Washington University in St. Louis
Peter Donnelly, University of Oxford
Dannie Durand, Carnegie Mellon University
Nadia El-Mabrouk, University of Montreal
Robert Giegerich, Bielefeld University
Carole Goble, University of Manchester
Concettina Guerra, Universita’ di Padova
Dan Gusfield, University of California, Davis
Michael Hallett , McGill University
Sridhar Hannenhalli, University of Pennsylvania
Daniel Huson, Tbingen University
Gavin Huttley, Australian National Univeristy
Jenn-Kang Hwang, National Chiao Tung University
Tao Jiang, University of California - Riverside
Uri Keich, Cornell University
Anand Kumar, University of Leipzig
Tak Wah Lam, The University of Hong Kong
Doheon Lee, KAIST, Korea
Jinyan Li, Institute for Infocomm Research
Wentian Li, Feinstein Institute for Medical Research
Guohui Lin, University of Alberta
Michal Linial, The Hebrew University of Jerusalem
Zhijie Liu, University of Georgia
Bin Ma, University of Western Ontario
Satoru Miyano, The University of Tokyo
Laxmi Parida, IBM Thomas J. Watson Research Center
Mark Ragan, University of Queensland
Marie-France Sagot, University Claude Bernard, Lyon I
Akinori Sarai, Kyushu Institute of Technology
Vincent Schachter , Genoscope
Steven Skiena, State University of New York at Stony Brook
Edward Susko, Dalhousie University
Yun Song, University of California, Davis
Robert Stevens, University of Manchester
Alfonso Valencia, Centro Nacional de Biotechnologia
Michael Waterman, University of Southern California
 ix

Ken Wolfe, University of Dublin

Stacia Wyman, Williams College
Hong Yan, City University of Hong Kong
Qiang Yang, Hong Kong University of Science and Technology
Kaizhong Zhang, University of Western Ontario
Liqing Zhang, Virginia Tech
Louxin Zhang, National University of Singapore
X

Additional Reviewers
Shandar Ahmad Marcos Jesus Arauzo Bravo Alexander Auch
Iris Bahir Richard Bean Pierre-Yves Bourguignon
Shihyen Chen Matteo Comin Mike Cornell
Tobias Dezulian Zhihong Ding Maxime Durot
James Eales Logan Everett Paul Fisher
Morihiro Hayashida Cornelia Hedeler Duncan Hull
Helen Hulme Shane Jensen Noam Kaplan
Gunnar W. Klau Kiyoung Lee Yaoyong Li
Jingping Liu Yaniv Loewenstein Suryani Lukman
Julia Mixtacki Jose Carlos Nacher Niranj an Nagara j an
Hiroshi Nakashima Kay Nieselt Elon Portugaly
Magnus Rattray Jonathan Schug Charles Semple
Baozhen Shan Yun S. Song Kristian Stevens
Ashish V. Tendulkar Victor Tong Roy Varshavsky
Balaji Venkatachalam Li-San Wang Michael Wilson
Katy Wolstencroft Yufeng Wu Lei Xin
Zheng Yuan Guanglan Zhang
 CONTENTS

Preface V

APBC 2007 Organization vii

Keynote Papers

Exploring Genomes of Distantly Related Mammals 1

J.A. Marshall Graves

Bugs, Guts and Fat - A Systems Approach to the Metabolic ‘Axis of Evil’ 3
J. Nadeau

Protein Identification via Spectral Networks Analysis 5

P. Pevzner

Contributed Papers

Metagenome Analysis using MEGAN 7

D.H. Huson, A.F. Auch, J. Qi, and S.C. Schuster

Algorithmic Approaches to Selecting Control Clones in DNA Array

Hybridization Experiments 17
Q. Fu, E. Bent, J . Borneman, M. Chrobak, and N. Young

Subtle Motif Discovery for Detection of DNA Regulatory Sites 27

M. Comin, and L. Parida

An Effective Promoter Detection Method using the Adaboost Algorithm 37

X . Xze, S. Wu, K.-M. Lam, and H. Yan

A New Strategy of Geometrical Biclustering for Microarray Data Analysis 47

H. Zhao, A. W.C. Liew, and H. Yan

xi
xii

Using Formal Concept Analysis for Microarray Data Comparison 57

V. Choi, Y. Huang, V. Lam, D. Potter, R . Laubenbacher, and K. Duca

An Efficient Biclustering Algorithm for Finding Genes with Similar

Patterns in Time-series Expression Data 67
S.C. Madeira, and A.L. Oliveira

Selecting Genes with Dissimilar Discrimination Strength for Sample

Class Prediction 81
Z. Cai, R. Goebel, M.R. Salavatipour, Y. Shi, L. Xu, and G. Lin

Computing the All-Pairs Quartet Distance on a Set of Evolutionary

Trees 91
M. Stissing, T . Mailund, C.N.S. Pedersen, G.S. Brodal,
and R. Fagerberg

Computing the Quartet Distance Between Evolutionary Trees of

Bounded Degree 101
M. Stissing, C.N.S. Pedersen, T . Mailund, G.S. Brodal,
and R. Fagerberg

A Global Maximum Likelihood Super-Quartet Phylogeny Method 111

P. Wang, B.B. Zhou, M. Taraeneh, D. Chu, C. Wang, A . Y. Zomaya,
and R.P. Brent

A Randomized Algorithm for Comparing Sets of Phylogenetic Trees 121

S.-J. Sul, and T.L. Williams

Protein Structure-Structure Alignment with Discrete Frkchet Distance 131

M. Jiang, Y. Xu, and B. Zhu

Deriving Protein Structure Topology from the Helix Skeleton in Low

Resolution Density Map using Rosetta 143
Y. Lu, J . He, and C.E.M. Strauss

Fitting Protein Chains to Cubic Lattice is NP-complete 153

J. Mafiuch, and D.R. Gaur

Inferring a Chemical Structure from a Feature Vector Based on

Frequency of Labeled Paths and Small Fragments 165
T. Alcutsu, and D. Fukagawa
 ...
Xlll

Exact and Heuristic Approaches for Identifying Disease-Associated

SNP Motifs 175
G. Huang, P. Jeavons, and D. Kwiatkowski

Genotype-Based Case-Control Analysis, Violation of Hardy-Weinberg

Equilibrium, and Phase Diagrams 185
Y.J. Suh, and W. L i

A Probabilistic Method to Identify Compensatory Substitutions for

Pathogenic Mutations 195
B.C. Easton, A. V. Isaev, G.A. Huttley, and P. Maxwell

Exploring Genome Rearrangements using Virtual Hybridization 205

M. Belcaid, A. Bergeron, A . Chateau, C. Chauve, Y. Gingras,
G. Poisson, and M. Vendette

Two Plus Two Does not Equal Three: Statistical Tests for Multiple
Genome Comparison 215
N . Raghupathy, R. Hoberman, and D. Durand

The Distance Between Randomly Constructed Genomes 227

w.xu
Computing the Breakpoint Distance between Partially
Ordered Genomes 237
Z. Fu,and T. Jiang

Inferring Gene Regulatory Networks by Machine Learning Methods 247

J. Supper, H. Frohlich, C. Spieth, A. Drager, and A . Zell

A Novel Clustering Method for Analysis of Biological Networks using

Maximal Components of Graphs 257
M.Hayashida, T. Akutsu, and H. Nagamochi

Gene Regulatory Network Inference via Regression Based Topological

Refinement 267
J. Supper, H. Frohlich, and A. Zell

Algorithm Engineering for Color-Coding to Facilitate Signaling

Pathway Detection 277
F. Huffner, S. Wernicke, and T. Zichner
xiv

De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge

Strong Tags 287
K. Ning, K.F. Chong, and H. W. Leong

Complexities and Algorithms for Glycan Structure Sequencing using

Tandem Mass Spectrometry 297
B. Shun, B. Ma, K. Zhang, and G. Lajoie

Semi-supervised Pattern Learning for Extracting Relations from

Bioscience Texts 307
S. Ding, M. Huang, and X . Zhu

Flow Model of the Protein-protein Interaction Network for Finding

Credible Interactions 317
K. Okada, K. Asai, and M. Arzta

All Hits All The Time: Parameter Free Calculation of Seed Sensitivity 327
D.Y.F. Mak. and G. Benson

Fast Structural Similarity Search Based on Topology String Matching 341

S.-H. Park, D. Gilbert, and K.H. Ryu

Simple and Fast Alignment of Metabolic Pathways by Exploiting

Local Diversity 353
S. Wernicke, and F. Rasche

Combining N-grams and Alignment in G-protein Coupling Specificity

Prediction 363
B. Y.M. Chen, and J. G. Carbonell

Author Index 373

 EXPLORING GENOMES OF DISTANTLY RELATED MAMMALS

JENNIFER A. MARSHALL GRAVES

ARC Centre for Kangaroo Genomics, Research School of Biological Sciences
Australian National Universi@,Canberra, ACT 2601, Australia

There are three groups of extant mammals, two of which abound in Australia. Marsupials (kangaroos
and their relatives) and monotremes (echidna and the fabulous platypus) have been evolving inde-
pendently for most of mammalian history. The genomes of marsupial and monotreme mammals are
particularly valuable because these alternative mammals fill a phylogenetic gap in vertebrate species
lined up for exhaustive genomic study. Human and mice (w70MY) are too close to distinguish signal,
whereas mammalibird comparisons ( ~ 3 1 0 M Y )are too distant to allow alignment. Kangaroos (180
MY) and platypus (210 MY) are just right. Sequence has diverged sufficiently for stringent detec-
tion of homologies that can reveal coding regions and regulatory signals. Importantly, marsupials and
monotremes share with humans many mammal-specific developmental pathways and regulatory sys-
tems such as sex determination, lactation and X chromosome inactivation.
The ARC Centre for Kangaroo Genomics is characterizing the genome of the model Australian
kangaroo Macropus eugenii (the tammar wallaby), which is being sequenced by AGRF in Australia,
and Baylor (funded by NIH) in the US. We are developing detailed physical and linkage maps of
the genome to complement sequencing, and will prepare and array cDNAs for functional studies,
especially of reproduction and development. Complete sequencing of the distantly related Brazilian
short-tailed opossum Monodelphis domestica by the NIH allows us to compare distantly related marsu-
pials. Sequencing of the genome of the platypus, Omithorhynchus anatinus by Washington University
(funded by the NIH) is complete, and our lab is anchoring contigs to the physical map. We have iso-
lated and completely characterized many BACs and cDNAs containing kangaroo and platypus genes
of interest, and demonstrate the value of comparisons to reveal conserved genome organization and
function, and new insights in the evolution of the mammalian genome, particularly sex chromosomes.

1
This page intentionally left blank
 BUGS, GUTS AND FAT - A SYSTEMS APPROACH
TO THE METABOLIC ‘AXIS OF EVIL’

JOE NADEAU
Department of Genetics and Centerf o r Computational Genomics and Systems Biology
Case Western Reserve University, Cleveland, Ohio,USA

Rapidly growing evidence suggests that complex and variable interactions between host genetic and
systems factors, diet, activity and lifestyle choices, and intestinal microbes control the incidence, sever-
ity and complexity of metabolic diseases. The dramatic increase in the world-wide incidence of these
diseases, including obesity, diabetes, hypertension, heart disease, and fatty liver disease, raises the
need for new ways to maintain health despite inherited and environmental risks. We are pursuing a
comprehensive approach based on diet-induced models of metabolic disease. During the course of
these studies, new and challenging statistical, analytical and computational problems were discovered.
We pioneered a new paradigm for genetic studies based on chromosome substitution strains of labora-
tory mice. These strains involve systematically substituting each chromosome in a host strain with the
corresponding chromosome from a donor strain. A genome survey with these strains therefore involves
testing a panel of individual, distinct and non-overlapping genotypes, in contrast to conventional stud-
ies of heterogeneous populations. Studies of diet-induced metabolic disease with these strains have
already led to striking observations. We discovered that most traits are controlled by a many genetic
variants each of which has unexpectedly large phenotypic effects and that act in a highly non-additive
manner. The non-additive nature of these variants challenges conventional models of the architecture
of complex traits. At every level of resolution from the entire genome to very small genetic intervals,
we discovered comparable levels of genetic complexity, suggesting a fractal property of complex traits.
Another remarkable property of these large-effect variants is their ability to switch complex systems
between alternative phenotypic states such as obese to lean and high to low cholesterol, suggesting
that biological traits might be organized in a small number of stable states rather than continuous
variability. Moreover, by studying correlations between non-genetic variation in pairs of traits (the
genetic control of non-genetic variation), we discovered a new way to dissect the functional architec-
ture of biological systems. Finally, a neglected aspect of these studies of metabolic disease involves
the intestingal microbes. Early studies suggest that diet and host physiology affect the numbers and
kinds of microbes, and that these microbes in turn affect host metabolism. These interactions between
’bugs, guts and fat’ extend systems studies from conventional aspects of genetics and biology to pop-
ulation considerations of the functional interactions between hosts, diet and our microbial passengers.
With these models of diet-induced metabolic disease in chromosome substitution strains, we are now
positioned find ways to tip complex systems from disease to health.

3
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