Warren Alden Kibbe | Scholars@Duke

Warren Alden Kibbe
Professor in Biostatistics & Bioinformatics

Warren A. Kibbe, PhD, is chief for Translational Biomedical Informatics in the Department of Biostatistics and Bioinformatics and Chief Data Officer for the Duke Cancer Institute. He joined the Duke University School of Medicine in August after serving as the acting deputy director of the National Cancer Institute (NCI) and director of the NCI’s Center for Biomedical Informatics and Information Technology where he oversaw 60 federal employees and more than 600 contractors, and served as an acting Deputy Director for NCI. As an acting Deputy Director, Dr. Kibbe was involved in the myriad of activities that NCI oversees as a research organization, as a convening body for cancer research, and as a major funder of cancer research, funding nearly $4B US annually in cancer research throughout the United States.

Current Research Interests

Cancer informatics, cancer genomics, clinical trial operations, precision oncology

Current Appointments & Affiliations

Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2022
Chief Data Officer, DCI, Biostatistics & Bioinformatics, Basic Science Departments 2017
Chief, Division of Translational Biomedical Informatics, Biostatistics & Bioinformatics, Basic Science Departments 2017
Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 2018

Contact Information

2424 Erwin Road, Suite 902, 9025 Hock Plaza, Durham, NC 27705
Duke Box 2721, Durham, NC 27710
warren.kibbe@duke.edu (919) 668-7384
Google Scholar
LinkedIn profile
ORCID profile
Twitter feed

Background
Education, Training, & Certifications
- Ph.D., California Institute of Technology 1990
Previous Appointments & Affiliations
- Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2021 - 2022
- Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2018 - 2020
- 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
Recognition
Awards & Honors
- Fellow of ACMI 2018. American Medical Informatics Association. 2018
Expertise
Subject Headings
Research
Selected Grants
- RADx-UP CDCC awarded by National Institutes of Health 2020 - 2024
- The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
- Study effects of COVID-19 infection on cancer patients on National COVID Cohort Collaborative (N3) awarded by University of Colorado Anschutz Medical Campus 2021 - 2022
External Relationships
- Case Comprehensive Cancer Center
- City of Hope
- Cleveland Computational Biology Institute
- N-POWER Medicine
- Sage Bionetworks
- University of Wisconsin School of Medicine and Public Health
- Virginia Commonwealth University
Publications & Artistic Works
Selected Publications
- Books
  - Fleming, M., L. Bresler, and J. O’Toole. Introduction, 2015.
- Academic Articles
  - Carrillo, Gabriel A., Michael Cohen-Wolkowiez, Emily M. D’Agostino, Keith Marsolo, Lisa M. Wruck, Laura Johnson, James Topping, Al Richmond, Giselle Corbie, and Warren A. Kibbe. “Standardizing, harmonizing, and protecting data collection to broaden the impact of COVID-19 research: the rapid acceleration of diagnostics-underserved populations (RADx-UP) initiative.” J Am Med Inform Assoc 29, no. 9 (August 16, 2022): 1480–88. https://doi.org/10.1093/jamia/ocac097.
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  - Herbert, Carly, Qiming Shi, Vik Kheterpal, Chris Nowak, Thejas Suvarna, Basyl Durnan, Summer Schrader, et al. “Use of a Digital Assistant to Report COVID-19 Rapid Antigen Self-test Results to Health Departments in 6 US Communities.” Jama Netw Open 5, no. 8 (August 1, 2022): e2228885. https://doi.org/10.1001/jamanetworkopen.2022.28885.
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  - Chen, Zhaoyi, Hansi Zhang, Thomas J. George, Yi Guo, Mattia Prosperi, Jingchuan Guo, Dejana Braithwaite, et al. “Simulating Colorectal Cancer Trials Using Real-World Data.” Jco Clin Cancer Inform 6 (July 2022): e2100195. https://doi.org/10.1200/CCI.21.00195.
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  - Soni, Apurv, Carly Herbert, Jonggyu Baek, Qiming Shi, Juan Marquez, Emma Harman, Vik Kheterpal, et al. “Association of Mass Distribution of Rapid Antigen Tests and SARS-CoV-2 Prevalence: Results from NIH-CDC funded Say Yes! Covid Test program in Michigan.” Medrxiv, April 2, 2022. https://doi.org/10.1101/2022.03.26.22272727.
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  - Herbert, Carly, Qiming Shi, Vik Kheterpal, Chris Nowak, Thejas Suvarna, Basyl Durnam, Summer Schrader, et al. “If you build it, will they use it? Use of a Digital Assistant for Self-Reporting of COVID-19 Rapid Antigen Test Results during Large Nationwide Community Testing Initiative.” Medrxiv, April 1, 2022. https://doi.org/10.1101/2022.03.31.22273242.
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  - Chow, Jonathan H., Ali Rahnavard, Mardi Gomberg-Maitland, Ranojoy Chatterjee, Pranay Patodi, David P. Yamane, Andrea R. Levine, et al. “Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19.” Jama Netw Open 5, no. 3 (March 1, 2022): e223890. https://doi.org/10.1001/jamanetworkopen.2022.3890.
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  - Schapiro, Denis, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, et al. “MITI minimum information guidelines for highly multiplexed tissue images.” Nat Methods 19, no. 3 (March 2022): 262–67. https://doi.org/10.1038/s41592-022-01415-4.
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  - Ciccone, Emily J., Donaldson F. Conserve, Gaurav Dave, Christoph P. Hornik, Marlena L. Kuhn, Jessica L. Herling, Michelle Song, et al. “Correction to: At-home testing to mitigate community transmission of SARS-CoV-2: protocol for a public health intervention with a nested prospective cohort study.” Bmc Public Health 22, no. 1 (January 21, 2022): 151. https://doi.org/10.1186/s12889-021-12442-9.
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  - Ciccone, Emily J., Donaldson F. Conserve, Gaurav Dave, Christoph P. Hornik, Marlena L. Kuhn, Jessica L. Herling, Michelle Song, et al. “At-home testing to mitigate community transmission of SARS-CoV-2: protocol for a public health intervention with a nested prospective cohort study.” Bmc Public Health 21, no. 1 (December 4, 2021): 2209. https://doi.org/10.1186/s12889-021-12007-w.
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  - Noyd, David H., Amy Berkman, Claire Howell, Steve Power, Susan G. Kreissman, Andrew P. Landstrom, Michel Khouri, Kevin C. Oeffinger, and Warren A. Kibbe. “Leveraging Clinical Informatics Tools to Extract Cumulative Anthracycline Exposure, Measure Cardiovascular Outcomes, and Assess Guideline Adherence for Children With Cancer.” Jco Clin Cancer Inform 5 (October 2021): 1062–75. https://doi.org/10.1200/CCI.21.00099.
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  - Kerlavage, Anthony R., Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, Karlyne Reilly, Gregory Reaman, et al. “Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer.” Jco Clin Cancer Inform 5 (August 2021): 881–96. https://doi.org/10.1200/CCI.21.00040.
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  - Yu, Peter, and Warren Kibbe. “Cancer Data Science and Computational Medicine.” Jco Clin Cancer Inform 5 (May 2021): 487–89. https://doi.org/10.1200/CCI.21.00006.
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  - Haendel, Melissa A., Christopher G. Chute, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Philip R. O. Payne, et al. “The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.” J Am Med Inform Assoc 28, no. 3 (March 1, 2021): 427–43. https://doi.org/10.1093/jamia/ocaa196.
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  - Bent, Brinnae, Oana M. Enache, Benjamin Goldstein, Warren Kibbe, and Jessilyn P. Dunn. “Reply: Matters Arising 'Investigating sources of inaccuracy in wearable optical heart rate sensors'.” Npj Digit Med 4, no. 1 (February 26, 2021): 39. https://doi.org/10.1038/s41746-021-00409-4.
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  - Flaherty, Keith T., Robert Gray, Alice Chen, Shuli Li, David Patton, Stanley R. Hamilton, Paul M. Williams, et al. “The Molecular Analysis for Therapy Choice (NCI-MATCH) Trial: Lessons for Genomic Trial Design.” J Natl Cancer Inst 112, no. 10 (October 1, 2020): 1021–29. https://doi.org/10.1093/jnci/djz245.
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  - Rozenblatt-Rosen, Orit, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E. Rood, Orr Ashenberg, et al. “The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.” Cell 181, no. 2 (April 16, 2020): 236–49. https://doi.org/10.1016/j.cell.2020.03.053.
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  - Bent, Brinnae, Benjamin A. Goldstein, Warren A. Kibbe, and Jessilyn P. Dunn. “Investigating sources of inaccuracy in wearable optical heart rate sensors.” Npj Digit Med 3, no. 1 (February 10, 2020): 18. https://doi.org/10.1038/s41746-020-0226-6.
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  - Barnholtz-Sloan, Jill S., Dana E. Rollison, Amrita Basu, Alexander D. Borowsky, Alex Bui, Jack DiGiovanna, Montserrat Garcia-Closas, et al. “Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.” Jco Clin Cancer Inform 4 (February 2020): 108–16. https://doi.org/10.1200/CCI.19.00166.
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  - Bent, Brinnae, Benjamin A. Goldstein, Warren A. Kibbe, and Jessilyn P. Dunn. “Investigating sources of inaccuracy in wearable optical heart rate sensors.” Npj Digit Med 3 (2020): 18. https://doi.org/10.1038/s41746-020-0226-6.
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  - Zheng, Yinan, Ryan A. Hlady, Brian T. Joyce, Keith D. Robertson, Chunyan He, Drew R. Nannini, Warren A. Kibbe, et al. “DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma.” Clin Epigenetics 11, no. 1 (October 21, 2019): 145. https://doi.org/10.1186/s13148-019-0733-y.
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  - Lee, Jerry Ssu-Hsien, Warren Alden Kibbe, and Robert Lee Grossman. “Data Harmonization for a Molecularly Driven Health System.” Cell 174, no. 5 (August 23, 2018): 1045–48. https://doi.org/10.1016/j.cell.2018.08.012.
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  - Davis, Andrew A., Amy E. McKee, Warren A. Kibbe, and Victoria M. Villaflor. “Complexity of Delivering Precision Medicine: Opportunities and Challenges.” Am Soc Clin Oncol Educ Book 38 (May 23, 2018): 998–1007. https://doi.org/10.1200/EDBK_200279.
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  - Hinkson, I. V., T. M. Davidsen, J. D. Klemm, I. Chandramouliswaran, A. R. Kerlavage, and W. A. Kibbe. “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). https://doi.org/10.3389/fcell.2017.00108.
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  - Kibbe, Warren, Juli Klemm, and John Quackenbush. “Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research.” Cancer Res 77, no. 21 (November 1, 2017): e1–2. https://doi.org/10.1158/0008-5472.CAN-17-2212.
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  - Zheng, Yinan, Brian T. Joyce, Lei Liu, Zhou Zhang, Warren A. Kibbe, Wei Zhang, and Lifang Hou. “Prediction of genome-wide DNA methylation in repetitive elements.” Nucleic Acids Res 45, no. 15 (September 6, 2017): 8697–8711. https://doi.org/10.1093/nar/gkx587.
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  - Hsu, E. R., J. D. Klemm, A. R. Kerlavage, D. Kusnezov, and W. A. Kibbe. “Cancer Moonshot Data and Technology Team: Enabling a National Learning Healthcare System for Cancer to Unleash the Power of Data.” Clin Pharmacol Ther 101, no. 5 (May 2017): 613–15. https://doi.org/10.1002/cpt.636.
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  - Hinkson, Izumi V., Tanja M. Davidsen, Juli D. Klemm, Anthony R. Kerlavage, Warren A. Kibbe, and Ishwar Chandramouliswaran. “A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine.” Front Cell Dev Biol 5 (2017): 83. https://doi.org/10.3389/fcell.2017.00083.
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  - Grossman, Robert L., Allison P. Heath, Vincent Ferretti, Harold E. Varmus, Douglas R. Lowy, Warren A. Kibbe, and Louis M. Staudt. “Toward a Shared Vision for Cancer Genomic Data.” N Engl J Med 375, no. 12 (September 22, 2016): 1109–12. https://doi.org/10.1056/NEJMp1607591.
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  - Zheng, Yinan, Brian T. Joyce, Elena Colicino, Lei Liu, Wei Zhang, Qi Dai, Martha J. Shrubsole, et al. “Blood Epigenetic Age may Predict Cancer Incidence and Mortality.” Ebiomedicine 5 (March 2016): 68–73. https://doi.org/10.1016/j.ebiom.2016.02.008.
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  - Zhang, Zhou, Yinan Zheng, Xu Zhang, Cong Liu, Brian Thomas Joyce, Warren A. Kibbe, Lifang Hou, and Wei Zhang. “Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.” Hum Genet 135, no. 2 (February 2016): 223–32. https://doi.org/10.1007/s00439-015-1628-4.
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  - Groza, Tudor, Sebastian Köhler, Dawid Moldenhauer, Nicole Vasilevsky, Gareth Baynam, Tomasz Zemojtel, Lynn Marie Schriml, et al. “The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.” Am J Hum Genet 97, no. 1 (July 2, 2015): 111–24. https://doi.org/10.1016/j.ajhg.2015.05.020.
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  - Kibbe, Warren A., Cesar Arze, Victor Felix, Elvira Mitraka, Evan Bolton, Gang Fu, Christopher J. Mungall, et al. “Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.” Nucleic Acids Res 43, no. Database issue (January 2015): D1071–78. https://doi.org/10.1093/nar/gku1011.
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  - Wu, Tsung-Jung, Lynn M. Schriml, Qing-Rong Chen, Maureen Colbert, Daniel J. Crichton, Richard Finney, Ying Hu, et al. “Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.” Database (Oxford) 2015 (2015): bav032. https://doi.org/10.1093/database/bav032.
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  - Wood, Andrew R., Tonu Esko, Jian Yang, Sailaja Vedantam, Tune H. Pers, Stefan Gustafsson, Audrey Y. Chu, et al. “Defining the role of common variation in the genomic and biological architecture of adult human height.” Nat Genet 46, no. 11 (November 2014): 1173–86. https://doi.org/10.1038/ng.3097.
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  - Ng, Maggie C. Y., Daniel Shriner, Brian H. Chen, Jiang Li, Wei-Min Chen, Xiuqing Guo, Jiankang Liu, et al. “Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes.” Plos Genet 10, no. 8 (August 2014): e1004517. https://doi.org/10.1371/journal.pgen.1004517.
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  - Bao, Riyue, Lei Huang, Jorge Andrade, Wei Tan, Warren A. Kibbe, Hongmei Jiang, and Gang Feng. “Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.” Cancer Inform 13, no. Suppl 2 (2014): 67–82. https://doi.org/10.4137/CIN.S13779.
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  - Basu, Siddhartha, Petra Fey, Yogesh Pandit, Robert Dodson, Warren A. Kibbe, and Rex L. Chisholm. “DictyBase 2013: integrating multiple Dictyostelid species.” Nucleic Acids Res 41, no. Database issue (January 2013): D676–83. https://doi.org/10.1093/nar/gks1064.
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  - Gene Ontology Consortium, M., J. A. Blake, M. Dolan, H. Drabkin, D. P. Hill, Ni Li, D. Sitnikov, et al. “Gene Ontology annotations and resources.” Nucleic Acids Res 41, no. Database issue (January 2013): D530–35. https://doi.org/10.1093/nar/gks1050.
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  - Peng, Kai, Wei Xu, Jianyong Zheng, Kegui Huang, Huisong Wang, Jiansong Tong, Zhifeng Lin, et al. “The Disease and Gene Annotations (DGA): an annotation resource for human disease.” Nucleic Acids Res 41, no. Database issue (January 2013): D553–60. https://doi.org/10.1093/nar/gks1244.
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  - Zhang, Xiao, Andrew D. Wallace, Pan Du, Simon Lin, Andrea A. Baccarelli, Hongmei Jiang, Nadereh Jafari, et al. “Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro.” Environ Toxicol Pharmacol 34, no. 3 (November 2012): 959–68. https://doi.org/10.1016/j.etap.2012.07.012.
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  - Hinchcliff, Monique, Eric Just, Sofia Podlusky, John Varga, Rowland W. Chang, and Warren A. Kibbe. “Text data extraction for a prospective, research-focused data mart: implementation and validation.” Bmc Med Inform Decis Mak 12 (September 13, 2012): 106. https://doi.org/10.1186/1472-6947-12-106.
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  - Zhang, Xiao, Andrew D. Wallace, Pan Du, Warren A. Kibbe, Nadereh Jafari, Hehuang Xie, Simon Lin, Andrea Baccarelli, Marcelo Bento Soares, and Lifang Hou. “DNA methylation alterations in response to pesticide exposure in vitro.” Environ Mol Mutagen 53, no. 7 (August 2012): 542–49. https://doi.org/10.1002/em.21718.
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  - Feng, Gang, Pamela Shaw, Steven T. Rosen, Simon M. Lin, and Warren A. Kibbe. “Using the bioconductor GeneAnswers package to interpret gene lists.” Methods Mol Biol 802 (2012): 101–12. https://doi.org/10.1007/978-1-61779-400-1_7.
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  - Gene Ontology Consortium, Maninder. “The Gene Ontology: enhancements for 2011.” Nucleic Acids Res 40, no. Database issue (January 2012): D559–64. https://doi.org/10.1093/nar/gkr1028.
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  - Schriml, Lynn Marie, Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, and Warren Alden Kibbe. “Disease Ontology: a backbone for disease semantic integration.” Nucleic Acids Res 40, no. Database issue (January 2012): D940–46. https://doi.org/10.1093/nar/gkr972.
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  - Xu, Wei, Huisong Wang, Wenqing Cheng, Dong Fu, Tian Xia, Warren A. Kibbe, and Simon M. Lin. “A framework for annotating human genome in disease context.” Plos One 7, no. 12 (2012): e49686. https://doi.org/10.1371/journal.pone.0049686.
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  - Good, Benjamin M., Douglas G. Howe, Simon M. Lin, Warren A. Kibbe, and Andrew I. Su. “Mining the Gene Wiki for functional genomic knowledge.” Bmc Genomics 12 (December 13, 2011): 603. https://doi.org/10.1186/1471-2164-12-603.
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  - Weber, Griffin M., William Barnett, Mike Conlon, David Eichmann, Warren Kibbe, Holly Falk-Krzesinski, Michael Halaas, et al. “Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms.” J Am Med Inform Assoc 18 Suppl 1 (December 2011): i157–60. https://doi.org/10.1136/amiajnl-2011-000200.
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  - McCarty, Catherine A., Rex L. Chisholm, Christopher G. Chute, Iftikhar J. Kullo, Gail P. Jarvik, Eric B. Larson, Rongling Li, et al. “The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies.” Bmc Med Genomics 4 (January 26, 2011): 13. https://doi.org/10.1186/1755-8794-4-13.
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  - Gaudet, Pascale, Petra Fey, Siddhartha Basu, Yulia A. Bushmanova, Robert Dodson, Kerry A. Sheppard, Eric M. Just, Warren A. Kibbe, and Rex L. Chisholm. “dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.” Nucleic Acids Res 39, no. Database issue (January 2011): D620–24. https://doi.org/10.1093/nar/gkq1103.
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  - Du, Pan, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe, Lifang Hou, and Simon M. Lin. “Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.” Bmc Bioinformatics 11 (November 30, 2010): 587. https://doi.org/10.1186/1471-2105-11-587.
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  - Feng, Gang, Pan Du, Nancy L. Krett, Michael Tessel, Steven Rosen, Warren A. Kibbe, and Simon M. Lin. “A collection of bioconductor methods to visualize gene-list annotations.” Bmc Res Notes 3 (January 19, 2010): 10. https://doi.org/10.1186/1756-0500-3-10.
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  - Desai, Jairav, Jared M. Flatow, Jie Song, Lihua J. Zhu, Pan Du, Chiang-Ching Huang, Hui Lu, Simon M. Lin, and Warren A. Kibbe. “Visual presentation as a welcome alternative to textual presentation of gene annotation information.” Adv Exp Med Biol 680 (2010): 709–15. https://doi.org/10.1007/978-1-4419-5913-3_79.
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  - Gene Ontology Consortium, Tara L. E. “The Gene Ontology in 2010: extensions and refinements.” Nucleic Acids Res 38, no. Database issue (January 2010): D331–35. https://doi.org/10.1093/nar/gkp1018.
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  - Osborne, John D., Jared Flatow, Michelle Holko, Simon M. Lin, Warren A. Kibbe, Lihua Julie Zhu, Maria I. Danila, Gang Feng, and Rex L. Chisholm. “Annotating the human genome with Disease Ontology.” Bmc Genomics 10 Suppl 1 (July 7, 2009): S6. https://doi.org/10.1186/1471-2164-10-S1-S6.
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  - Du, Pan, Gang Feng, Jared Flatow, Jie Song, Michelle Holko, Warren A. Kibbe, and Simon M. Lin. “From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.” Bioinformatics 25, no. 12 (June 15, 2009): i63–68. https://doi.org/10.1093/bioinformatics/btp193.
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  - Fey, Petra, Pascale Gaudet, Tomaz Curk, Blaz Zupan, Eric M. Just, Siddhartha Basu, Sohel N. Merchant, et al. “dictyBase--a Dictyostelium bioinformatics resource update.” Nucleic Acids Res 37, no. Database issue (January 2009): D515–19. https://doi.org/10.1093/nar/gkn844.
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  - Wen, Jing, Xishu Wang, Warren Kibbe, Simon Lin, and Hui Lu. “Visual annotation of the gene database.” Annu Int Conf Ieee Eng Med Biol Soc 2009 (2009): 4175–77. https://doi.org/10.1109/IEMBS.2009.5333931.
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  - Du, Pan, Warren A. Kibbe, and Simon M. Lin. “lumi: a pipeline for processing Illumina microarray.” Bioinformatics 24, no. 13 (July 1, 2008): 1547–48. https://doi.org/10.1093/bioinformatics/btn224.
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  - Lin, Simon M., Pan Du, Wolfgang Huber, and Warren A. Kibbe. “Model-based variance-stabilizing transformation for Illumina microarray data.” Nucleic Acids Res 36, no. 2 (February 2008): e11. https://doi.org/10.1093/nar/gkm1075.
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  - Gene Ontology Consortium, Monte. “The Gene Ontology project in 2008.” Nucleic Acids Res 36, no. Database issue (January 2008): D440–44. https://doi.org/10.1093/nar/gkm883.
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  - Lee, Chia-Ju, Dong Fu, Pan Du, Hongmei Jiang, Simon M. Lin, and Warren Kibbe. “A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.” Int J Comput Biol Drug Des 1, no. 4 (2008): 396–405. https://doi.org/10.1504/ijcbdd.2008.022209.
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  - Kibbe, Warren A. “OligoCalc: an online oligonucleotide properties calculator.” Nucleic Acids Res 35, no. Web Server issue (July 2007): W43–46. https://doi.org/10.1093/nar/gkm234.
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  - Du, Pan, Warren A. Kibbe, and Simon M. Lin. “nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays.” Biol Direct 2 (May 31, 2007): 16. https://doi.org/10.1186/1745-6150-2-16.
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  - Osborne, John D., Simon Lin, and Warren A. Kibbe. “Other riffs on cooperation are already showing how well a wiki could work.” Nature 446, no. 7138 (April 19, 2007): 856. https://doi.org/10.1038/446856a.
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  - Osborne, J. D., L. Zhu, S. M. Lin, and W. A. Kibbe. “Interpreting microarray results with gene ontology and MeSH.” Methods in Molecular Biology 377 (March 24, 2007): 223–41. https://doi.org/10.1385/1-59745-390-0:223.
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  - Arshinoff, Bradley I., Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, and Roy D. Welch. “Xanthusbase: adapting wikipedia principles to a model organism database.” Nucleic Acids Res 35, no. Database issue (January 2007): D422–26. https://doi.org/10.1093/nar/gkl881.
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  - Osborne, John D., Lihua Julie Zhu, Simon M. Lin, and Warren A. Kibbe. “Interpreting microarray results with gene ontology and MeSH.” Methods Mol Biol 377 (2007): 223–42. https://doi.org/10.1007/978-1-59745-390-5_14.
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  - Osborne, John D., Simon Lin, Lihua Zhu, and Warren A. Kibbe. “Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).” Methods Mol Biol 408 (2007): 153–69. https://doi.org/10.1007/978-1-59745-547-3_9.
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  - Du, Pan, Warren A. Kibbe, and Simon M. Lin. “Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.” Bioinformatics 22, no. 17 (September 1, 2006): 2059–65. https://doi.org/10.1093/bioinformatics/btl355.
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  - Lin, Simon M., Jyothi Devakumar, and Warren A. Kibbe. “Improved prediction of treatment response using microarrays and existing biological knowledge.” Pharmacogenomics 7, no. 3 (April 2006): 495–501. https://doi.org/10.2217/14622416.7.3.495.
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  - Chisholm, R. L., P. Gaudet, E. M. Just, K. E. Pilcher, P. Fey, S. N. Merchant, and W. A. Kibbe. “dictyBase, the model organism database for Dictyostelium discoideum.” Nucleic Acids Research 34, no. Database issue (January 1, 2006). https://doi.org/10.1093/nar/gkj090.
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  - Chisholm, Rex L., Pascale Gaudet, Eric M. Just, Karen E. Pilcher, Petra Fey, Sohel N. Merchant, and Warren A. Kibbe. “dictyBase, the model organism database for Dictyostelium discoideum.” Nucleic Acids Res 34, no. Database issue (January 1, 2006): D423–27. https://doi.org/10.1093/nar/gkj090.
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  - Ge, Xijin, Yong-Chul Jung, Qingfa Wu, Warren A. Kibbe, and San Ming Wang. “Annotating nonspecific SAGE tags with microarray data.” Genomics 87, no. 1 (January 2006): 173–80. https://doi.org/10.1016/j.ygeno.2005.08.014.
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  - Gene Ontology Consortium, Masafumi. “The Gene Ontology (GO) project in 2006.” Nucleic Acids Res 34, no. Database issue (January 1, 2006): D322–26. https://doi.org/10.1093/nar/gkj021.
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  - Lin, Simon M., Lihua Zhu, Andrew Q. Winter, Maciek Sasinowski, and Warren A. Kibbe. “What is mzXML good for?” Expert Rev Proteomics 2, no. 6 (December 2005): 839–45. https://doi.org/10.1586/14789450.2.6.839.
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  - Lin, Simon M., and Warren Alden Kibbe. “Irrational exuberance in clinical proteomics.” Clin Cancer Res 11, no. 22 (November 15, 2005): 7963–64. https://doi.org/10.1158/1078-0432.CCR-05-1744.
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  - Kaput, Jim, Jose M. Ordovas, Lynnette Ferguson, Ben van Ommen, Raymond L. Rodriguez, Lindsay Allen, Bruce N. Ames, et al. “The case for strategic international alliances to harness nutritional genomics for public and personal health.” Br J Nutr 94, no. 5 (November 2005): 623–32. https://doi.org/10.1079/bjn20051585.
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  - Goldowitz, Dan, Wayne N. Frankel, Joseph S. Takahashi, Martha Holtz-Vitaterna, Carol Bult, Warren A. Kibbe, Jay Snoddy, et al. “Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function.” Brain Res Mol Brain Res 132, no. 2 (December 20, 2004): 105–15. https://doi.org/10.1016/j.molbrainres.2004.09.016.
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  - Kaput, Jim, Karin G. Klein, Eric J. Reyes, Warren A. Kibbe, Craig A. Cooney, Borko Jovanovic, Willard J. Visek, and George L. Wolff. “Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet x genotype interactions.” Physiol Genomics 18, no. 3 (August 11, 2004): 316–24. https://doi.org/10.1152/physiolgenomics.00065.2003.
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  - Bult, Carol, Warren A. Kibbe, Jay Snoddy, Martha Vitaterna, Doug Swanson, Stephanie Pretel, Yanxia Li, et al. “A genome end-game: understanding gene function in the nervous system.” Nat Neurosci 7, no. 5 (May 2004): 484–85. https://doi.org/10.1038/nn0504-484.
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  - Harris, M. A., J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, et al. “The Gene Oncology (GO) database and informatics resource.” Nucleic Acids Research 32, no. DATABASE ISS. (January 1, 2004).
  - Kreppel, L., P. Fey, P. Gaudet, E. Just, W. A. Kibbe, R. L. Chisholm, and A. R. Kimmel. “dictyBase: A new Dictyostelium discoideum genome database.” Nucleic Acids Research 32, no. DATABASE ISS. (January 1, 2004).
  - Harris, M. A., J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, et al. “The Gene Ontology (GO) database and informatics resource.” Nucleic Acids Res 32, no. Database issue (January 1, 2004): D258–61. https://doi.org/10.1093/nar/gkh036.
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  - Kreppel, Lisa, Petra Fey, Pascale Gaudet, Eric Just, Warren A. Kibbe, Rex L. Chisholm, and Alan R. Kimmel. “dictyBase: a new Dictyostelium discoideum genome database.” Nucleic Acids Res 32, no. Database issue (January 1, 2004): D332–33. https://doi.org/10.1093/nar/gkh138.
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  - Jovanovic, Borko D., Raymond C. Bergan, and Warren A. Kibbe. “Some aspects of analysis of gene array data.” Cancer Treat Res 113 (2002): 71–89. https://doi.org/10.1007/978-1-4757-3571-0_5.
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  - Zhang-Keck, Z. Y., W. A. Kibbe, W. S. Moye-Rowley, and C. S. Parker. “The SV40 core sequence functions as a repressor element in yeast.” J Biol Chem 266, no. 32 (November 15, 1991): 21362–67.
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  - Wiederrecht, G., D. J. Shuey, W. A. Kibbe, and C. S. Parker. “The Saccharomyces and Drosophila heat shock transcription factors are identical in size and DNA binding properties.” Cell 48, no. 3 (February 13, 1987): 507–15. https://doi.org/10.1016/0092-8674(87)90201-7.
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- Book Sections
  - Kibbe, W. A., L. Hengst, and D. Gallwitz. “The YPT protein family in yeast.” In The Ras Superfamily of GTPases, 367–85, 2017. https://doi.org/10.1201/9780203709931.
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  - Kibbe, W. A. “The Informatics and Bioinformatics Infrastructure of a Nutrigenomics Biobank.” In Nutritional Genomics: Discovering the Path to Personalized Nutrition, 353–74, 2006. https://doi.org/10.1002/0471781797.ch16.
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- Conference Papers
  - Noyd, D., A. Berkman, C. Howell, S. Power, A. Landstrom, S. Kreissman, K. Oeffinger, and W. Kibbe. “Clinical Informatics Tools to Extract Cumulative Anthracycline Exposure from the EHR, Measure Cardiovascular Outcomes, and Assess Adherence to Guideline Recommendations for Children with Cancer.” In Pediatric Blood & Cancer, 68:S429–30, 2021.
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  - Du, P., S. M. Lin, W. A. Kibbe, and H. Wang. “Application of wavelet transform to the MS-based proteomics data preprocessing.” In Proceedings of the 7th Ieee International Conference on Bioinformatics and Bioengineering, Bibe, 680–86, 2007. https://doi.org/10.1109/BIBE.2007.4375634.
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  - Kibbe, W. A., W. W. Wolf, M. E. Smith, J. S. Allen, and R. L. Chisholm. “The NUgene Project: Biospecimen informatics system design.” In Cell Preservation Technology, 4:230–31. MARY ANN LIEBERT INC, 2006.
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  - Wolf, W. W., M. E. Smith, W. A. Kibbe, J. S. Allen, and R. L. Chisholm. “The NUgene Project: eMR-facilitated biobanking.” In Cell Preservation Technology, 4:232–232. MARY ANN LIEBERT INC, 2006.
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  - Pinto, L. H., M. Vitaterna, S. Siepka, K. Shimomura, W. Kibbe, R. Mullins, E. Heffron, E. Stone, V. Sheffield, and J. S. Takahashi. “Mapping and characterization of Noerg-1 mutation in mouse.” In Investigative Ophthalmology & Visual Science, 45:U513–U513. ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2004.
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  - Wolf, W. A., M. J. Doyle, S. A. Aufox, T. M. Frezzo, M. E. Smith, W. A. Kibbe, and R. L. Chisholm. “DNA banking study in an ethnically diverse urban university hospital.” In American Journal of Human Genetics, 73:423–423. UNIV CHICAGO PRESS, 2003.
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  - Pinto, L. H., N. Grabowski, W. A. Kibbe, A. Lotery, S. Lumayag, R. Mullens, E. Stone, et al. “Chemically induced mutations in the mouse that affect the fundus and electroretinogram.” In Neural Basis of Early Vision, edited by A. Kaneko, 11:188–89. SPRINGER-VERLAG TOKYO, 2003.
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  - Gwaltney, K., C. Chute, D. Hageman, W. Kibbe, K. McCormick, D. Reeves, and L. Wright. “An assessment of cancer clinical trials vocabulary and IT infrastructure in the U.S.” In Proc Amia Symp, 224–28, 2001.
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