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
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Time |
Room 1 |
Room 2 |
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07:00 - 09:00 AM |
Registration + Poster Setup |
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09:00 - 09:15 AM |
Opening Ceremony |
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09:15 - 10:15 AM |
Keynote 1 – Jenny Graves, La Trobe University “Weird
Animal Genomes and Sex” Session Chair: Phoebe Chen |
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10:15 – 10:30 AM |
Group Photo 1 + Morning Tea + Poster (A) Setup |
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A1: Genome Evolution (Session Chair: Kiwon Lee) |
A2: Regulatory Studies (Session Chair: Wen-Chi Chang) |
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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) |
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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) |
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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) |
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12:00 – 01:30 PM |
Lunch + Posters (A) |
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01:30 – 02:30 PM |
Invited Speaker 1 – Narayanaswamy
Srinivasan, IIS “Evolution of structure, stability and domain architectures of multi-domain proteins” Session
Chair: Mark Ragan |
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A3: Gene Network Modelling (Session Chair: Hiroshi Matsuno) |
A4: Micro / RNA Modelling (Session Chair: Wen-chang Lin) |
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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) |
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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) |
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03:30 – 04:00 PM |
Afternoon Tea + Posters (A) |
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A5: Database and
Data Models (Session
Chair: Rahul Singh) |
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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 |
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04:30 – 05:00 PM |
A5.2 Christopher Langmead, Hetunandan Kamisetty and Narges Sharif Razavian.
Learning Generative Models of Molecular Dynamics (P 106) |
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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) |
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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) |
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7:00 PM |
APBC Steering Committee |
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Wednesday 18th January 2012
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Time |
Room
1 |
Room
2 |
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07:30 - 08:30 AM |
Registration + Poster Setup |
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08:30
- 09:30AM |
Keynote
2 – Peer Bork, EMBL Heidelberg, Session
Chair: Steven Jones |
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09:30
– 9:45 AM |
Group Photo 2 + Morning
Tea + Poster (B) Setup |
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A5: Database and Data Models (continued) (Session Chair: Hsien-Da Huang) |
B2:
Protein Structural Prediction (Session Chair:
Lusheng Wang) |
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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) |
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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) |
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B1:
Protein – Protein Interaction (Session Chair: Ramanathan Sowdhamini) |
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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) |
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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) |
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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) |
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12:15
– 01:30 PM |
Lunch
+ Posters (B) |
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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 |
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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 |
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03:30
– 04:00 PM |
Afternoon
Tea + Posters (B) |
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B1:
Protein – Protein Interaction (continued) |
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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 |
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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) |
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C1:
Algorithmic Optimisation and Evaluation (Session Chair: Nihar Mahapatra) |
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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) |
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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) |
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07:00PM |
Conference
Dinner – Banquet Speech Professor Steven Jones |
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Thursday 19th January 2012
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Time |
Room 1 |
Room 2 |
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08:00 - 09:00AM |
Registration + Poster Setup |
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09:00 - 10:00AM |
Keynote
3 – Terry Speed, WEHI, UC Berkeley “Removing
Unwanted Variation from gene expression data” Session Chair: Phoebe Chen |
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10:00 – 10:30 AM |
Morning Tea + Poster (C) Setup |
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C2. Knowledge Reconstruction (Session Chair: Janusz Bujnicki) |
C3. Knowledge Modelling (Session Chair: Hae Ja Shin) |
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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) |
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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) |
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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) |
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12:00 – 01:00 PM |
Lunch + Posters (C) |
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D1 Protein Drug Applications (Session Chair: Christopher
Langmead) |
D2 Protein Binding Studies (Session Chair: Zengyou
He) |
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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) |
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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) |
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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) |
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02:30 – 03:00 PM |
Afternoon Tea + Posters (C) |
Tutorial 3 – Zengyou He & Weichuan Yu Protein
Inference: Concepts, Algorithms and Software Tools |
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D3 Sequencing and Prediction Applications (Session Chair: Brian Fristensky) |
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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) |
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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) |
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04:00 – 04:30 PM |
Conference Closing & Award Drawing |
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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
24 Yikan Wang, Edmund Crampin and Cristin
Print A REGULATORY MODEL FOR PREDICTING THE CLINICAL OUTCOMES OF INDIVIDUAL
BREAST CANCER PATIENTS
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