APBC 2012 Program

The Tenth Asia Pacific Bioinformatics Conference

Melbourne, Australia, 17-19 January 2012

Conference Venue: Rydges Melbourne, 186 Exhibition Street, Melbourne VIC 3000.


Tue 17th January 2012


Room 1

Room 2

07:00 - 09:00 AM

Registration + Poster Setup

09:00 - 09:15 AM

Opening Ceremony

09:15 - 10:15 AM

Keynote 1 – Jenny Graves, La Trobe University “Weird Animal Genomes and Sex”

Session Chair: Phoebe Chen

10:15 – 10:30 AM

Group Photo 1 + Morning Tea + Poster (A) Setup


A1: Genome Evolution

(Session Chair:  Kiwon Lee)

A2: Regulatory Studies

(Session Chair:  Wen-Chi Chang)

10:30 - 11:00 AM

A1.1 Yiwei Zhang, Fei Hu and Jijun Tang. A Mixture Framework for Inferring Ancestral Gene Orders

(P 29)

A2.1 Tzong-Yi Lee and Wen-Chi Chang. GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group

(P 1)

11:00 - 11:30 AM

A1.2 Gloria Fu and Wen-Chang Lin. Identification of gene-oriented exon orthology between human and mouse

(P 44)

A2.2 Alena Mysickova and Martin Vingron. Detection of interacting transcription factors in human tissues using predicted DNA binding affinity (P 31)

11:30 – 12:00 PM

A1.3 David Sankoff, Chunfang Zheng and Baoyong Wang. A model for biased fractionation after whole genome duplication (P 117)

A2.3 Tien-Hao Chang, Chi-Yeh Wu and Chen-Yu Fan. A study of promoter characteristics of head-to-head genes in Saccharomyces cerevisiae (P 33)

12:00 – 01:30 PM

Lunch + Posters (A)

01:30 – 02:30 PM

Invited Speaker 1Narayanaswamy Srinivasan, IIS “Evolution of structure, stability and domain

architectures of multi-domain proteins” Session Chair: Mark Ragan


A3: Gene Network Modelling

(Session Chair:  Hiroshi Matsuno)

A4: Micro / RNA Modelling

(Session Chair:  Wen-chang Lin)

02:30 – 03:00 PM

A3.1 Yukito Watanabe, Shigeto Seno, Yoichi Takenaka and Hideo Matsuda. An Estimation Method for Inference of Gene Regulatory Network Using Bayesian Network with Uniting of Partial Problems (P 2)

A4.1 Sung-Chou Li, Yu-Lun Liao, Meng-Ru Ho, Kuo-Wang Tsai, Chun-Hung Lai and Wen-Chang Lin. miRNA arm selection and isomiR distribution in gastric cancer (P 17)

03:00 – 03:30 PM

A3.2 Kaname Kojima, Seiya Imoto, Rui Yamaguchi, Andre Fujita, Mai Yamauchi, Noriko Gotoh and Satoru Miyano. Identifying Regulational Alterations in Gene Regulatory Networks by State Space Representation of Vector Autoregressive Models and Variational Annealing (P 86)

A4.2 Guoqing Lei, Yong Dou and Wen Wan. CPU-GPU Hybrid Accelerating The Zuker Algorithm for RNA Secondary Structure Prediction Applications (P 35)

03:30 – 04:00 PM

Afternoon Tea + Posters (A)


A5: Database and Data Models

(Session Chair: Rahul Singh)


04:00 – 04:30 PM

A5.1 Hyokyeong Lee, Asher Moody-Davis, Utsab Saha, Brian Suzuki, Daniel Asarnaw, Steve Chen, Michelle Arkin, Conor Caffrey and Rahul Singh. Quantification and Clustering of Phenotypic Screening Data Using Time-Series Analysis for Chemotherapy of Schistosomiasis (P 120)

Tutorial 1   Limsoon Wong.

Analysis of Gene Expression and Proteomic Profiles based on Biological Networks


04:30 – 05:00 PM

A5.2 Christopher Langmead, Hetunandan Kamisetty and Narges Sharif Razavian. Learning Generative Models of Molecular Dynamics (P 106)

05:00 – 05:30 PM

A5.3 Trupti Joshi, Kapil Patil, Michael R. Fitzpatrick, Levi D. Franklin, Qiuming Yao, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry Nguyen and Dong Xu. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics (P 74)

05:30 – 06:00 PM

D5.4 Yanxia Lin. The Algorithm of Equal Acceptance Region for detecting Copy Number Alterations: Applications to  Next-Generation Sequencing Data

(P 68)

7:00 PM

APBC Steering Committee



Wednesday 18th January 2012


Room 1

Room 2

07:30 - 08:30 AM

Registration + Poster Setup

08:30 - 09:30AM

Keynote 2 – Peer Bork, EMBL Heidelberg,

Session Chair: Steven Jones

09:30 – 9:45 AM

Group Photo 2 + Morning Tea + Poster (B) Setup


A5: Database and Data Models (continued)

(Session Chair: Hsien-Da Huang)

B2:  Protein Structural Prediction

(Session Chair: Lusheng Wang)

09:45 – 10:15 AM

A5.5 Nai-Jyuan Wang, Chi-Ching Lee, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Chen and Ping-Chiang Lyu. Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB) (P 81)

B2.1 Keunwan Park and Dongsup Kim. Structure-based Rebuilding of Coevolutionary Information Reveals Functional Modules in Rhodopsin Structure (P 37)

10:15 – 10:45 PM

A5.6 Hatice Ulku Osmanbeyoglu, Ryan Hartmaierr, Steffi Oesterreich and Xinghua Lu. Improving ChIP-seq peak-calling for functional secondary co-activator binding by integrating multiple sources of biological information (P 112)

B2.2 Wenji Ma, Craig Mcanulla and Lusheng Wang. A Protein Complex Prediction Improving Method based on Maximum Matching (P 97)


B1:  Protein – Protein Interaction

(Session Chair:  Ramanathan Sowdhamini)


10:45 - 11:15 AM

B1.1 Lin He, Xi Han and Bin Ma. De Novo Sequencing with Limited Number of Post-Translational Modifications per Peptide (P 104)

B2.3   Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel, and Pramod P. Wangikar. On Validating Genetic Network Reverse Engineering Algorithms Using Small Networks (P 8)

11:15 - 11:45 AM

B1.2 Tomoaki Yamamotoya, Hitomi Dose, Zhongyuan Tian, Adrien Faure, Yoshihiro Toya, Masayuki Honma, Kaori Igarashi, Kenji Nakahigashi, Tomoyoshi Soga, Hirotada Mori and Hiroshi Matsuno. Glycogen is the primary source of glucose during the lag phase of E. coli proliferation (P 52)

B2.4 Abhinav Grover, Shashank Katiyar, Sanjeev Singh and D Sundar. A leishmaniasis study: Structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase (P 62)

11:45 - 12:15 PM

B1.3 Marcin Magnus, Marcin Pawlowski and Janusz Bujnicki. MetaLocGramN: a meta-predictor of protein subcellular localization for Gram-negative bacteria (P 113)

B2.5 Qian Liu, Limsoon Wong and Jinyan Li. Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state (P 73)

12:15 – 01:30 PM

Lunch + Posters (B)

01:30 – 02:30 PM

Invited Speaker 2 - Robin Gasser, University of Melbourne “Harnessing next-generation tools to explore

neglected parasites of major socioeconomic importance” Session Chair: Peer Bork

02:30 – 03:30 PM

Panel Discussion: Bioinformatics - Current Strategies and Future Directions

Panel  Chair: Terry Speed, Members: Steven Jones, Peer Bork, Mark Ragan, Limsoon Wang

Moderator: Phoebe Chen

03:30 – 04:00 PM

Afternoon Tea  + Posters (B)


B1:  Protein – Protein Interaction (continued)


04:00 – 04:30 PM

B1.4 Periyanaina Kesika and Krishnaswamy Balamurugan. Shigella boydii infection in Caenorhabditis elegans and comparative immune regulatory protein interactions  (P 80)

Tutorial 2

Andrew Lonie

Introduction to NGS informatics


04:30 – 05:00 PM

B1.5 Yi Tsung Tang and Hung-Yu Kao. Augmented Transitive Relationships with High Impact Protein Distillation in Protein Interaction Prediction (P 60)


C1:   Algorithmic Optimisation and Evaluation

(Session Chair:  Nihar Mahapatra)

05:00 – 05:30 PM

C1.1 Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh and Yew Soon Ong. QuickVina: Accelerating AutoDock Vina using gradient-based heuristics for global optimization (P 124)

05:30 – 06:00 PM

C1.2 Hossam Ashtawy and Nihar Mahapatra. A Comparative Assessment of Ranking Powers of Conventional and Machine-Learning-Based Scoring Functions on Diverse and Homogeneous Test Sets (P 126)


Conference Dinner – Banquet Speech Professor Steven Jones


Thursday 19th January 2012


Room 1

Room 2

08:00 - 09:00AM

Registration + Poster Setup

09:00 - 10:00AM

Keynote 3 – Terry Speed, WEHI, UC Berkeley “Removing Unwanted Variation from gene expression data”

Session Chair: Phoebe Chen

10:00 – 10:30 AM

Morning Tea + Poster (C) Setup


C2. Knowledge Reconstruction

(Session Chair:  Janusz Bujnicki)

C3. Knowledge Modelling

(Session Chair:  Hae Ja Shin)

10:30 - 11:00 AM

C2.1 Lin Wan and Fengzhu Sun. CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq  (P 28)

C3.1 Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing Zhou and Yee Hwa Yang. Improving X!Tandem on peptide identification from mass spectrometry by integrating empirical modeling and semi-supervised learning (P 15)

11:00 - 11:30 PM

C2.2 Richard Röttger, Ulrich Rückert, Jan Taubert and Jan Baumbach. How little do we actually know? - On the size of gene regulatory networks (P 71)

C3.2  Jikai Lei, Prapaporn Techa-Angkoon and Yanni Sun. NCRNA homology search based on an extended two-dimensional chain algorithm (P 108)

11:30 - 12:00 PM

C2.3 Ngoc Tu Le, Tu Bao Ho and Bich Hai Ho. Computational reconstruction of transcriptional relationships from ChIP-Chip data (P 82)

C3.3 Pradipta Maji and Sushmita Paul. Rough-Fuzzy Clustering for Grouping Functionally Similar Genes from Microarray Data (P 96)

12:00 – 01:00 PM

Lunch + Posters (C)


D1 Protein Drug Applications

(Session Chair:  Christopher Langmead)

D2 Protein Binding Studies

(Session Chair:  Zengyou He)

01:00 -01:30 PM

D1.1 Wilson Wen Bin Goh, Yiehou Lee, Zubaidah Ramdzan, Maxey Chung, Limsoon Wong and Marek Sergot. A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression (P 12)

D2.1 Zhenhua Li, Ying He, Longbing Cao, Limsoon Wong and Jinyan Li. Conservation of water molecules in protein binding interfaces (P 91)

01:30 – 02:00 PM

D1.2 Wei-Chih Huang, Feng-Mao Lin, Tzu-Hao Chang and Hsien-Da Huang. Identifying Cancer Highly-expressed Membrane Receptors for Targeted Drug Delivery (P 21)

D2.2 Sriganesh Srihari and Hon Wai Leong. Employing functional interactions for characterization and detection of sparse complexes from yeast PPI networks (P 5)

02:00 – 02:30 PM

D1.3 Sumit Kumar Jha, Raj G. Dutta, Christopher Langmead and Susmit Jha. Synthesis of Insulin Pump Controllers from Safety Specifications using Bayesian Model Validation (P 116)

D3.3 Yang Zhao, Morihiro Hayashida, Jose Nacher, Hiroshi Nagamochi and Tatsuya Akutsu. Protein complex prediction via improved verification methods using constrained domain-domain matching (P 78)

02:30 – 03:00 PM

Afternoon Tea + Posters (C)

Tutorial 3 – Zengyou He &  Weichuan Yu

Protein Inference: Concepts, Algorithms and Software Tools


D3 Sequencing and Prediction Applications

(Session Chair:  Brian Fristensky)

03:00 -03:30 PM

D3.1 Abu Dayem Ullah, Sudhakar Sahoo, Kathleen Steinhofel and Andreas Albrecht. Derivative Scores from Site Accessibility and Ranking of miRNA Target Predictions (P 57)

03:30 – 04:00 PM

D3.2 Hao Jiang, Wai-Ki Ching and De Lin Chu Discriminant Analysis in Pairwise Kernel Learning for SVM Classification

(P 16)

04:00 – 04:30 PM

Conference Closing & Award Drawing






















Poster Part (A) (Poster Session Chair: Zhirong Sun)
2 Zahra Nourmohammadi, Masoud Sheidai and Somayeh Ghasemzadeh Baraki Comparison of ISSR and RAPD patterns of Sargassum species in Oman Sea and Persian Gulf
3 Wen Li and Zhirong Sun, Systematic Analysis of Chip-Seq Data Indicates That specific Patterns of Histone Modifications Are Associated With Transcription Factor Binding
4 Wenting Li and Zhirong Sun Integrated analyses of cancer genomes and transcriptomes revealed driver modules with correlated geno-phenotypic changes for cancer development
5 Kenichi Yoshida Discrimination between apoptosis and autophagy by expression changes of autophagy-related genes
7 Masoud Sheidaei Phylogeny of the genus Cirsium (Asteraceae) based on genome size, morphometry and molecular analyses
9 Chao Wu and Xuegong Zhang Prioritizing putative regulatory hub genes in cancer by protein-protein interaction and gene expression data
12 Chang Jui Yu, Yan Yu Chen, Shih Chi Peng, David Shan Hill Wong and Yung Jen Chuang Core Network Identification Using Parametric Sensitivity and Multi-way Principal Component Analysis
13 Da Young Lee, Duck Gyoun Shin, Woon Ki Lim and Hae Ja Shin Comparison of the Recombinant Microbial Biosensor Systems for Assessment of Phenolic compounds
14 Veena Pande, Sushil Midha, Nitin Sharma, Usha T, Biplab Bhattacharjae Bhattacharjae, Mayank Pandey and Nagaveni Mb SCREENING OF NATURAL INHIBITORS OF NEURAMINIDASE TYPE 1 IN H1N1 FOR TREATMENT OF SWINE FLU- AN INSILICO APPROACH
17 Graham Alvare, Abiel Roche-Lima and Brian Fristensky BioLegato: A Programmable, Object-Oriented Graphic User Interface
18 Kalpana Raja, Suresh Subramani and Jeyakumar Natarajan Naggner – A hybrid named entity tagger for tagging human proteins/genes
Poster Part (B)
(Poster Session Chair: Sheidaei Masoud)
19 Stephen Goodswen, Paul Kennedy and John Ellis Evaluation of high-throughput ab initio gene finding in apicomplexan genomes
20 Joana P. Gonçalves and Sara Madeira Time-coherent triclustering algorithm: mining local transcriptional patterns in multiple expression time series
23 Adrien Fauré, Barbara Vreede, Élio Sucena and Claudine Chaouiya Logical modelling of the regulatory network controlling the formation of the egg appendages in Drosophila
25 Bing Liu, Danielle Santarelli, Paul Tooney, Carlotta Duncan, Peter Schofield and Murray J. Cairns Integration analysis of miRNA and mRNA in the mouse brain following treatment with clozapine, haloperidol, and olanzapine in the mechanism of antipsychotic drug action
27 Xi Wang, Jing Qin Wu, Paul Tooney and Murray Cairns An RNA-seq data analysis pipeline and its application to real data from schizophrenia brain samples versus controls
28 Song Gao, Denis Bertrand and Niranjan Nagarajan Improved Eukaryotic Genome Assembly with Multiple Large-insert Libraries and an Optimal Scaffolder

29 Yuki Murakami, Qi-Wei Ge and Hiroshi Matsuno, Petri net model construction of signaling pathway and its delay time estimation.
32 Timothy Vaughan, Peter Drummond and Alexei Drummond Inter-strain correlation dynamics during within-host viral evolution
33 Phataraporn Khumphai and David Gordon Evolution of Bacteriocin Plasmids in the RepFIB and RepFIIA Groups in Escherichia coli
34 Piyush Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Antonio Reverter and Mark A. Ragan Gene regulatory networks in cancer systems biology
36 Sung Jin Cho, Jea Woon Ryu and Hak Yong Kim Conversion of directed flow network from undirected protein network
Poster Part (C ) (Poster Session Chair: Crampin Edmund)
37 Yi-Han Bai, Tien-Hao Chang and Chen-Yu Fan Predicting protein-protein interactions based frequent short sequences in proteins
38 Benjamin Goudey, Qiao Wang, Armita Zarnegar, Eder Kikianty, John Markham, Dave Rawlinson, Benjamin Goudey, Geoff Macintyre, Gad Abraham, Fan Shi, Linda Stern, Michael Inouye, Izhak Haviv and Adam Kowalczyk Replication of epistatic DNA loci in five case-control GWAS studies
39 Geoff Macintyre, James Bailey, Adam Kowalczyk and Izhak Haviv Identifying CNVs of regulatory elements which impact overall survival in serous cystadenocarcinoma
40 Yu-Jung Chang, Chien-Chih Chen, Chuen-Liang Chen and Jan-Ming Ho CloudBrush: A String Graph Approach of De Novo Assembly for High-Throughput Sequencing Data with Cloud Computing
41 Sean O'Callaghan, Malcolm Mcconville, Antony Bacic and Vladimir A. Likic Automated peak annotation in non-targeted GC-MS based metabolomics using PyMS
42 Young Ju Suh Combined genome-wide linkage and association analyses for the fasting glucose level in Korean healthy twin and their families
47 Niels W. Hanson, Kishori M. Konwar, Antoine P. Pagé, Charles G. Howes and Steven J. Hallam Metabolic Interaction Networks for the Whole Community
49 David Salgado, Marc Depaule, Elodie Drula and Christophe Marcelle MyoBase: Multi organism muscle database
50 Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida and Yutaka Akiyama Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method
51 Ruijie Liu, Rafael Irizarry and Matthew Ritchie Improved genotype calling for rare variants
52 Pengyi Yang, Penghao Wang, Bing Zhou and Jean Yang Self-boosted Percolator incorporates X!Tandem, MASCOT, and SEQUEST, and integrated with ProteinPropeht in Trans-Proteomic Pipeline