Call for Papers

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    Functional genomics is a sub-field of molecular biology that makes use of the enormous amounts of data produced by genomic projects to describe some dynamic aspects such as gene transcription, translation, and protein-protein interactions. Because these phenomena are typically characterized by large and increasing amounts of data, diverse and unusual data types, and complex relationships, interpreting such data requires novel approaches that include multiple tools, new algorithms, resources, etc. in an integrated fashion. Data Mining is the process of automatic discovery of novel, understandable and potentially useful models from such massive amounts of data. Organized in conjunction with BIBM 2008, the objective of this workshop is to facilitate collaboration between data mining researchers and bioinformaticians by presenting cutting-edge research topics and methodologies in the areas of functional genomics and data mining. While such research has an interdisciplinary character, this workshop emphasizes on the application of various data mining techniques such as data pre-processing, data visualization, model evaluation, classification and cluster analysis to research problems that arise in functional genomics. We encourage papers that employ data mining techniques for tasks related to functional genomics. Research papers are solicited in, but not limited to the following topics:

• Microarray Expression Analysis
• Protein Structure Prediction
• Protein-Protein Interactions
• Sub-cellular Localization
• Proteomics
• Mass spectrometry
• Integration of Heterogeneous data
• Gene Ontology

Paper Submission

Papers should be at most 8 pages long, including all figures, tables, and references. Papers should be submitted electronically by email to the workshop chairs in .pdf format. All papers accepted for this workshop will be included in the Workshop Proceedings published by the IEEE Computer Society Press, which are indexed by EI. Paper submission form is available at Data Mining in Functional Genomics Submission Form

Important Dates

Final Workshop Program - 8:00AM - 12:00PM

Session I - 8:00AM - 10:00AM

• Yun Xiong, Qing Yang, Boren Qiu, and Yangyong Zhu, "An Integrated Approach of Sequence and Text Mining Technology for the Identification of Transcription Factor Binding Sites"
• Jingyu liu, Joel Bixler, and vince calhoun, "A multimodality ICA study - integrating genomic single nucleotide polymorphisms with functional neuroimaging data"
• Elina Tjioe, Michael Berry, and Ramin Homayouni, "Using a Literature-based NMF Model for Discovering Gene Functional Relationships"
• Huitao Sheng, Kishan Mehrotra, Chilukuri Mohan, and Ramesh Raina, "Classification of Gene Expression Levels Using Activator and Repressor Motifs"
• Vincent Guillemot, Laurent Le Brusquet, Arthur Tenenhaus, and Vincent Frouin, "Graph-Constrained Discriminant Analysis of functional genomics data"
• Hao Sun, Milena Nicoloso, George Caline, Anirban Bhattacharyya, and Ramana Davuluri, "In silico prediction of target SNPs affecting miR-mRNA interaction"
• Venkata Rama Kumar Swamy Yedida, Chien-Chung Chan, and Zhong-Hui Duan, "Protein Function Prediction Using Decision Trees"

Session I - 10:15AM - 12:00PM

• Huang-Cheng Kuo, Ping-Lin Ong, Jung-Chang Lin, and Jen-Peng Huang, "A Prediction of Protein-Protein Recognition Using Support Vector Machine Based on Feature Vectors"
• Stefan Gremalschi, Gulsah Altun, Irina Astrovskaya, Alexander Zelikovsky,"Mean Square Residue Biclustering with Missing Data and Row Inversions"
• Chengwei Lei and Jianhua Ruan, "A Particle Swarm Optimization Algorithm for Finding DNA Sequence Motifs"
• Xiyi Hang, "Cancer Classification by Sparse Representation using Microarray Gene Expression Data"
• Chen Yiming, "Predicting Consistently Protein Function Based on MKL"
• Sofia Mosci, Annalisa Barla, Alessandro Verri, and Lorenzo Rosasco, "Finding structured gene signatures"

Organizers

Program Committee

Registration

One registration covers everything so that the workshop attendances can attend any regular sessions of the main conference as well as other workshops.