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Alan Wee-Chung Liew
Bao-Liang Lu
Bin Ma
Christopher James Langmead
David Dagan Feng
Francis Y. L. Chin
Guohui Lin
Henry C. M. Leung
Hong Yan
Jinyan Li
Ján Manuch
Limsoon Wong
Luay Nakhleh
Lusheng Wang
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APBC (apbc)
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Publications
Viewing Publication 1 - 100 from 240
2008
Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach
Mohamed Ibrahim Abouelhoda
,
Robert Giegerich
,
Behshad Behzadi
,
Jean-Marc Steyaert
.
apbc 2008
:
261-272
[doi]
GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts
Tyler S. Alioto
,
Roderic Guigó
,
Ernesto Picardi
,
Graziano Pesole
.
apbc 2008
:
363-372
[doi]
Supervised Ensembles of Prediction Methods for Subcellular Localization
Johannes Aßfalg
,
Jing Gong
,
Hans-Peter Kriegel
,
Alexey Pryakhin
,
Tiandi Wei
,
Arthur Zimek
.
apbc 2008
:
29-38
[doi]
Predicting Nucleolar Proteins Using Support-Vector Machines
Mikael Bodén
.
apbc 2008
:
19-28
[doi]
Preface
Alvis Brazma
,
Satoru Miyano
,
Tatsuya Akutsu
.
apbc 2008
:
[doi]
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan
Alvis Brazma
,
Satoru Miyano
,
Tatsuya Akutsu
, editors,
Volume 6 of
Advances in Bioinformatics and Computational Biology
, Imperial College Press,
2008.
A Fixed-Parameter Approach for Weighted Cluster Editing
Sebastian Böcker
,
Sebastian Briesemeister
,
Quang Bao Anh Bui
,
Anke Truß
.
apbc 2008
:
211-220
[doi]
Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from SNP Fragments
Zhixiang Chen
,
Bin Fu
,
Robert T. Schweller
,
Boting Yang
,
Zhiyu Zhao
,
Binhai Zhu
.
apbc 2008
:
333-342
[doi]
Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency
Francis Y. L. Chin
,
Henry C. M. Leung
,
Man-Hung Siu
,
Siu-Ming Yiu
.
apbc 2008
:
343-352
[doi]
Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP
Bhaskar DasGupta
,
Jin Jun
,
Ion I. Mandoiu
.
apbc 2008
:
353-362
[doi]
Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions
Melissa J. Davis
,
Andrew Newman
,
Imran Khan
,
Jane Hunter
,
Mark A. Ragan
.
apbc 2008
:
145-154
[doi]
Recent Progress in Phylogenetic Combinatorics
Andreas W. M. Dress
.
apbc 2008
:
1-4
[doi]
Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress
Yannick Haudry
,
Chuang Kee Ong
,
Laurence Ettwiller
,
Hugo Berube
,
Ivica Letunic
,
Misha Kapushesky
,
Paul-Daniel Weeber
,
Xi Wang
,
Julien Gagneur
,
Charles Girardot
,
Detlev Arendt
,
Peer Bork
,
Alvis Brazma
,
Eileen E. M. Furlong
,
Joachim Wittbrodt
,
Thorsten Henrich
.
apbc 2008
:
373-382
[doi]
Image Compression-based Approach to Measuring the Similarity of Protein Structures
Morihiro Hayashida
,
Tatsuya Akutsu
.
apbc 2008
:
221-230
[doi]
KEGG for Medical and Pharmaceutical Applications
Minoru Kanehisa
.
apbc 2008
:
5
[doi]
Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers
Alireza Hadj Khodabakhshi
,
Ján Manuch
,
Arash Rafiey
,
Arvind Gupta
.
apbc 2008
:
49-58
[doi]
From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature
Jin-Dong Kim
,
Tomoko Ohta
,
Kanae Oda
,
Jun-ichi Tsujii
.
apbc 2008
:
165-176
[doi]
Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations
Dmitry A. Konovalov
,
Dik Heg
.
apbc 2008
:
321-332
[doi]
Discrimination of Native Folds Using Network Properties of Protein Structures
Alper Küçükural
,
Osman Ugur Sezerman
,
Aytul Ercil
.
apbc 2008
:
59-68
[doi]
Symbolic Approaches for Finding Control Strategies in Boolean Networks
Christopher James Langmead
,
Sumit Kumar Jha
.
apbc 2008
:
307-320
[doi]
Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies
Juntao Li
,
Majid Eshaghi
,
Jianhua Liu
,
Karuturi R. Krishna Murthy
.
apbc 2008
:
383-392
[doi]
Semantic Similarity Definition over Gene Ontology by Further Mining of the Information Content
Yuan-Peng Li
,
Bao-Liang Lu
.
apbc 2008
:
155-164
[doi]
Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks
Yunlei Li
,
Dick de Ridder
,
Marco J. L. de Groot
,
Marcel J. T. Reinders
.
apbc 2008
:
273-286
[doi]
Interacting Amino Acid Preferences of 3D Pattern Pairs at the Binding Sites of Transient and Obligate Protein Complexes
Suryani Lukman
,
Kelvin Sim
,
Jinyan Li
,
Yi-Ping Phoebe Chen
.
apbc 2008
:
69-78
[doi]
Seed Optimization Is No Easier than Optimal Golomb Ruler Design
Bin Ma
,
Hongyi Yao
.
apbc 2008
:
133-144
[doi]
A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment
Ryuichiro Nakato
,
Osamu Gotoh
.
apbc 2008
:
101-110
[doi]
fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information for Pairs with Low Sequence Identity
Huzefa Rangwala
,
George Karypis
.
apbc 2008
:
111-122
[doi]
Structural Descriptors of Protein-Protein Binding Sites
Oliver Sander
,
Francisco S. Domingues
,
Hongbo Zhu
,
Thomas Lengauer
,
Ingolf Sommer
.
apbc 2008
:
79-88
[doi]
Chemical Compound Classification with Automatically Mined Structure Patterns
Aaron M. Smalter
,
Jun Huan
,
Gerald H. Lushington
.
apbc 2008
:
39-48
[doi]
Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes
Krister M. Swenson
,
William Arndt
,
Jijun Tang
,
Bernard M. E. Moret
.
apbc 2008
:
241-250
[doi]
Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics
Satish Tadepalli
,
Naren Ramakrishnan
,
Layne T. Watson
,
Bhubaneshwar Mishra
,
Richard F. Helm
.
apbc 2008
:
297-306
[doi]
SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions
Cuong Than
,
Luay Nakhleh
.
apbc 2008
:
251-260
[doi]
Finding Non-coding RNAs Through Genome-Scale Clustering
Huei-Hun Tseng
,
Zasha Weinberg
,
Jeremy Gore
,
Ronald R. Breaker
,
Walter L. Ruzzo
.
apbc 2008
:
199-210
[doi]
Protein Interactions Extracted from Genomes and Papers
Alfonso Valencia
.
apbc 2008
:
7
[doi]
Genome Halving with Double Cut and Join
Robert Warren
,
David Sankoff
.
apbc 2008
:
231-240
[doi]
Analysis of Structural Strand Asymmetry in Non-coding RNAs
Jiayu Wen
,
Brian J. Parker
,
Georg F. Weiller
.
apbc 2008
:
187-198
[doi]
A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots
Thomas K. F. Wong
,
Y. S. Chiu
,
Tak Wah Lam
,
Siu-Ming Yiu
.
apbc 2008
:
89-100
[doi]
String Kernels with Feature Selection for SVM Protein Classification
Wen-Yun Yang
,
Bao-Liang Lu
.
apbc 2008
:
9-18
[doi]
Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds
Jialiang Yang
,
Louxin Zhang
.
apbc 2008
:
123-132
[doi]
Classification of Protein Sequences Based on Word Segmentation Methods
Yang Yang
,
Bao-Liang Lu
,
Wen-Yun Yang
.
apbc 2008
:
177-186
[doi]
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks
Xing-Ming Zhao
,
Rui-Sheng Wang
,
Luonan Chen
,
Kazuyuki Aihara
.
apbc 2008
:
287-296
[doi]
2007
Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments
Tatsuya Akutsu
,
Daiji Fukagawa
.
apbc 2007
:
165-174
[doi]
Exploring Genome Rearrangements using Virtual Hybridization
M. Belcaid
,
Anne Bergeron
,
Annie Chateau
,
Cedric Chauve
,
Yannick Gingras
,
Guylaine Poisson
,
M. Vendette
.
apbc 2007
:
205-214
[doi]
Selecting Genes with Dissimilar Discrimination Strength for Sample Class Prediction
Zhipeng Cai
,
Randy Goebel
,
Mohammad R. Salavatipour
,
Yi Shi
,
Lizhe Xu
,
Guohui Lin
.
apbc 2007
:
81-90
[doi]
Combining N-grams and Alignment in G-protein Coupling Specificity Prediction
Betty Yee Man Cheng
,
Jaime G. Carbonell
.
apbc 2007
:
363-372
[doi]
Using Formal Concept Analysis for Microarray Data Comparison
V. Choi
,
Y. Huang
,
Vy Lam
,
D. Potter
,
Reinhard C. Laubenbacher
,
Karen Duca
.
apbc 2007
:
57-66
[doi]
Subtle Motif Discovery for Detection of DNA Regulatory Sites
Matteo Comin
,
Laxmi Parida
.
apbc 2007
:
27-36
[doi]
Semi-supervised Pattern Learning for Extracting Relations from Bioscience Texts
Shilin Ding
,
Minlie Huang
,
Xiaoyan Zhu
.
apbc 2007
:
307-316
[doi]
A Probabilistic Method to Identify Compensatory Substitutions for Pathogenic Mutations
B. C. Easton
,
A. V. Isaev
,
Gavin A. Huttley
,
Peter Maxwell
.
apbc 2007
:
195-204
[doi]
Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization Experiments
Qi Fu
,
Elizabeth Bent
,
James Borneman
,
Marek Chrobak
,
Neal E. Young
.
apbc 2007
:
17-26
[doi]
Computing the Breakpoint Distance between Partially Ordered Genomes
Zheng Fu
,
Tao Jiang
.
apbc 2007
:
237-246
[doi]
Exploring Genomes of Distantly Related Mammals
Jennifer A. Marshall Graves
.
apbc 2007
:
1
[doi]
A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs
Morihiro Hayashida
,
Tatsuya Akutsu
,
Hiroshi Nagamochi
.
apbc 2007
:
257-266
[doi]
Exact and Heuristic Approaches for Identifying Disease-Associated SNP Motifs
Gaofeng Huang
,
Peter Jeavons
,
Dominic Kwiatkowski
.
apbc 2007
:
175-184
[doi]
etagenome Analysis using Megan
Daniel H. Huson
,
Alexander F. Auch
,
Qi Ji
,
Stephan C. Schuster
.
apbc 2007
:
7-16
[doi]
Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection
Falk Hüffner
,
Sebastian Wernicke
,
Thomas Zichner
.
apbc 2007
:
277-286
[doi]
Protein Structure-Structure Alignment with Discrete Fr echet Distance
Minghui Jiang
,
Ying Xu
,
Binhai Zhu
.
apbc 2007
:
131-141
[doi]
Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta
Yonggang Lu
,
Jing He
,
Charlie E. M. Strauss
.
apbc 2007
:
143-151
[doi]
An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data
Sara C. Madeira
,
Arlindo L. Oliveira
.
apbc 2007
:
67-80
[doi]
All Hits All The Time: Parameter Free Calculation of Seed Sensitivity
Denise Y. F. Mak
,
Gary Benson
.
apbc 2007
:
327-340
[doi]
Fitting Protein Chains to Cubic Lattice is NP-Complete
Ján Manuch
,
Daya Ram Gaur
.
apbc 2007
:
153-164
[doi]
Bugs, Guts and Fat - A Systems Approach to the Metabolic Axis of Evil
Joseph H. Nadeau
.
apbc 2007
:
3
[doi]
De Novo Peptide Sequencing for Mass Spectra Based on Multi-Charge Strong Tags
Kang Ning
,
Ket Fah Chong
,
Hon Wai Leong
.
apbc 2007
:
287-296
[doi]
Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions
Kinya Okada
,
Kiyoshi Asai
,
Masanori Arita
.
apbc 2007
:
317-326
[doi]
Fast Structural Similarity Search Based on Topology String Matching
Sung-Hee Park
,
David Gilbert
,
Keun Ho Ryu
.
apbc 2007
:
341-351
[doi]
Protein Identification via Spectral Networks Analysis
Pavel A. Pevzner
.
apbc 2007
:
5
[doi]
Two Plus Two Does not Equal Three: Statistical Tests for Multiple Genome Comparison
Narayanan Raghupathy
,
Rose Hoberman
,
Dannie Durand
.
apbc 2007
:
215-225
[doi]
Preface
David Sankoff
,
Lusheng Wang
,
Francis Chin
.
apbc 2007
:
[doi]
Proceedings of 5th Asia-Pacific Bioinformatics Conference, APBC 2007, 15-17 January 2007, Hong Kong, China
David Sankoff
,
Lusheng Wang
,
Francis Chin
, editors,
Volume 5 of
Advances in Bioinformatics and Computational Biology
, Imperial College Press,
2007.
Complexities and Algorithms for Glycan Structure Sequencing using Tandem Mass Spectrometry
Baozhen Shan
,
Bin Ma
,
Kaizhong Zhang
,
Gilles Lajoie
.
apbc 2007
:
297-306
[doi]
Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree
M. Stissing
,
Christian N. S. Pedersen
,
Thomas Mailund
,
Gerth Stølting Brodal
,
Rolf Fagerberg
.
apbc 2007
:
101-110
[doi]
Computing the All-Pairs Quartet Distance on a Set of Evolutionary Trees
M. Stissing
,
Thomas Mailund
,
Christian N. S. Pedersen
,
Gerth Stølting Brodal
,
Rolf Fagerberg
.
apbc 2007
:
91-100
[doi]
Genotype-Based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase Diagrams
Young Ju Suh
,
Wentian Li
.
apbc 2007
:
185-194
[doi]
A Randomized Algorithm for Comparing Sets of Phylogenetic Trees
Seung-Jin Sul
,
Tiffani L. Williams
.
apbc 2007
:
121-130
[doi]
Inferring Gene Regulatory Networks by Machine Learning Methods
Jochen Supper
,
Holger Fröhlich
,
Christian Spieth
,
Andreas Dräger
,
Andreas Zell
.
apbc 2007
:
247-256
[doi]
Gene Regulatory Network Inference via Regression Based Topological Refinement
Jochen Supper
,
Holger Fröhlich
,
Andreas Zell
.
apbc 2007
:
267-276
[doi]
A Global Maximum Likelihood Super-Quartet Phylogeny Method
Pinghao Wang
,
Bing Bing Zhou
,
Monther Tarawneh
,
Daniel Chu
,
Chen Wang
,
Albert Y. Zomaya
,
Richard P. Brent
.
apbc 2007
:
111-120
[doi]
Simple and Fast Alignment of Metabolic Pathways by Exploiting Local Diversity
Sebastian Wernicke
,
Florian Rasche
.
apbc 2007
:
353-362
[doi]
An Effective Promoter Detection Method using the Adaboost Algorithm
Xudong Xie
,
Shuanhu Wu
,
Kin-Man Lam
,
Hong Yan
.
apbc 2007
:
37-46
[doi]
The Distance Between Randomly Constructed Genomes
Wei Xu
.
apbc 2007
:
227-236
[doi]
A New Strategy of Geometrical Biclustering for Microarray Data Analysis
Hongya Zhao
,
Alan Wee-Chung Liew
,
Hong Yan
.
apbc 2007
:
47-56
[doi]
2006
Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach
Marcos J. Araúzo-Bravo
,
Satoshi Fujii
,
Hidetoshi Kono
,
Akinori Sarai
.
apbc 2006
:
227-236
[doi]
Structure-Based Chemical Shift Prediction Using Random Forests Non-Linear Regression
K. Arun
,
Christopher James Langmead
.
apbc 2006
:
317-326
[doi]
An Efficient Algorithm for String Motif Discovery
Francis Y. L. Chin
,
Henry C. M. Leung
.
apbc 2006
:
79-88
[doi]
Trends in Codon and Amino Acid Usage in Human Pathogen Tropheryma Whipplei, the only Known Actinobacteria with Reduced Genome
Sabyasachi Das
,
Sandip Paul
,
Chitra Dutta
.
apbc 2006
:
139-148
[doi]
Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes
Shao-Shan Huang
,
Debra L. Fulton
,
David J. Arenillas
,
Paul Perco
,
Shannan J. Ho Sui
,
James R. Mortimer
,
Wyeth W. Wasserman
.
apbc 2006
:
247-256
[doi]
Accuracy of Four Heuristics for the Full Sibship Reconstruction Problem in the Presence of Genotype Errors
Dmitry A. Konovalov
.
apbc 2006
:
7-16
[doi]
A Randomized Algorithm for Learning Mahalanobis Metrics: Application to Classification and Regression of Biological Data
Christopher James Langmead
.
apbc 2006
:
217-226
[doi]
On the Inference of Regulatory Elements, Circuits, and Modules
Wen-Hsiung Li
.
apbc 2006
:
1
[doi]
System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis Thaliana
C. W. Li
,
W. C. Chang
,
B. S. Chen
.
apbc 2006
:
27-37
[doi]
Inference of Gene Regulatory Networks from Microarray Data: A Fuzzy Logic Approach
Patrick C. H. Ma
,
Keith C. C. Chan
.
apbc 2006
:
17-26
[doi]
A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis
Michael K. Ng
.
apbc 2006
:
129-138
[doi]
Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses
Sandip Paul
,
Sabyasachi Das
,
Chitra Dutta
.
apbc 2006
:
149-158
[doi]
Automating the Search for Lateral Gene Transfer
Mark A. Ragan
.
apbc 2006
:
3
[doi]
Techniques for Assessing Phylogenetic Branch Support: A Performance Study
Derek A. Ruths
,
Luay Nakhleh
.
apbc 2006
:
187-196
[doi]
RECOMP: A Parsimony-Based Method for Detecting Recombination
Derek A. Ruths
,
Luay Nakhleh
.
apbc 2006
:
59-68
[doi]
Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica)
M. Shashikanth
,
A. Snethalatharani
,
S. K. Mubarak
,
K. Ulaganathan
.
apbc 2006
:
277-286
[doi]
Property-Dependent Analysis of Aligned Proteins from Two Or More Populations
Steinar Thorvaldsen
,
Elinor Ytterstad
,
Tor Flå
.
apbc 2006
:
169-178
[doi]
Whole Genome Optical Mapping
Michael S. Waterman
.
apbc 2006
:
5
[doi]
A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid Preference
Zhong-Ru Xie
,
Ming-Jing Hwang
.
apbc 2006
:
237-246
[doi]
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