Warren Kibbe

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Warren Kibbe, Ph.D.

WAK2005.jpg Research 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

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

Research Synopsis

Dr Kibbe is a Research Professor in the Feinberg School of Medicine and is also the Director of Cancer Informatics and CIO for the Robert H. Lurie Comprehensive Cancer Center at Northwestern University. Dr. Kibbe received his Ph.D. in Chemistry from Caltech, and was a visiting scientist at the Max Plank Institute for Biophysical Chemistry in Göttingen, Germany before joining the faculty at Northwestern. Dr. Kibbe is an active member of the open biomedical ontologies community and is part of the Gene Ontology Consortium, a member of the CTSA Ontology Working Group, and was a founder as well as PI of an NIH-funded project to build the Human Disease Ontology. Dr. Kibbe was the PI of the caBIG Patient Study Calendar module software development project, which developed a syntactically and semantically harmonized interoperable patient study calendar using CDISC Study Data Tabulation Model and BRIDG terminology standards. Dr. Kibbe is the co-PI of the NIH-funded Dictyostelium Model Organism Database dictyBase (http://dictybase.org) with Dr. Rex Chisholm serving as PI. 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 and the open source eNOTIS cloud-enabled clinical trial information management system used to track clinical study participation at Northwestern, with more than 4000 studies and 100,000 participants, and by the 10,000 patient genotype/phenotype biorepository NUgene (http://www.nugene.org). Dr. Kibbe was an active member of the NCI-funded caBIG project, and was a member of the steering committee for the caBIG Clinical Trial Management Systems Workspace. He is also a key participant in building a computable research representation of clinical data, through his work with the Northwestern Medicine Enterprise Data Warehouse, and ontology efforts. Dr. Kibbe is the PI of the National Children’s Study NCS Navigator Information Management Hub, which is used as the data management and coordination system for ten National Children’s Study locations. Dr. Kibbe was named a Top 25 Innovative Healthcare CIO for 2012 by InformationWeek.

Recent Projects

Personal Projects

Disease Ontology (DO) sourceforge site; DO wiki

LatticeGrid Collaboration Assessment and Publications tool

Documentation [1]
Downloads github repository
Feinberg Publications public site
RHLCCC Publications public site

Cancer Center Clinical Trials Abstracts production

Cancer Center Members Profiles production requires login

NUCATS Assist - internal competitions page production

Oligonucleotide Properties Calculator

Collaborations and Projects

NUBIC open source project sharing site

NCS Navigator Information Management Hub

dictyBase MOD and wiki

nuID data

VST/RSN microarray analysis package for Illumina data

caBIG™ Patient Study Calendar Project demo site NCI Wiki

IPBS Prostate SPOREs/caBIG™ caTISSUE Suite Adoption NCI Wiki

Publications 2004-2013

  • Basu S, Fey P, Pandit Y, Dodson R, Kibbe WA, Chisholm RL. dictyBase 2013: integrating multiple Dictyostelid species. Nucleic Acids Res, 41:D676-D683, 2013. [PubMed ID 23172289]; PMC3531180; 10.1093/nar/gks1064
  • Peng K, Xu W, Zheng J, Huang K, Wang H, Tong J, Lin Z, Liu J, Cheng W, Fu D, Du P, Kibbe WA, Lin SM, Xia T. The disease and gene annotations (DGA): an annotation resource for human disease. Nucleic Acids Res, 41:D553-D560, 2013. [PubMed ID 23197658]; PMC3531051; 10.1093/nar/gks1244
  • Hinchcliff ME, Just E, Podlusky S, Varga J, Chang RW, Kibbe WA. Text data extraction for a prospective, research-focused data mart: implementation and validation. BMC Med Inform Decis Mak (2012) 12:106. [PubMed ID 22970696]
  • Zhang X, Wallace AD, Du P, Kibbe WA, Jafari N, Xie H, Lin S, Baccarelli A, Soares MB, Hou L. DNA methylation alterations in response to pesticide exposure in vitro. Environ Mol Mutagen (2012) 53:542-549. [PubMed ID 22847954]
  • Zhang X, Wallace AD, Du P, Lin S, Baccarelli AA, Jiang H, Jafari N, Zheng Y, Xie H, Soares MB, Kibbe WA, Hou L. Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro. Environ Toxicol Pharmacol (2012) In process. [PubMed ID 22964155]
  • Feng G, Shaw P, Rosen ST, Lin SM, Kibbe WA. Using the Bioconductor GeneAnswers Package to Interpret Gene Lists. Methods Mol Bio. (2012) 802:101-112. [PubMed ID 22130876]
  • Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res (2012) 40:D940-D946. [PubMed ID 22080554]
  • Good BM, Howe DG, Lin SM, Kibbe WA, Su AI. Mining the Gene Wiki for functional genomic knowledge. BMC Genomics. (2011) 12:603. [PubMed ID 22165947]
  • Weber GM, Barnett W, Conlon M, Eichmann D, Kibbe WA, Falk-Krzesinski H, Halaas M, Johnson L, Meeks E, Mitchell D, Schleyer T, Stallings S, Warden M, Kahlon M. Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms. J Am Med Inform Assoc. (2011) 18 Suppl 1:i157-i160. [PubMed ID 22037890]
  • 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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