|BIOKDD '11 Workshop, "Data Mining Challenges in Next‐generation Sequencing (NGS)"|
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 inherent uncertainties in data collection processes, 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.
Data Mining approaches seem ideally suited for Bioinformatics, since they are data-driven and do not require 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 (BIOKDD 2001-2010), held annually or biannually in conjunction with the ACM SIGKDD Conference. This will be the 10th year for the workshop.
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 a panel/invited talk.
Information on past workshops is available at:
The goal of this workshop is to encourage KDD researchers to take on the numerous challenges that Bioinformatics offers. This year, the workshop will feature the theme of “Data Mining Challenges in Next‐generation Sequencing (NGS)”. NGS is revolutionizing biological, biomedical, and health research. There are enormous data analysis and knowledge discovery challenges in the NGS technology, including expression analysis, mutational analysis, alternative slicing pattern discovery, whole transcription sequence alignment, epigenetics site discovery, storing and compression of high volume sequence data and clustering and classification of structural variations in a population.
We encourage papers that propose novel data mining techniques for post-genome bioinformatics studies in areas such as the following, although excellent papers without the use of NGS will also be considered:
Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Paper should be submitted in PDF/PS format through Easychar at the following link: http://www.easychair.org/conferences?conf=biokdd2011
Camera-ready format papers may be referenced from previous BIOKDD conference proceedings (e.g., BIOKDD10)
All papers will be published at the workshop proceedings and at the ACM digital library.
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.
Publication of proceeding and expanded papers. Expanded version of selected high-quality papers from the workshop will be invited for publication in a special issue of a major bioinformatics/biocomputing journal (in 2007, it was Journal of Bioinformatics and Computational Biology; in 2008, it was ACM/IEEE Transactions on Computational Biology and Bioinformatics; in 2010, it was BMC Bioinformatics). Details of the journal/book publication will be announced online after the workshop.
Please use the following Google Checkout to pay the workshop publication fees.
8:25-8:30: Opening Remarks
8:30-9:25: Invited Speaker presentation 1
Session I (9:30 am – 10:10 am)
9:30 – 9:55 [L] Zhen Hu and Raj Bhatnagar. Algorithm for Low-Variance Biclusters to Identify Coregulation Modules in Sequencing Datasets
9:55 – 10:10 [S] Mina Maleki, Md. Mominul Aziz and Luis Rueda. Analysis of Obligate and Non-obligate Complexes using Desolvation Energies in Domain-domain Interactions
10:10-10:30 Coffee Break
10:30-11:25: Invited speaker presentation 2
Session II (11:30 am – 12:35 pm)
11:30 – 11:55 [L] K.S.M. Tozammel Hossain, Chris Bailey-Kellogg, Alan Friedman, Michael Bradley, Nathan Baker and Naren Ramakrishnan. Using Physicochemical Properties of Amino Acids to induce Graphical Models of Residue Couplings
11:55 – 12:20 [L] Hamching Lam and Daniel Boley. Analyze Influenza Virus Sequences Using Binary Encoding Approach
12:20 – 12:35 pm [S] Ankit Agrawal, Sanchit Misra, Ramanathan Narayanan, Lalith Polepeddi and Alok Choudhary. A Lung Cancer Outcome Calculator Using Ensemble Data Mining on SEER Data
12:35 – 12:45 Closing Remarks