BIOKDD Workshop Home

Biological Knowledge Discovery and Data Mining (BIOKDD) Workshop Site


Bioinformatics is the science of managing, mining, and interpreting information from biological data. Various genome projects have contributed to an exponential growth in DNA and protein sequence databases. Advances in high-throughput technology such as microarrays and mass spectrometry have further created the fields of functional genomics and proteomics, in which one can monitor quantitatively the presence of multiple genes, proteins, metabolites, and compounds in a given biological state. The ongoing influx of these data, the presence of biological answers to data observed despite noises, and the gap between data collection and knowledge curation have collectively created exciting opportunities for data mining researchers.

While tremendous progress has been made over the years, many of the fundamental problems in bioinformatics, such as protein structure prediction, gene-environment interaction, and regulatory pathway mapping, are still open. Data mining will play essential roles in understanding these fundamental problems and development of novel therapeutic/diagnostic solutions in post-genome medicine.

Workshop History (2001-present)

Data Mining approaches seem ideally suited for Bioinformatics, since it is data-rich, but lacks a comprehensive theory of life's organization at the molecular level. The extensive databases of biological information create both challenges and opportunities for developing novel KDD methods. To highlight these avenues we organized the Workshops on Data Mining in Bioinformatics, held annually in conjunction with the ACM SIGKDD Conference.

Past workshops attracted 50-100 participants, from academia, industry and government labs, underscoring the surge of interest in this exciting and rapidly expanding field.  The program of the workshops included 10-11 contributed papers, and 1-2 invited talks.
Information on past workshops is available at:

General Call for Papers

The goal of this workshop is to encourage KDD researchers to take on the numerous challenges that Bioinformatics offers. The workshop will feature invited talks from noted experts in the field, and the latest data mining research in bioinformatics. We encourage papers that propose novel data mining techniques for post-genome bioinformatics studies in areas such as:

  • Phylogenetics and comparative Genomics
  • DNA microarray data analysis
  • RNAi and microRNA Analysis
  • Protein/RNA structure prediction
  • Sequence and structural motif finding
  • Modeling of biological networks and pathways
  • Statistical learning methods in bioinformatics
  • Computational proteomics
  • Computational biomarker discoveries
  • Computational drug discoveries
  • Biomedical text mining
  • Biological data management techniques
  • Semantic webs and ontology-driven biological data integration methods

Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides.  Paper in PDF/PS format can be sent to both of the co-chairs by email. Camera-ready format papers may be referenced from previous BIOKDD conference proceedings


Submission of accepted papers. For accepted workshop papers, we require that each camera-ready paper be formatted strictly according to the official ACM Proceedings Format. Please submit PDF file only. To prepare for the camera-ready PDF file submission, you may use either the Microsoft word template or the Latex files preparation instructions found here. All final camera-ready submissions must be accompanied by a completed digital copy (scanned Okay) of the ACM copyright transfer form, or else the paper cannot be included in the final workshop proceedings.


  [an error occurred while processing this directive]