Warren Kibbe
From PublicWiki
Contents |
Warren Kibbe, Ph.D.
| Research Associate Professor Feinberg School of Medicine
|
The Robert H. Lurie Comprehensive Cancer Center
Feinberg School of Medicine
Northwestern University
676 St Clair Suite 1200
Chicago, IL 60611
Phone: 847-380-2656
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
Recent Projects
Personal Projects
Disease Ontology public site;
NU-CATS Publications public site; dev site accessible to only NU IPs
RHLCCC Publications public site dev site accessible to only NU IPs
Cancer Center Clinical Trials Abstracts production
Cancer Center Members Profiles production requires login
Animal Models of Disease production NU only IPs
Oligonucleotide Properties Calculator
Collaborations and Projects
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
Publications 2004-2008
- Lin SM, Du P, WA Kibbe. Heuristic-based Baseline Removal Algorithm for SELDI Proteomics Data. Bioinformatics, submitted.
- Lin SM, Du P, Huber W, WA Kibbe. Model-based Variance-stabilizing Transformation for Illumina Microarray Data. Nucleic Acids Res., (2008) 36:e11.
- Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics (2008) 24:1547-8.
- Gene Ontology Consortium. The Gene Ontology (GO) project in 2008. Nucleic Acids Res. (2008) 36:D440-4.
- 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.
- Du P, Kibbe WA, SM Lin. nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays. Biol. Direct. (2007) 2:16.
- 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.
- Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol. (2007) 377:223-42.
- Kibbe WA. OligoCalc – an online Oligonucleotide Properties Calculator. Nucleic Acids Res. (2007 Webserver issue).
- Osborne JD, Lin SM, and Kibbe WA Other riffs on cooperation are already showing how well a wiki could work. Nature (2007) 446:856.
- 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.
- 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).
- 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.
- 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.
