Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., California Institute of Technology 1990
• 

  Duke Appointment History

  • Instructor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2017 - 2018
• 

  Leadership & Clinical Positions at Duke

  • Duke Cancer Institute Chief Data Officer
• 

  Academic Positions Outside Duke

  • Professor, Northwestern University. 1995 - 2013
• Expertise
• 

  Subject Headings

  • Bioinformatics
  • Clinical medicine--Research
  • Informatics
  • Medical Informatics
  • Software
  • Software Design
  • Software Validation
• Publications & Artistic Works
• 

  Selected Publications

  • Books

    • Fleming, M, Bresler, L, and O'Toole, J. Introduction. July 30, 2015.

  • Academic Articles

    • Lee, JS-H, Kibbe, WA, and Grossman, RL. "Data Harmonization for a Molecularly Driven Health System." Cell 174, no. 5 (August 2018): 1045-1048.  Full Text
    • Davis, AA, McKee, AE, Kibbe, WA, and Villaflor, VM. "Complexity of Delivering Precision Medicine: Opportunities and Challenges." American Society of Clinical Oncology Educational Book. American Society of Clinical Oncology. Annual Meeting , no. 38 (May 2018): 998-1007. (Review)  Full Text  Open Access Copy
    • Hinkson, IV, Davidsen, TM, Klemm, JD, Chandramouliswaran, I, Kerlavage, AR, and Kibbe, WA. "Corrigendum: A comprehensive infrastructure for big data in cancer research: Accelerating cancer research and precision medicine [Front. Cell Dev. Biol, 5, (83)] doi: 10.3389/fcell.2017.00083." Frontiers in Cell and Developmental Biology 5, no. DEC (December 7, 2017).  Full Text
    • Kibbe, W, Klemm, J, and Quackenbush, J. "Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research." Cancer Research 77, no. 21 (November 2017): e1-e2.  Full Text
    • Hinkson, IV, Davidsen, TM, Klemm, JD, Kerlavage, AR, and Kibbe, WA. "A comprehensive infrastructure for big data in cancer research: Accelerating cancer research and precision medicine." Frontiers in Cell and Developmental Biology 5, no. SEP (September 21, 2017).  Full Text  Open Access Copy
    • Zheng, Y, Joyce, BT, Liu, L, Zhang, Z, Kibbe, WA, Zhang, W, and Hou, L. "Prediction of genome-wide DNA methylation in repetitive elements." Nucleic acids research 45, no. 15 (September 2017): 8697-8711.  Full Text
    • Hsu, ER, Klemm, JD, Kerlavage, AR, Kusnezov, D, and Kibbe, WA. "Cancer Moonshot Data and Technology Team: Enabling a National Learning Healthcare System for Cancer to Unleash the Power of Data." Clinical pharmacology and therapeutics 101, no. 5 (May 2017): 613-615. (Review)  Full Text
    • Grossman, RL, Heath, AP, Ferretti, V, Varmus, HE, Lowy, DR, Kibbe, WA, and Staudt, LM. "Toward a Shared Vision for Cancer Genomic Data." The New England Journal of Medicine 375, no. 12 (September 2016): 1109-1112.  Full Text
    • Zheng, Y, Joyce, BT, Colicino, E, Liu, L, Zhang, W, Dai, Q, Shrubsole, MJ, Kibbe, WA, Gao, T, Zhang, Z, Jafari, N, Vokonas, P, Schwartz, J, Baccarelli, AA, and Hou, L. "Blood Epigenetic Age may Predict Cancer Incidence and Mortality." Ebiomedicine 5 (March 2016): 68-73.  Full Text
    • Zhang, Z, Zheng, Y, Zhang, X, Liu, C, Joyce, BT, Kibbe, WA, Hou, L, and Zhang, W. "Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines." Human genetics 135, no. 2 (February 2016): 223-232.  Full Text
    • Groza, T, Köhler, S, Moldenhauer, D, Vasilevsky, N, Baynam, G, Zemojtel, T, Schriml, LM, Kibbe, WA, Schofield, PN, Beck, T, Vasant, D, Brookes, AJ, Zankl, A, Washington, NL, Mungall, CJ, Lewis, SE, Haendel, MA, Parkinson, H, and Robinson, PN. "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease." American Journal of Human Genetics 97, no. 1 (July 2015): 111-124.  Full Text
    • Kibbe, WA, Arze, C, Felix, V, Mitraka, E, Bolton, E, Fu, G, Mungall, CJ, Binder, JX, Malone, J, Vasant, D, Parkinson, H, and Schriml, LM. "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data." Nucleic Acids Research 43, no. Database issue (January 2015): D1071-D1078.  Full Text
    • Wu, T-J, Schriml, LM, Chen, Q-R, Colbert, M, Crichton, DJ, Finney, R, Hu, Y, Kibbe, WA, Kincaid, H, Meerzaman, D, Mitraka, E, Pan, Y, Smith, KM, Srivastava, S, Ward, S, Yan, C, and Mazumder, R. "Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis." Database : the Journal of Biological Databases and Curation 2015 (January 2015): bav032-null.  Full Text
    • Ng, MCY, Shriner, D, Chen, BH, Li, J, Chen, W-M, Guo, X, Liu, J, Bielinski, SJ, Yanek, LR, Nalls, MA, Comeau, ME, Rasmussen-Torvik, LJ, Jensen, RA, Evans, DS, Sun, YV, An, P, Patel, SR, Lu, Y, Long, J, Armstrong, LL, Wagenknecht, L, Yang, L, Snively, BM, Palmer, ND, Mudgal, P, Langefeld, CD, Keene, KL, Freedman, BI, Mychaleckyj, JC, Nayak, U, Raffel, LJ, Goodarzi, MO, Chen, Y-DI, Taylor, HA, Correa, A, Sims, M, Couper, D, Pankow, JS, Boerwinkle, E, Adeyemo, A, Doumatey, A, Chen, G, Mathias, RA, Vaidya, D, Singleton, AB, Zonderman, AB, Igo, RP, Sedor, JR, FIND Consortium, , Kabagambe, EK, Siscovick, DS, McKnight, B, Rice, K, Liu, Y, Hsueh, W-C, Zhao, W, Bielak, LF, Kraja, A, Province, MA, Bottinger, EP, Gottesman, O, Cai, Q, Zheng, W, Blot, WJ, Lowe, WL, Pacheco, JA, Crawford, DC, eMERGE Consortium, , DIAGRAM Consortium, , Grundberg, E, MuTHER Consortium, , Rich, SS, Hayes, MG, Shu, X-O, Loos, RJF, Borecki, IB, Peyser, PA, Cummings, SR, Psaty, BM, Fornage, M, Iyengar, SK, Evans, MK, Becker, DM, Kao, WHL, Wilson, JG, Rotter, JI, Sale, MM, Liu, S, Rotimi, CN, Bowden, DW, and MEta-analysis of type 2 DIabetes in African Americans Consortium, . "Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes." Plos Genetics 10, no. 8 (August 7, 2014): e1004517-null.  Full Text
    • Bao, R, Huang, L, Andrade, J, Tan, W, Kibbe, WA, Jiang, H, and Feng, G. "Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing." Cancer Informatics 13, no. Suppl 2 (January 2014): 67-82. (Review)  Full Text
    • Basu, S, Fey, P, Pandit, Y, Dodson, R, Kibbe, WA, and Chisholm, RL. "DictyBase 2013: integrating multiple Dictyostelid species." Nucleic Acids Research 41, no. Database issue (January 2013): D676-D683.  Full Text
    • Gene Ontology Consortium, , Blake, JA, Dolan, M, Drabkin, H, Hill, DP, Li, N, Sitnikov, D, Bridges, S, Burgess, S, Buza, T, McCarthy, F, Peddinti, D, Pillai, L, Carbon, S, Dietze, H, Ireland, A, Lewis, SE, Mungall, CJ, Gaudet, P, Chrisholm, RL, Fey, P, Kibbe, WA, Basu, S, Siegele, DA, McIntosh, BK, Renfro, DP, Zweifel, AE, Hu, JC, Brown, NH, Tweedie, S, Alam-Faruque, Y, Apweiler, R, Auchinchloss, A, Axelsen, K, Bely, B, Blatter, M-C, Bonilla, C, Bouguerleret, L, Boutet, E, Breuza, L, Bridge, A, Chan, WM, Chavali, G, Coudert, E, Dimmer, E, Estreicher, A, Famiglietti, L, Feuermann, M, Gos, A, Gruaz-Gumowski, N, Hieta, R, Hinz, C, Hulo, C, Huntley, R, James, J, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, Martin, MJ, Masson, P, Mutowo-Muellenet, P, O'Donovan, C, Pedruzzi, I, Pichler, K, Poggioli, D, Porras Millán, P, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Foulgar, R, Lomax, J, Roncaglia, P, Khodiyar, VK, Lovering, RC, Talmud, PJ, Chibucos, M, Giglio, MG, Chang, H-Y, Hunter, S, McAnulla, C, Mitchell, A, Sangrador, A, Stephan, R, Harris, MA, Oliver, SG, Rutherford, K, Wood, V, Bahler, J, Lock, A, Kersey, PJ, McDowall, DM, Staines, DM, Dwinell, M, Shimoyama, M, Laulederkind, S, Hayman, T, Wang, S-J, Petri, V, Lowry, T, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, JM, Costanzo, MC, Dwight, SS, Engel, SR, Fisk, DG, Hitz, BC, Hong, EL, Karra, K, Miyasato, SR, Nash, RS, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Berardini, TZ, Huala, E, Mi, H, Thomas, PD, Chan, J, Kishore, R, Sternberg, P, Van Auken, K, Howe, D, and Westerfield, M. "Gene Ontology annotations and resources." Nucleic Acids Research 41, no. Database issue (January 2013): D530-D535.  Full Text
    • 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, and Xia, T. "The Disease and Gene Annotations (DGA): an annotation resource for human disease." Nucleic Acids Research 41, no. Database issue (January 2013): D553-D560.  Full Text
    • Zhang, X, Wallace, AD, Du, P, Lin, S, Baccarelli, AA, Jiang, H, Jafari, N, Zheng, Y, Xie, H, Soares, MB, Kibbe, WA, and Hou, L. "Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro." Environmental Toxicology and Pharmacology 34, no. 3 (November 2012): 959-968.  Full Text
    • Hinchcliff, M, Just, E, Podlusky, S, Varga, J, Chang, RW, and Kibbe, WA. "Text data extraction for a prospective, research-focused data mart: implementation and validation." Bmc Medical Informatics and Decision Making 12 (September 13, 2012): 106-null.  Full Text
    • Zhang, X, Wallace, AD, Du, P, Kibbe, WA, Jafari, N, Xie, H, Lin, S, Baccarelli, A, Soares, MB, and Hou, L. "DNA methylation alterations in response to pesticide exposure in vitro." Environmental and Molecular Mutagenesis 53, no. 7 (August 2012): 542-549.  Full Text
    • Feng, G, Shaw, P, Rosen, ST, Lin, SM, and Kibbe, WA. "Using the bioconductor GeneAnswers package to interpret gene lists." Methods in molecular biology (Clifton, N.J.) 802 (January 2012): 101-112.  Full Text
    • Gene Ontology Consortium, . "The Gene Ontology: enhancements for 2011." Nucleic Acids Research 40, no. Database issue (January 2012): D559-D564.  Full Text
    • Schriml, LM, Arze, C, Nadendla, S, Chang, Y-WW, Mazaitis, M, Felix, V, Feng, G, and Kibbe, WA. "Disease Ontology: a backbone for disease semantic integration." Nucleic Acids Research 40, no. Database issue (January 2012): D940-D946.  Full Text
    • Xu, W, Wang, H, Cheng, W, Fu, D, Xia, T, Kibbe, WA, and Lin, SM. "A framework for annotating human genome in disease context." PloS one 7, no. 12 (January 2012): e49686-.  Full Text
    • Good, BM, Howe, DG, Lin, SM, Kibbe, WA, and Su, AI. "Mining the Gene Wiki for functional genomic knowledge." BMC genomics 12 (December 13, 2011): 603-.  Full Text
    • Weber, GM, Barnett, W, Conlon, M, Eichmann, D, Kibbe, W, Falk-Krzesinski, H, Halaas, M, Johnson, L, Meeks, E, Mitchell, D, Schleyer, T, Stallings, S, Warden, M, Kahlon, M, and Direct2Experts Collaboration, . "Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms." Journal of the American Medical Informatics Association : Jamia 18 Suppl 1 (December 2011): i157-i160.  Full Text
    • McCarty, CA, Chisholm, RL, Chute, CG, Kullo, IJ, Jarvik, GP, Larson, EB, Li, R, Masys, DR, Ritchie, MD, Roden, DM, Struewing, JP, Wolf, WA, and eMERGE Team, . "The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies." Bmc Medical Genomics 4 (January 26, 2011): 13-null. (Letter)  Full Text
    • Gaudet, P, Fey, P, Basu, S, Bushmanova, YA, Dodson, R, Sheppard, KA, Just, EM, Kibbe, WA, and Chisholm, RL. "dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa." Nucleic Acids Research 39, no. Database issue (January 2011): D620-D624.  Full Text
    • Du, P, Zhang, X, Huang, C-C, Jafari, N, Kibbe, WA, Hou, L, and Lin, SM. "Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis." Bmc Bioinformatics 11 (November 30, 2010): 587-null.  Full Text
    • Feng, G, Du, P, Krett, NL, Tessel, M, Rosen, S, Kibbe, WA, and Lin, SM. "A collection of bioconductor methods to visualize gene-list annotations." BMC research notes 3 (January 19, 2010): 10-.  Full Text
    • "The Gene Ontology in 2010: extensions and refinements." Nucleic Acids Research 38, no. Database issue (January 2010): D331-D335.  Full Text
    • Desai, J, Flatow, JM, Song, J, Zhu, LJ, Du, P, Huang, C-C, Lu, H, Lin, SM, and Kibbe, WA. "Visual presentation as a welcome alternative to textual presentation of gene annotation information." Advances in experimental medicine and biology 680 (January 2010): 709-715.  Full Text
    • Osborne, JD, Flatow, J, Holko, M, Lin, SM, Kibbe, WA, Zhu, LJ, Danila, MI, Feng, G, and Chisholm, RL. "Annotating the human genome with Disease Ontology." Bmc Genomics 10 Suppl 1 (July 7, 2009): S6-null.  Full Text
    • Du, P, Feng, G, Flatow, J, Song, J, Holko, M, Kibbe, WA, and 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 (Oxford, England) 25, no. 12 (June 2009): i63-i68.  Full Text
    • Fey, P, Gaudet, P, Curk, T, Zupan, B, Just, EM, Basu, S, Merchant, SN, Bushmanova, YA, Shaulsky, G, Kibbe, WA, and Chisholm, RL. "dictyBase--a Dictyostelium bioinformatics resource update." Nucleic Acids Research 37, no. Database issue (January 2009): D515-D519.  Full Text
    • Wen, J, Wang, X, Kibbe, W, Lin, S, and Lu, H. "Visual annotation of the gene database." Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 2009 (January 2009): 4175-4177.  Full Text
    • Du, P, Kibbe, WA, and Lin, SM. "lumi: a pipeline for processing Illumina microarray." Bioinformatics (Oxford, England) 24, no. 13 (July 2008): 1547-1548.  Full Text
    • Lin, SM, Du, P, Huber, W, and Kibbe, WA. "Model-based variance-stabilizing transformation for Illumina microarray data." Nucleic Acids Research 36, no. 2 (February 2008): e11-null.  Full Text
    • Gene Ontology Consortium, . "The Gene Ontology project in 2008." Nucleic Acids Research 36, no. Database issue (January 2008): D440-D444.  Full Text
    • Lee, C-J, Fu, D, Du, P, Jiang, H, Lin, SM, and Kibbe, W. "A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays." International journal of computational biology and drug design 1, no. 4 (January 2008): 396-405.  Full Text
    • Kibbe, WA. "OligoCalc: an online oligonucleotide properties calculator." Nucleic Acids Research 35, no. Web Server issue (July 2007): W43-W46.  Full Text
    • Osborne, JD, Lin, S, and Kibbe, WA. "Other riffs on cooperation are already showing how well a wiki could work." Nature 446, no. 7138 (April 2007): 856-null. (Letter)  Full Text
    • Osborne, JD, Zhu, L, Lin, SM, and Kibbe, WA. "Interpreting microarray results with gene ontology and MeSH." Methods in Molecular Biology 377 (March 24, 2007): 223-241.  Full Text
    • Arshinoff, BI, Suen, G, Just, EM, Merchant, SM, Kibbe, WA, Chisholm, RL, and Welch, RD. "Xanthusbase: adapting wikipedia principles to a model organism database." Nucleic Acids Research 35, no. Database issue (January 2007): D422-D426.  Full Text
    • Du, P, Kibbe, WA, and Lin, SM. "nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays." Biology Direct 2 (January 2007): 16-null.  Full Text
    • Osborne, JD, Lin, S, Zhu, L, and Kibbe, WA. "Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS)." Methods in molecular biology (Clifton, N.J.) 408 (January 2007): 153-169.  Full Text
    • Osborne, JD, Zhu, LJ, Lin, SM, and Kibbe, WA. "Interpreting microarray results with gene ontology and MeSH." Methods in molecular biology (Clifton, N.J.) 377 (January 2007): 223-242. (Review)  Full Text
    • Du, P, Kibbe, WA, and Lin, SM. "Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching." Bioinformatics (Oxford, England) 22, no. 17 (September 2006): 2059-2065.  Full Text
    • Lin, SM, Devakumar, J, and Kibbe, WA. "Improved prediction of treatment response using microarrays and existing biological knowledge." Pharmacogenomics 7, no. 3 (April 2006): 495-501.  Full Text
    • Chisholm, RL, Gaudet, P, Just, EM, Pilcher, KE, Fey, P, Merchant, SN, and Kibbe, WA. "dictyBase, the model organism database for Dictyostelium discoideum." Nucleic Acids Research 34, no. Database issue (January 2006): D423-D427.  Full Text
    • Chisholm, RL, Gaudet, P, Just, EM, Pilcher, KE, Fey, P, Merchant, SN, and Kibbe, WA. "dictyBase, the model organism database for Dictyostelium discoideum." Nucleic Acids Research 34, no. Database issue (January 1, 2006).
    • Ge, X, Jung, Y-C, Wu, Q, Kibbe, WA, and Wang, SM. "Annotating nonspecific SAGE tags with microarray data." Genomics 87, no. 1 (January 2006): 173-180.  Full Text
    • Gene Ontology Consortium, . "The Gene Ontology (GO) project in 2006." Nucleic Acids Research 34, no. Database issue (January 2006): D322-D326.  Full Text
    • Lin, SM, Zhu, L, Winter, AQ, Sasinowski, M, and Kibbe, WA. "What is mzXML good for?." Expert review of proteomics 2, no. 6 (December 2005): 839-845. (Review)  Full Text
    • Lin, SM, Zhu, L, Winter, AQ, Sasinowski, M, and Kibbe, WA. "What is mzXML good for?." EXPERT REVIEW OF PROTEOMICS 2, no. 6 (December 2005): 839-845.  Full Text  Link to Item
    • Kaput, J, Ordovas, JM, Ferguson, L, van Ommen, B, Rodriguez, RL, Allen, L, Ames, BN, Dawson, K, German, B, Krauss, R, Malyj, W, Archer, MC, Barnes, S, Bartholomew, A, Birk, R, van Bladeren, P, Bradford, KJ, Brown, KH, Caetano, R, Castle, D, Chadwick, R, Clarke, S, Clément, K, Cooney, CA, Corella, D, Manica da Cruz, IB, Daniel, H, Duster, T, Ebbesson, SOE, Elliott, R, Fairweather-Tait, S, Felton, J, Fenech, M, Finley, JW, Fogg-Johnson, N, Gill-Garrison, R, Gibney, MJ, Gillies, PJ, Gustafsson, J-A, Hartman, JL, He, L, Hwang, J-K, Jais, J-P, Jang, Y, Joost, H, Junien, C, Kanter, M, Kibbe, WA, Koletzko, B, Korf, BR, Kornman, K, Krempin, DW, Langin, D, Lauren, DR, Ho Lee, J, Leveille, GA, Lin, S-J, Mathers, J, Mayne, M, McNabb, W, Milner, JA, Morgan, P, Muller, M, Nikolsky, Y, van der Ouderaa, F, Park, T, Pensel, N, Perez-Jimenez, F, Poutanen, K, Roberts, M, Saris, WHM, Schuster, G, Shelling, AN, Simopoulos, AP, Southon, S, Tai, ES, Towne, B, Trayhurn, P, Uauy, R, Visek, WJ, Warden, C, Weiss, R, Wiencke, J, Winkler, J, Wolff, GL, Zhao-Wilson, X, and Zucker, J-D. "The case for strategic international alliances to harness nutritional genomics for public and personal health." The British Journal of Nutrition 94, no. 5 (November 2005): 623-632. (Review)  Full Text
    • Kaput, J, Ordovas, JM, Ferguson, L, van Ommen, B, Rodriguez, RL, Allen, L, Ames, BN, Dawson, K, German, B, Krauss, R, Malyj, W, Archer, MC, Barnes, S, Bortholomew, A, Birk, R, van Bladeren, P, Bradford, KJ, Brown, KH, Caetano, R, Castle, D, Chadwick, R, Clarke, S, Clemént, K, Cooney, CA, Corella, D, da Cruz, IBM, Daniel, H, Duster, T, Ebbesson, SOE, Elliott, R, Fairweather-Tait, S, Felton, J, Fenech, M, Finley, JW, Fogg-Johnson, N, Gill-Garrison, R, Gibney, MJ, Gillies, PJ, Gustafsson, JA, Hartman IV, JL, He, L, Hwang, JK, Jais, JP, Jang, Y, Joost, H, Junien, C, Kanter, M, Kibbe, WA, Koletzko, B, Korf, BR, Kornman, K, Krempin, DW, Langin, D, Lauren, DR, Lee, JH, Leveille, GA, Lin, SJ, Mathers, J, Mayne, M, McNabb, W, Milner, JA, Morgan, P, Muller, M, Nikolsky, Y, van der Ouderaa, F, Park, T, Pensel, N, Perez-Jimenez, F, Poutanen, K, Roberts, M, Saris, WHM, Schuster, G, Shelling, AN, Simopoulos, AP, Southon, S, Shyong Tai, E, Towne, B, Trayhurn, P, Uauy, R, Visek, WJ, Warden, C, Weiss, R, Wiencke, J, Winkler, J, Wolff, GL, Zhao-Wilson, X, and Zucker, JD. "The case for strategic international alliances to harness nutritional genomics for public and personal health." British Journal of Nutrition 94, no. 5 (November 1, 2005): 623-632.  Full Text
    • Lin, SM, and Kibbe, WA. "Irrational exuberance in clinical proteomics." Clinical cancer research : an official journal of the American Association for Cancer Research 11, no. 22 (November 2005): 7963-7964.  Full Text
    • Goldowitz, D, Frankel, WN, Takahashi, JS, Holtz-Vitaterna, M, Bult, C, Kibbe, WA, Snoddy, J, Li, Y, Pretel, S, Yates, J, and Swanson, DJ. "Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function." Brain Research. Molecular Brain Research 132, no. 2 (December 2004): 105-115. (Review)  Full Text
    • Kaput, J, Klein, KG, Reyes, EJ, Kibbe, WA, Cooney, CA, Jovanovic, B, Visek, WJ, and Wolff, GL. "Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet x genotype interactions." Physiological Genomics 18, no. 3 (August 11, 2004): 316-324.  Full Text
    • Bult, C, Kibbe, WA, Snoddy, J, Vitaterna, M, Swanson, D, Pretel, S, Li, Y, Hohman, MM, Rinchik, E, Takahashi, JS, Frankel, WN, and Goldowitz, D. "A genome end-game: understanding gene function in the nervous system." Nature Neuroscience 7, no. 5 (May 2004): 484-485.  Full Text
    • Harris, MA, Clark, J, Ireland, A, Lomax, J, Ashburner, M, Foulger, R, Eilbeck, K, Lewis, S, Marshall, B, Mungall, C, Richter, J, Rubin, GM, Blake, JA, Bult, C, Dolan, M, Drabkin, H, Eppig, JT, Hill, DP, Ni, L, Ringwald, M, Balakrishnan, R, Cherry, JM, Christie, KR, Costanzo, MC, Dwight, SS, Engel, S, Fisk, DG, Hirschman, JE, Hong, EL, Nash, RS, Sethuraman, A, Theesfeld, CL, Botstein, D, Dolinski, K, Feierbach, B, Berardini, T, Mundodi, S, Rhee, SY, Apweiler, R, Barrell, D, Camon, E, Dimmer, E, Lee, V, Chisholm, R, Gaudet, P, Kibbe, W, Kishore, R, Schwarz, EM, Sternberg, P, Gwinn, M, Hannick, L, Wortman, J, Berriman, M, Wood, V, de la Cruz, N, Tonellato, P, Jaiswal, P, Seigfried, T, White, R, and Gene Ontology Consortium, . "The Gene Ontology (GO) database and informatics resource." Nucleic Acids Research 32, no. Database issue (January 2004): D258-D261.  Full Text
    • Harris, MA, Clark, J, Ireland, A, Lomax, J, Ashburner, M, Foulger, R, Eilbeck, K, Lewis, S, Marshall, B, Mungall, C, Richter, J, Rubin, GM, Blake, JA, Bult, C, Dolan, M, Drabkin, H, Eppig, JT, Hill, DP, Ni, L, Ringwald, M, Balakrishnan, R, Cherry, JM, Christie, KR, Costanzo, MC, Dwight, SS, Engel, S, Fisk, DG, Hirschman, JE, Hong, EL, Nash, RS, Sethuraman, A, Theesfeld, CL, Botstein, D, Dolinski, K, Feierbach, B, Berardini, T, Mundodi, S, Rhee, SY, Apweiler, R, Barrell, D, Camon, E, Dimmer, E, Lee, V, Chisholm, R, Gaudet, P, Kibbe, W, Kishore, R, Schwarz, EM, Sternberg, P, Gwinn, M, Hannick, L, and Wortman, J. "The Gene Oncology (GO) database and informatics resource." Nucleic Acids Research 32, no. DATABASE ISS. (January 1, 2004).
    • Kreppel, L, Fey, P, Gaudet, P, Just, E, Kibbe, WA, Chisholm, RL, and Kimmel, AR. "dictyBase: a new Dictyostelium discoideum genome database." Nucleic Acids Research 32, no. Database issue (January 2004): D332-D333.  Full Text
    • Kreppel, L, Fey, P, Gaudet, P, Just, E, Kibbe, WA, Chisholm, RL, and Kimmel, AR. "dictyBase: A new Dictyostelium discoideum genome database." Nucleic Acids Research 32, no. DATABASE ISS. (January 1, 2004).
    • Jovanovic, BD, Bergan, RC, and Kibbe, WA. "Some aspects of analysis of gene array data." Cancer treatment and research 113 (January 2002): 71-89. (Review)
    • Zhang-Keck, ZY, Kibbe, WA, Moye-Rowley, WS, and Parker, CS. "The SV40 core sequence functions as a repressor element in yeast." The Journal of biological chemistry 266, no. 32 (November 1991): 21362-21367.
    • Wiederrecht, G, Shuey, DJ, Kibbe, WA, and Parker, CS. "The Saccharomyces and Drosophila heat shock transcription factors are identical in size and DNA binding properties." Cell 48, no. 3 (February 1987): 507-515.  Full Text

  • Book Sections

    • Kibbe, WA. "The Informatics and Bioinformatics Infrastructure of a Nutrigenomics Biobank." In Nutritional Genomics: Discovering the Path to Personalized Nutrition, 353-374. May 10, 2006.  Full Text

  • Conference Papers

    • Du, P, Lin, SM, Kibbe, WA, and Wang, H. "Application of wavelet transform to the MS-based proteomics data preprocessing." December 1, 2007.  Full Text
    • Kibbe, WA, Wolf, WW, Smith, ME, Allen, JS, and Chisholm, RL. "The NUgene Project: Biospecimen informatics system design." 2006.  Link to Item
    • Wolf, WW, Smith, ME, Kibbe, WA, Allen, JS, and Chisholm, RL. "The NUgene Project: eMR-facilitated biobanking." 2006.  Link to Item
    • Pinto, LH, Vitaterna, M, Siepka, S, Shimomura, K, Kibbe, W, Mullins, R, Heffron, E, Stone, E, Sheffield, V, and Takahashi, JS. "Mapping and characterization of Noerg-1 mutation in mouse." April 2004.  Link to Item
    • Wolf, WA, Doyle, MJ, Aufox, SA, Frezzo, TM, Smith, ME, Kibbe, WA, and Chisholm, RL. "DNA banking study in an ethnically diverse urban university hospital." November 2003.  Link to Item
    • Pinto, LH, Grabowski, N, Kibbe, WA, Lotery, A, Lumayag, S, Mullens, R, Stone, E, Siepka, S, Vitatema, MH, Sheffield, V, and Takahashi, JS. "Chemically induced mutations in the mouse that affect the fundus and electroretinogram." 2003.  Link to Item
    • Gwaltney, K, Chute, C, Hageman, D, Kibbe, W, McCormick, K, Reeves, D, and Wright, L. "An assessment of cancer clinical trials vocabulary and IT infrastructure in the U.S." January 2001.

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