Warren Kibbe, PhD
Research Associate Professor
Director of Bioinformatics for the Center for Genetic Medicine
Director of Bioinformatics for the Robert H. Lurie Comprehensive Cancer Center
Associate Director of the Northwestern University Biomedical Informatics Center (NUBIC)
Feinberg School of Medicine
Research Interests:
Dr. Kibbe is involved in the caBIG® Clinical Trial Management Systems Workspace where he is the PI of the Patient Study Calendar module software development project, the caBIG development project that has developed a syntactically and semantically harmonized interoperable patient study calendar using agile design practices. Also in caBIG, he is also a member of the caBIG Tissue Banks and Pathology Tools Workspace, the Integrative Cancer Research Workspace, the Data Sharing and Intellectual Capital Workspace, and the Architecture Cross-cutting workspace. Dr. Kibbe is the co-PI of the NIH-funded Dictyostelium Model Organism Database, dictyBase (dictybase.org). He was co-Investigator and director of bioinformatics for the NIH-funded Northwestern ENU Mutagenesis Center, and the NIH-funded Neuromice consortium involving the ENU centers at Northwestern, the Jackson Laboratory, and the University of Tennessee. He is a proponent of Agile software development methodologies and the Agile Unified Process Framework and the application of these to biomedical research problems. Dr. Kibbe's group has developed NOTIS, the clinical trial information management system used for all cancer trials at Northwestern and by the genotype/phenotype biorepository NUgene (www.nugene.org) as the source of identified information on participant in NUgene. He is also a key participant in building a computable research representation of clinical data, through his work with the Northwestern Clinical Enterprise Data Warehouse, the caBIG Clinical Annotations Engine (which is designed to build a computable representation of pathology reports from the Cerner and Epic EMR systems), and ontology efforts, including being a co-founder of the Disease Ontology (diseaseontology.sourceforge.net) and the semantically computable BRIDG domain analysis model that is being jointly developed by members of HL7, CDISC and caBIG to represent clinical research information and the semantics necessary to conduct clinical trials.
Selected Publications:
Fey, P., Gaudet, P., Curk, T., Zupan, B., Just, E. M., Basu, S., Merchant, S. N., Bushmanova, Y. A., Shaulsky, G., Kibbe, W. A. et al. (2009). dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res 37, D515-9.
Du, P., Kibbe, W. A. and Lin, S. M. (2008). lumi: a pipeline for processing Illumina microarray. Bioinformatics 24, 1547-8.
Lin, S. M., Du, P., Huber, W. and Kibbe, W. A. (2008). Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36, e11.
Du, P., Kibbe, W. A. and Lin, S. M. (2007). nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. Biol Direct 2, 16.
Kibbe, W. A. (2007). OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35, W43-6.
Osborne, J. D., Lin, S. and Kibbe, W. A. (2007a). Other riffs on cooperation are already showing how well a wiki could work. Nature 446, 856.
Osborne, J. D., Lin, S., Zhu, L. and Kibbe, W. A. (2007b). Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol 408, 153-69.
Osborne, J. D., Zhu, L. J., Lin, S. M. and Kibbe, W. A. (2007c). Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol 377, 223-42.
