Warren Kibbe

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Warren Kibbe, Ph.D.

Research Associate Professor
Feinberg School of Medicine


Director of Cancer Informatics and CIO, The Robert H. Lurie Comprehensive Cancer Center
Director of Bioinformatics, Center for Genetic Medicine at Northwestern University
Associate Director of the Northwestern University Biomedical Informatics Center (NUBIC)

Northwestern University Biomedical Informatics Center
Feinberg School of Medicine
Northwestern University
750 Lake Shore Drive
Rubloff Building 11-162
Chicago, IL 60611

Phone: +1-312-503-3229
email

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Education

Postdoctoral fellow in Molecular Genetics, Max Plank Institute for Biophysical Chemistry, Göttingen, Germany, 1990-1992

PhD in Chemistry, California Institute of Technology (Caltech), Pasadena, CA,1990

BS in Chemistry, Michigan Technological University, Houghton, MI, 1982

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Research Synopsis

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 (http://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 (http://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 (http://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.

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Recent Projects

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Personal Projects

Disease Ontology (DO) sourceforge site; DO wiki

LatticeGrid Collaboration Assessment and Publications tool

Documentation docs
Downloads github repository
NUCATS Publications public site
RHLCCC Publications public site

Cancer Center Clinical Trials Abstracts production

Cancer Center Members Profiles production requires login

Animal Models of Disease production NU only IPs

Oligonucleotide Properties Calculator

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Collaborations and Projects

NUBIC open source project sharing site

NCS Greater Chicago Study Center

dictyBase MOD and wiki

nuID data

nuID-based Illumina Associations website

VST/RSN microarray analysis package for Illumina data

caBIG™ Patient Study Calendar Project demo site gForge site

caBIG™ caGRID Bioconductor Project gForge site developers gForge site

IPBS Prostate SPOREs/caBIG™ caTISSUE Suite Adoption gForge site

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Publications 2004-2011

  • Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, Sheppard KA, Just EM, Kibbe W, Chisholm RL. dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. Nucleic Acids Res. (2011) 39(Database issue):D620-4. [PubMed ID 21087999]
  • Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics (2010) 11:587. [PubMed ID 21118553]
  • Feng G, Du P, Krett NL, Tessel M, Rosen S, Kibbe WA, Lin SM. A collection of bioconductor methods to visualize gene-list annotations. BMC Res Notes. (2010) 19:3:10. [PubMed ID 20180973]
  • Wen J, Wang X, Kibbe W, Lin S, Lu H. Visual annotation of the gene database. Conf Proc IEEE Eng Med Biol Soc. (2009) 2009:4175-7. [PubMed ID 19964623]
  • Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. (2010) 38(Database issue):D331-5. [PubMed ID 19920128]
  • Desai J, Flatow JM, Song J, Zhu LJ, Du P, Huang CC, Lu H, Lin SM, Kibbe WA. Visual presentation as a welcome alternative to textual presentation of gene annotation information. Adv Exp Med Biol. (2010) 680:709-15. [PubMed ID 20865558]
  • Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. Annotating the human genome with Disease Ontology. BMC Genomics. (2009) 10 Suppl 1:S6. [PubMed ID 19594883]
  • Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics (2009) 25:i63-8. [PubMed ID 19478018]
  • Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL. dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res. (2009) 37:D515-9. [PubMed ID 18974179]
  • Lin SM, Du P, Huber W, WA Kibbe. Model-based Variance-stabilizing Transformation for Illumina Microarray Data. Nucleic Acids Res., (2008) 36:e11. [PubMed ID 18178591]
  • Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics (2008) 24:1547-8. [PubMed ID 18467348]
  • Gene Ontology Consortium. The Gene Ontology (GO) project in 2008. Nucleic Acids Res. (2008) 36:D440-4. [PubMed ID 17984083]
  • Osborne JD, Lin SM, Zhu LJ, Kibbe WA. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol. (2007) 408:153-69. [PubMed ID 18314582]
  • Du P, Kibbe WA, SM Lin. nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays. Biol. Direct. (2007) 2:16. [PubMed ID 17540033]
  • Arshinoff BI, Suen G, Just EM, Merchant SM, Kibbe WA, Chisholm RL, Welch RD. Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. (2007) 35: D422-D426. [PubMed ID 17090585]
  • Du P, Kibbe WA, SM Lin. Application of wavelet transform to the MS-based proteomics data preprocessing. Proceedings of the 7th IEEE International Symposium on Bioinformatics and Bioengineering. (2007) I-II:680-686.
  • Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol. (2007) 377:223-42. [PubMed ID 17634620]
  • Kibbe WA. OligoCalc – an online Oligonucleotide Properties Calculator. Nucleic Acids Res. (2007) 35:W43-6. [PubMed ID 17452344]
  • Osborne JD, Lin SM, and Kibbe WA Other riffs on cooperation are already showing how well a wiki could work. Nature (2007) 446:856. [PubMed ID 17443163]
  • Ge X, Jung YC, Wu Q, Kibbe WA, Wang SM. Annotating nonspecific SAGE tags with microarray data. Genomics. 2006 Jan; 87(1):173-80.
  • Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.
  • Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA. dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D423-7.
  • WA Kibbe “The Bioinformatics of Biobanks – designing Next Generation Biobanks”, book chapter in Nutritional Genomics: Discovering the path to personalized nutrition, Editors: R. Rodriguez and J. Kaput; J Wiley, 2006.
  • Osborne J, Zhu LH, Lin SM, and Kibbe WA. Interpreting Microarray Results with Gene Ontology and MeSH Ontology. In Korenberg M. ed. Methods in Microarray Data Analysis. Humana Press (2006).
  • Lin SM, Devakumar J, and Kibbe WA. Improved prediction of treatment response using microarrays and existing biological knowledge, Pharmacogenomics (2006) 7:495-501.
  • Du P, Kibbe WA, Lin SM. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics (2006) 22:2059-65.
  • Osborne J, Zhu LH, Lin SM, and Kibbe WA. Interpreting Microarray Results with Gene Ontology and MeSH Ontology. In Korenberg M. ed. Methods in Microarray Data Analysis. Humana Press (2006).
  • Kaput J, et al The case for strategic international alliances to harness nutritional genomics for public and personal health. Br J Nutr. 2005 Nov;94(5):623-32.
  • Lin SM, Kibbe WA. Irrational exuberance in clinical proteomics. Clin Cancer Res. 2005 Nov 15;11(22):7963-4.
  • Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA. What is mzXML good for? Expert Rev Proteomics. 2005 Dec; 2(6):839-45.
  • Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR. dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res. 2004 32: D332-3.
  • Harris MA et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 32: D258-61.
  • Bult C, Kibbe WA, Snoddy J, Vitaterna M, Swanson D, Pretel S, Li Y, Hohman MM, Rinchik E, Takahashi JS, Frankel WN, Goldowitz D. A genome end-game: understanding gene function in the nervous system. Nat Neurosci. 2004 May; 7(5):484-5.
  • Kaput J, Klein KG, Reyes EJ, Kibbe WA, Cooney CA, Jovanovic B, Visek WJ, Wolff GL. Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet x genotype interactions. Physiol Genomics. 2004 Aug 11; 18(3):316-24.
  • Goldowitz D, Frankel WN, Takahashi JS, Holtz-Vitaterna M, Bult C, Kibbe WA, Snoddy J, Li Y, Pretel S, Yates J, Swanson DJ. Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function. Brain Res Mol Brain Res. 2004 Dec 20; 132(2):105-15.
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