Second Call for Papers


ACM First International Workshop on Text Mining in Bioinformatics

TMBIO 2006

November 10, 2006


In conjunction with ACM Fifteenth Conference on Information and Knowledge Management (CIKM)

November 6-11, 2006, Sheraton Crystal City Hotel

 Arlington, VA  22202 USA


A fundamental issue that biological researchers encounter today is how to make effective use of the enormous amount of biomedical data to improve their understanding of complex biological systems. The biomedical data repositories are formed from various ways such as bibliographic information from electronic medical journals, gene expression data from Microarray experiments, protein identification and quantification data from proteomics experiments, and genomic sequences gathered by the Human Genome Project. The ability to automatically and effectively extract, integrate, understand and make use of information embedded in such heterogeneous unstructured data remains a challenging task.


Topic of Interests

The relevant topics include the following (but not limited to):

    *   Application and assessment of Text Mining (TM) algorithms,

    *   Information extraction from biomedical literatures,

    *   TM dealing with large and distributed biomedical data sets,

    *   Entities extraction from unstructured biomedical data sets,

    *   Improving and assessing data quality in TM,

    *   Application of ontologies to biomedical domains,

    *   Integration of Information Retrieval to TM in biomedical domains,

    *   Case studies,

    *   Evaluation methods for TM,

    *   Information integration for TM,

    *   Mining multi-relational data.


Goals and Intended Audience

In order to build Text Mining systems that contribute to our understanding of biological systems, solutions to the above problems have to be assembled into efficient and scalable systems. The workshop aims at facilitating this process, and at enhancing the exchange of knowledge between computational biologists and knowledge discovery researchers. Accordingly, our intended audiences are both computational biologists and Text Mining researchers.


A Special Journal Issue

Expanded versions of the best accepted papers will be invited to appear in a special issue of International Journal of Data Mining and Bioinformatics.


Submission Guidelines

Authors are invited to submit original, unpublished research papers that are not being considered for publication in any other forum. Manuscripts should be submitted electronically, in PDF format and formatted using the ACM camera-ready templates available at


A website with camera-ready instructions is available at


Please send your submission electronically to by the deadline listed below.


Important Dates

Paper Submission Due: July 21, 2006

Notification of Acceptance: August 15, 2006

Camera-ready Paper Due: August 31, 2006

Workshop: November 10, 2006


Program Chair

Min Song, New Jersey Institute of Technology, U.S.A.

Zoran Obradovic, Temple University, U.S.A.


Program Committee

Robert B. Allen, Drexel University, U.S.A.

Steffen Bickel, Humboldt University, Germany

Christian Blaschke, Bioalma, Spain

Aaron M. Cohen, Oregon Health & Science University, U.S.A.

Milton Corn, NIH, U.S.A.

David J. Foran, The Cancer Institute of New Jersey - UMDNJ, U.S.A.

Xiaohua Tony Hu, Drexel University, U.S.A.

Tapas Kanungo, IBM Almaden Research Center, U.S.A.

Hongfang Liu, Georgetown University, U.S.A.

Martin Middendorf, University of Leipzig, Germany

Haesun Park, Georgia Tech, U.S.A.

Predrag Radivojac, Indiana University, U.S.A.

Melissa Rogers, UMDNJ - NJ Medical School, U.S.A.

Hagit Shatkay, Queen’s University, Canada

Padmini Srinivasan, University of Iowa, U.S.A.

Alfonso Valencia, Spanish National Cancer Research Centre, Spain

Slobodan Vucetic, Temple University, U.S.A.

Jason T. L. Wang, New Jersey Institute of Technology, U.S.A.

Brook Wu, New Jersey Institute of Technology, U.S.A.