Exploring the frontiers of computational biology through the lens of APBC2009
In January 2009, just months after the dazzling display of the Beijing Olympics, another kind of global competition was unfolding at Tsinghua University—this time in the race to decode the mysteries of life itself. The Seventh Asia Pacific Bioinformatics Conference (APBC2009) brought together over 300 researchers from 21 nations and regions, representing a who's who of computational biology and bioinformatics 1 .
APBC2009 represented the coming of age of bioinformatics as a discipline indispensable to modern biological research.
Researchers
Submissions
Acceptance Rate
Nations Represented
| Aspect | Details |
|---|---|
| Dates | January 13-16, 2009 |
| Location | Tsinghua University, Beijing, China |
| Participants | 300+ researchers from 21 nations/regions |
| Submissions | 204 |
| Acceptance Rate | 37% |
| Presentation Formats | 2 keynotes, 5 invited talks, 76 selected talks, 120 posters, 4 tutorials |
| Proceedings | Published in BMC Bioinformatics, Volume 10, Supplement 1 |
Advanced algorithms for handling data-intensive challenges from second-generation deep sequencing technology 1 .
Novel computational pipelines for predicting previously unknown non-coding RNAs 4 .
Integration of biological pathways, networks, and systems biology approaches 1 .
| Research Area | Specific Topics | Biological Applications |
|---|---|---|
| Sequence Analysis | Sequence alignment, comparative genomics, sequence assembly | Understanding evolution, genome reconstruction |
| Gene Regulation | Transcriptional regulation, microarray analysis, alternative splicing | Disease gene identification, regulatory mechanisms |
| RNA Structure & Function | Non-coding RNAs, microRNAs, RNAi | Gene silencing, regulatory networks |
| Proteins & Proteomics | Protein structure, function, mass spectrometry data | Drug target identification, functional annotation |
| Pathways & Systems Biology | Biological pathways, networks, systems biology | Cellular processes modeling, disease mechanisms |
A novel functional data analysis (FDA) approach achieved 88% accuracy in classifying direct miR-124 targets, outperforming conventional methods 6 .
Discrete gene expression measurements converted into continuous curves using mathematical smoothing techniques 6 .
Identification of major patterns of expression variation over time 6 .
Genes classified based on expression curves using fuzzy classification approach 6 .
| Stage | Conventional Approach | FDA Approach | Advantage |
|---|---|---|---|
| Data Treatment | Discrete time points | Continuous curves | Captures temporal patterns |
| Feature Extraction | Values at each time | Patterns over time | Identifies response latency & shape |
| Classification | Binary classification | Fuzzy membership | Handles ambiguous cases |
| Application | Limited to conserved targets | Works without conservation | Broader applicability |
Provided genome-wide transcriptional profiling for identifying transcripts from unannotated genomic regions 4 .
The CRISP-DM (Cross-Industry Standard Process for Data Mining) methodology provided a systematic framework for many computational discoveries presented at APBC2009 2 . This logical, iterative structure guided researchers through complex data analysis challenges.
Translating biological questions into defined success criteria and research objectives 2 .
Identifying, collecting, and analyzing datasets from public repositories and experimental sources 2 .
Cleaning, constructing, and formatting data for modeling - the most time-consuming phase 2 .
The conference emphasized balancing algorithmic rigor with biological relevance, signaling the maturation of bioinformatics as a discipline 1 .
The conference fostered cross-pollination of ideas across computer science, biology, statistics, and other disciplines 1 .
APBC2009 not only showcased the state of the art in 2009 but also helped chart the course for the future of biological discovery in the digital age, addressing challenges that remain central to bioinformatics today.