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Sixth International
Conference on Bioinformatics

HKUST, Hong Kong
Hanoi, Vietnam and
Nansha, PR China

An APBioNet Meeting

InCoB History








HKUST Event 1

Getting around HK


HKSTP GalaDinner

Hanoi Event 2

Nansha Event 3

Call for Participation



Planning your trip:FAQs

Endorsed by

ISCB International Society for Computational Biology



Supported by

HongKong University of Science and Technology

HongKong Event
Sponsored by

KC Wong Education Foundation

Hong Kong Research Grants Council RGC

Hong Kong Science and Technology Parks

Inforsense Inc


KOOPrime KOOPrime Consulting

ISCB International Society for Computational Biology

Hanoi Event
Sponsored by

United Nations Educational, Scientific and Cultural Organisation

IUBMB International Union of Biochemistry and Molecular Biology

FAOBMB Federation of Asian and Oceanian Biochemists and Molecular Biologists

Institute of Biotechnology IBT

Nansha Event
Sponsored by

HKUST Fok Ying Tung Graduate School

Publication Partners

BioMedCentral Bioinformatics

BMF Biomolecular Frontiers

Internet2 Partners

Asian Institute of Technology, Thailand

TransEurasia Information Network TEIN


27 - 31 August 2007


Highlights of the InCoB2007 Programme

  • 5 plenary speakers
  • Invited speakers and session chairs
  • Oral presentations, selected from submitted abstracts.
  • 4 Tutorials sessions
    • EGEE Grid Computing for Life Sciences using gLITE
      Jose R Valverde, Scientific Computing Service, CNB/CSIC, Spain.
    • Building Bioinformation: The BioWiki Initiative
      Jong Bhak, Director, Korean Bioinformation Network (KOBIC), Korea.
    • Configuring P2P for Wide Area Narrow Band Large Dataset Dissemination
      Darran Nathan, Progeniq; Unitsa; Professor Amornrat Phongdara, Prince Songkla University, Thailand
    • Integrated Bioinformatics in Genomics and Proteomics Studies

Tentative Schedule (All times displayed in HongKong Local Time)
Note that Hanoi/Bangkok time is one hour behind, ie. 9am HK is 8am Hanoi.

August 27 (Day 1) InCoB2007 - HKUST
08:00-17:00 Registration for "Workshops on Bioinformatics"
Session 1
Tutorial 1:
EGEE Grid Computing for Life Sciences using gLITE
Jose R Valverde | Tutorial 1 PPT (20Mbs - Large)
Tutorial 2:
Building Bioinformation: the BioWiki Initiative
Jong Bhak | Tutorial 2 talk | competition
10:30-11:00 Break
Session 2
Tutorial 1: cont'd
Jose R Valverde
Tutorial 2: cont'd
Jong Bhak
12:30-13:30 Lunch
Session 3
Tutorial 3:
Configuring P2P for
Wide Area Narrow Band
Large Dataset Dissemination

Amornrat Phongdara
Tutorial 3 material
Tutorial 4:
Integrated Bioinformatics in Genomics and Proteomics Studies:
Coordinated Regulation of Molecular Networks underlying Targeted Therapy in Leukemia

Zhang Ji, Kankan Wang
15:00-15:30 Break
Session 4
Tutorial 3: cont'd
Amornrat Phongdara
Tutorial 4: cont'd
Zhang Ji, Kankan Wang
August 28 (Day 2) InCoB2007 - HKUST
08:00-17:00 Registration
09:00-09:30 Opening Ceremony
Chiang Chen Lecture Theatre (LT-J)
  • Welcoming remarks by Prof. Tony Eastham | PPT |
    Acting Vice-President for Research and Development, HKUST
  • Speech from Guest of Honour
    Mrs Regina Ip, Chairperson of Board of Governors, Savantas Policy Institute
  • Official Speech - President, ISCB, Professor Burkhart Rost
    Delivered by Professor Shoba Ranganathan
  • Official Speech - President, APBioNet and InCoB Co-Chairperson
    Professor Shoba Ranganathan | PPT |
  • Greetings from Hanoi by Prof Dr Nguyen Huu Duc, Rector, Coltech, Vietnam National University | Opening Speech from Hanoi |
  • Group Photo Taking
09:30-10:30 Session 1
Session Chair: C1 Shoba Ranganathan

Plenary Keynote: P1
How Bioinformatics Helped Reveal the Human Metabolome
Professor David Wishart
University of Alberta | PDF |
10:30-11:00 Break
. Session 2:
Data Storage and Data Mining
Session Chair: C2
Pak-Chung Sham
Dept of Psychiatry, HKU
Session 3:
Sequence Analysis
Session Chair: C3
Michael Ng
Dept of Mathematics, HKBU
11:00-11:30 Invited Speaker: I1
Bioinformatics Workflow Integration info
Yike Guo
Imperial College London; Shanghai Bioinformatics Institute
and Inforsense

Invited Speaker: I2
A Novel Knowledge Based Method for the Prediction of Transcription Factor Targets
Yu-Dong Cai
| PPT | CAS-MPG Partner Institute for Computational Biology, Shanghai
and Ziliang Qian
Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

11:30-13:00 Oral Presentations: 01-04
  • Exploitation of Structural Similarity in Semi-Structured Bioinformatics Data for Efficient Storage Construction
    Dongkyoo Shin | PPT |
  • Analyzing the Simplicial Decomposition of Spatial Protein Structures
    Rafael Ordog | PPT |
  • Improved General Regression Network for Protein Domain Boundary Prediction
    Paul D. Yoo | PPT |
  • Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis
    Olivo Miotto | PPT |

Oral Presentations: 05-08
  • CrossWA: A new approach of combining pairwise and three-sequence alignments to improve the accuracy for highly divergent sequences alignment
    Che-Lun Hung | PPT |
  • Using a Robust Homolog Peptide Search Method to Improve Protein Secondary Structure Prediction
    Ei-Wen Yang and Wen-Lian Hsu | PPT |
  • Tandem Duplication, Circular Permutation, Molecular Adaptation: How Solanaceae Resist Pests via Inhibitors
    Lesheng Kong | PPT |
  • A Bioinformatics Approach to Improving Prediction of Programmed Ribosomal Frameshifting
    Chin Lung Lu and Yen Lin Huang | PPT |

13:00-14:00 Lunch and
| APBioNet AGM agenda | PPT report |
Report on BioWiki Competition - Jong Bhak
Report on BioWorkflow Competition - Yike Guo or representative |info|
. Session 4:
Bio-Ontologies and Vocabularies
Session Chair: C4
Mary Waye
Dept of Biochemisty, CUHK
Session 5:
Genome Analysis
Session Chair: C5
Man-Yu Wong
Dept of Mathematics, HKUST
14:00-14:30 Invited Speaker: I3
Data Mining for Bioinformatics: Some Challenging Problems
Qiang Yang

Invited Speaker: I4
Finding distinct biclusters from background in gene expression matrices Zhengpeng Wu
Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
14:30-16:10 Oral Presentations: 09-O11
  • Rule-based Knowledge Aggregation for Large-Scale Protein Sequence Analysis of Influenza A Viruses
    Olivo Miotto | PPT |
  • Being a Binding-Site: Characterizing Residue-Composition of Binding Sites on Proteins
    Zoltan Szabadka and Vince Grolmusz | PPT |
  • Towards ontology-driven navigation of the lipid bibliosphere
    Christopher Baker and Low Hong Sang | PPT |

Oral Presentations: 012-015
  • Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments
    Hongya Zhao
  • A Bayesian Framework for Eucaryotic Promoter Recognition
    Jia Zeng
  • On sparse Fisher Discriminant Method for microarray data analysis
    Eric Fung
  • Unique Probe Selector (UPS): A Comprehensive Web Service for Probe Design and Oligo Nucleotide Arrays
    Cheng-Yen Li

16:10-16:30 Break
Session 6
Session Chair: C6 Hannah H Xue

Plenary Keynote: P2
Topic: The complexity of the human genome transcriptional landscape
Professor Roderic Guigó
Head, Bioinformatics and Genomics Program, Center for Genomic Regulation, Professor, Universitat Pompeu Fabra, Barcelona, Spain. |
17:30-18:30 Posters (odd numbers)
August 29 (Day 3) InCoB2007 - HKUST (late afternoon and evening at HK Science Park)
08:00-17:00 Registration
09:00-10:00 Session 7
Session Chair: C7 Shoba Ranganathan

Plenary Keynote: P3
Topic: Evolution teaches predicting protein function
Professor Burkhard Rost
Columbia University | PDF |
10:00-10:30 Break
. Session 8:
Text Mining
Session Chair: C8
Hong Yan
Dept of Computer Engineering, CityU
Session 9:
Structural Bioinformatics
Session Chairs: C9
Chandra Verma
Bioinformatics Institute, Singapore
Guang Zhu
Dept of Biochemistry, HKUST
10:30-11:00 Invited Speaker: I5
Latent Structure Models and Statistical Foundation for Traditional Chinese Medicine
Nevin Zhang*
The Hong Kong University of Science & Technology | PPT |
Invited Speaker: I6
Bioinformatics-guided Target Selection in Human Liver Structural Proteomics Project
Zhi-Jie Liu
Institute of Biophysics, Chinese Academy of Sciences
Bioinformatics of Disease: immune epitope prediction
Shoba Ranganathan
Macquarie University | PPT
11:00-12:30 Oral Presentations: 016-020
  • Transmembrane helix prediction using amino acid property features and latent semantic analysis
    Madhavi Ganapathiraju | PPT |
  • Effective Reranking for Extracting Protein-protein Interactions from Biomedical Literature
    Deyu Zhou and Chee Keong Kwoh | PPT|
  • Functional Gene Clustering via Gene Annotation Sentences, MeSH and GO Keywords from Biomedical Literature
    Jeyakumar Natarajan | PPT|
  • Exploiting Likely-Positive and Unlabeled Data to Improve the Identification of Protein-Protein Interaction Articles
    Richard Tsai and Wen-lian Hsu | PPT|
  • A Cascaded Approach to Normalising Gene Mentions in Biomedical Literature
    Hui Yang (pre-recorded) | PPT|

Oral Presentations: 021-025
  • Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
    Justin Choo, JC Tong and Shoba Ranganathan | PPT |
  • Homology Modeling of GPR30 Receptor and Identification of Allosteric Inhibitors to GPR30 Receptor, with reference to its role in ER-ve Breast Cancer
    Ayush Saxena
  • Modelling the structures of G protein-coupled receptor aided by three-dimensional validation
    Siavoush Dastmalchi | PPT |
  • Functional Site Prediction Selects Correct Protein Models
    Vijayalakshmi Chelliah | PPT |
  • Preferential Binding of Allosteric Modulators to Active and Inactive Conformational States of Metabotropic Glutamate Receptors
    Naveena Yanamala | PPT |

12:30-13:00 Lunch and
BioWiki Presentation | PPT|
InCoB ExCo Meeting (by invitation only)
Selection and Voting of the InCoB 2008 Venue
13:00-13:30 ISCB Student Council presentation
on ISCB-SC and Regional Student Group RSG-Korea

by Sungsoo Kang and Joshua Yang | PPT |
(All are Welcome)
. Session 10:
Pathways, Networks & Systems Biology
Session Chair: C10
Shea-Ping YIP
Dept of Health Technology & Informatics, PolyU
Session 11:
Transcriptome Analysis
Session Chair: C11
Nelson Tang Dept of Chemical Pathology, CUHK
13:30-14:00 Invited Speaker: I7
Motif-directed network component analysis for regulatory network inference
Jianhua Xuan
Department of Electrical and Computer Engineering, Virginia | PPT |
Invited Speaker: I8
Organization of the Caenorhabditis elegans small non-coding transcriptome by Rnomics, tiling array and bioinformatics
Runsheng Chen
Institute of Biophysics, Chinese Academy of Sciences | PPT|
14:00-15:40 Oral Presentations: 026-O29
  • SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
    Sungsoo Kang | PPT |
  • Pattern Detection and Co-methylation Analysis of Epigenetic Features in Human Embryonic Stem Cells
    Ben Niu | PPT |
  • ARPPI: A knowledge-based model for protein-protein interactions
    Jinn-Moon Yang | PPT|
  • MicroRNA regulation in Arabidopsis thaliana
    Qing Zhang and Diane Guo | PPT|

Oral Presentations: 030-033
  • Improving the Prediction of RNA Secondary Structure by Detecting and Assessing Conserved Stems
    Xiaoyong Fang | PPT
  • In silico analysis of expressed sequence tags (EST) from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with database searches
    Shivashankar H. Nagaraj | PPT |
  • Micro Designer- a standalone tool for designing micro-RNA
    Chandrasekharan Hariharan
  • GS2PATH: An Integrated Analysis Tool for Finding Functional Relationships Using Gene Ontology and Pathways
    Jin Ok Yang | PPT |

15:40-16:00 Posters (even numbers)
Note: all posters to be removed by 1610h
16:10-16:45 Travel by 3 coaches from HKUST to HK Science Park for
  • Special Plenary Keynote by Professor Minoru Kanehisa at HKSTP New Auditorium
  • Special Tour of HK Science Park sponsored by HKSTP
  • InCoB 2007 Gala Dinner at HK Science Park Happiness Cuisine Restaurant sponsored by HKSTP.

Session 12
Session Chair: C12 Shoba Ranganathan

Plenary Keynote: P4
Topic: Genome to Life and Environment
Professor Minoru Kanehisa | PDF |
Director, Bioinformatics Center,
Institute for Chemical Research, Kyoto University, Japan
18:00-19:00 HK Science Park Video Show and Special Tour
19:00-21:30 Conference Gala Dinner (HK Science Park)
Return Trip at 21:30 - Buses will take you back, one to HKUST, to Kowloon Tong KCR Station and to TsimShaTsui MTR Station.
August 30 (Day 4) InCoB2007 - HKUST
08:00-10:00 Registration
. Session 13:
Bioinformatics of Disease
Session Chair: C13
Weichuan Yu
Dept of Electronic & Computer Engineering, HKUST
Session 14:
Evolution and Phylogenetics
Session Chair: C14
Qiang Yang
Dept of Computer Science & Engineering, HKUST
09:00-09:30 Invited Speaker: I9
Computational Identification of Natural Antisense Transcripts in Arabidopsis thaliana
Xiu-Jie Wang
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences | PPT|
Invited Speaker: I10
Delineation of Root of Life and Origin of Eukaryotes from Transfer RNA Sequences
Jeffrey Tze-Fei Wong
Hong Kong University of Science & Technology
| PPT|
09:30-10:45 Oral Presentations: 034-038
  • Iterative local Gaussian clustering for expressed genes identification linked to malignancy of human colorectal carcinoma
    Ito Wasito | PPT|
  • Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
    Asif M. Khan | PPT|
  • T-cell epitopes prediction of hemagglutinin, neuraminidase and matrix protein of influenza A virus using support vector machine and hidden Markov models
    Vo Cam Quy | PPT|
  • Training and applying hidden Markov models and support vector machines for prediction of T cell epitopes
    Van Hai Van | PPT|
  • Stability of the core domain of p53: insights from computer simulations.
    A.Madhumalar, D J Smith and Chandra Verma | PPT|

Oral Presentations: 039-043
  • Speedup Bioinformatics Applications on Multicore-based Processor using Vectorizing & Multithreading Strategies
    Kridsadakorn Chaichoompu | PPT|
  • SNP@Promoter: A database of human SNPs (Single Nucleotide Polymorphisms) within putative promoter region
    Byoung-Chul Kim | PPT|
  • Phyloinformatics of Neuraminidase at Micro and Macro Levels using Grid-enabled HPC Technologies
    Bertil Schmidt | PPT|
  • A Generic Evolutionary Method Optimizes Soft Energy Functions for Protein Structure Prediction
    Jinn-Moon Yang
  • G-protein Coupled Receptor Subfamilies Prediction Based on Nearest Neighbor Approach
    Mudassir Khan

10:45-11:15 Break
11:15-12:15 Session 15
Session Chair: Tan Tin Wee

Plenary Keynote: P5
Topic: Estimating chromosomal copy number
Professor Terry Speed
Head, Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Australia and Department of Statistics and Program in Biostatistics, University of California at Berkeley | PPT |
12:15-12:45 InCoB 2007 Closing Ceremony
Announcement of Winners of BioWiki Competition, Dr Jong Bhak, KOBIC
Launch of BioWorkflow Competition, Dr Jack Lin and Dr Yike Guo, Inforsense
Invitation to InCoB2008
12:45-14:00 Invitation to Post-Conference Special Buffet Lunch-
cum-APBioNet Open Dialogue Session
Session Co-Chairs:
Professor Shoba Ranganathan, President APBioNet
Professor Hannah Xue, Board Director, ISCB
IMPT: Change in Programme New! Nansha Workshop relocated to HKUST
As Post-Conference Workshop, HKUST, Lecture Theatre J.
August 30 (Day 4) Post-InCoB07 Workshop - HKUST
14:00-16:00 Post Conference Workshop (Relocated from Nansha)
Session Chair: Tan Tin Wee

Topic: Workflow Integration in the Life Sciences | more info |
Dr Jack Jiancheng Lin, Zong-ming Guo and Jun Gao.
Workshop Closing Keynote Session
Session Chair: Professor Hannah Xue

Post-Conference Workshop Plenary Keynote
Topic: Causes of regulatory variation in the human genome
Dr Emmanouil (Manolis) Dermitzakis
The Wellcome Trust Sanger Institute, Cambridge, UK | PPT |
18:00-21:30 Special Outing to SeaFood Dinner
(Please contact registration desk to sign up)
August 31 (Day 5) Post-InCoB2007 Symposium - Nansha
Workshop 1: (Nansha Bioinformatics Lab) Transferred to HKUST
on day before (Thurs, Aug 30)

Workflow integration in the Life Sciences
| more info |
Yike Guo
Workshop 2:
Postponed ASEAN-China BioCyberinfrastructure Workshop
Tan Tin Wee
Nansha Symposium, Nansha IT Park
Post-Conference Symposium Keynote
Topic: Causes of regulatory variation in the human genome
Dr Emmanouil (Manolis) Dermitzakis
The Wellcome Trust Sanger Institute, Cambridge, UK
Workshop 3: (Postponed to 6-7 Sep 2007)
Traditional Chinese Medicine: Informatics
Hannah Xue Hong

First Created: April 2007 Tan Tin Wee
Last Updated: 1 Sep; 26, 20, 15, 6 Aug; 20 June; April 2007