Chi Wei Cliburn Chan
Professor of Biostatistics & Bioinformatics
Computational immunology (stochastic and spatial models and simulations, T cell signaling, immune regulation)
Statistical methodology for immunological laboratory techniques (flow cytometry, CFSE analysis, receptor-ligand binding and signaling kinetics)
Informatics of the immune system (reference and application ontologies, meta-programming, text mining and machine learning)
Statistical methodology for immunological laboratory techniques (flow cytometry, CFSE analysis, receptor-ligand binding and signaling kinetics)
Informatics of the immune system (reference and application ontologies, meta-programming, text mining and machine learning)
Current Appointments & Affiliations
- Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2022
- Research Professor of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2022
Contact Information
- 2424 Erwin Road Ste 1102, 11078 Hock Plaza Duke Box 2721, Durham, NC 27705
- Duke Box 2721, Durham, NC 27710
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cliburn.chan@duke.edu
(919) 668-2459
- Background
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Education, Training, & Certifications
- Ph.D., University College London (United Kingdom) 2002
- M.S., University College London (United Kingdom) 1998
- B.S., University of London (United Kingdom) 1997
- M.B.B.S., National University of Singapore (Singapore) 1991
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Previous Appointments & Affiliations
- Associate Research Professor of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2016 - 2022
- Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2021 - 2022
- Associate Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2014 - 2020
- Associate Professor in the Department of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2014 - 2016
- Assistant Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2007 - 2014
- Assistant Research Professor in the Department of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2013 - 2014
- Assistant Research Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2006 - 2007
- Research
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Selected Grants
- Clinical and Mechanistic Factors Impacting Transplant Outcomes (U01) awarded by National Institutes of Health 2022 - 2027
- R01_Monocyte-derived alveolar macrophage drives inflammatory response to lung ozone exposure awarded by National Institutes of Health 2022 - 2027
- Early life B cell responses and inflammation following SARS-CoV-2 infection awarded by National Institutes of Health 2021 - 2026
- Defining the Mechanisms of Epstein-Barr Virus Persistence and Recurrence awarded by National Institutes of Health 2016 - 2026
- Training Program in Bioinformatics at the Intersection of Cancer Immunology and Microbiome awarded by National Institutes of Health 2020 - 2025
- Defining the Landscape of HLA Risk Alleles in Primary Nephrotic Syndrome and Post Kidney Transplant Recurrence awarded by National Institutes of Health 2020 - 2025
- Pathogenesis of Neuroinflammation and Neurocognitive Impairment In HIV-infected Young Adult Cannabis Users awarded by National Institutes of Health 2019 - 2025
- EQAPOL - Years 2017 to 2024 - BASE awarded by National Institutes of Health 2017 - 2024
- Role of cannabis on HIV-related cognitive impairment: a brain connectomics study awarded by National Institutes of Health 2018 - 2024
- Resolving the Origins of Restricted Fates in Epstein-Barr Virus-Infected B Lymphocyte Proliferation awarded by American Cancer Society, Inc. 2022 - 2024
- Immune Correlates of Protection Against Congenital Cytomegalovirus Transmission in an HIV-Infected Mother-Infant Cohort awarded by National Institutes of Health 2020 - 2023
- Adjuvant Comparison for Peanut Allergy Immunotherapy awarded by National Institutes of Health 2022 - 2023
- Early life B cell responses and inflammation following SARS-CoV-2 infection awarded by Weill Cornell Medicine 2022 - 2023
- Quantitative Methods for HIV/AIDS Research awarded by National Institutes of Health 2018 - 2023
- Consequences of marijuana use on inflammatory pathways in HIV-infected youth awarded by National Institutes of Health 2017 - 2023
- Immunologic and Virologic Determinants of Congenital Cytomegalovirus Transmission and Disease in Rhesus Monkeys awarded by Weill Cornell Medicine 2020 - 2023
- Biomarkers predicting response to eculizumab in myasthenia gravis (fed) awarded by The George Washington University 2021 - 2023
- Immune Responses to Malaria, HIV and SARS-CoV-2 Infection and Immunization awarded by Seattle Children's Research Institute 2022 - 2023
- Neuro-inflammation in Postoperative Cognitive Dysfunction: CSF and fMRI Studies awarded by National Institutes of Health 2017 - 2023
- Impact of maternal HIV infection on immune priming of their uninfected infants awarded by National Institutes of Health 2020 - 2023
- VTEU Task D Option 2 Protocol FY.2015.A4D14.0033 awarded by National Institutes of Health 2015 - 2022
- R01: CXCL10/CXCR3 regulation of ozone-induced epithelial permeability awarded by National Institutes of Health 2017 - 2022
- GH-VAP: Duke Antibody Dynamics Core Extension; INV-008612 Supplement awarded by Bill and Melinda Gates Foundation 2019 - 2022
- Antigenome Signatures as Biomarkers for Subtyping Disease Heterogeneity in Lupus Patients awarded by Department of Defense 2019 - 2022
- Impact of immune-based intervention on viral rebound in orally SHIV infected infant monkeys : Statistical Core awarded by Weill Cornell Medicine 2020 - 2022
- Biomarkers predicting response to eculizumab in MG (NonFed) awarded by The George Washington University 2021 - 2022
- Biomarkers predicting response to eculizumab in myasthenia gravis awarded by The George Washington University 2021 - 2022
- A Systems Biology Approach to HIV-associated Neurocognitive Impairment: Role of Drug Abuse and Neuroinflammation awarded by National Institutes of Health 2016 - 2021
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Innate antiviral factors in breast milk and the oral HIV-1 reservoir awarded by National Institutes of Health 2015 - 2021
- Adjuvant Discovery Program (Option #3) awarded by National Institutes of Health 2014 - 2020
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- Immunological biomarker studies in myasthenia gravis awarded by National Institutes of Health 2014 - 2020
- Molecular Atlas of Lung Development - Data Coordinating Center awarded by National Institutes of Health 2014 - 2020
- Role of CD4 T cell subsets as drivers of MG disease awarded by Myasthenia Gravis Foundation 2016 - 2019
- Adjuvant Discovery Program (Option #2) awarded by National Institutes of Health 2014 - 2019
- Reversible Immunomodulation as a Strategy for Ischemia Tolerance in Hibernation awarded by Foundation for Anesthesia Education and Research 2017 - 2019
- Development of a Therapeutic for Brain Tumor Immunotherapy awarded by National Institutes of Health 2018 - 2019
- The impact of Epstein Barr virus infection on the immune response in pediatric transplant recipients awarded by Stanford University 2018 - 2019
- mHealth Peer Support to Reduce Rates of STIs in Black MSM PrEP Users awarded by National Institutes of Health 2018
- Duke CTSA (UL1) awarded by National Institutes of Health 2013 - 2018
- Adjuvant Discovery Program (Option #1) awarded by National Institutes of Health 2014 - 2017
- EQAPOL - 2016 to 2017 - Option 6 - FLOW awarded by National Institutes of Health 2010 - 2017
- EQAPOL Option 5 awarded by National Institutes of Health 2010 - 2017
- Innate immune adaptations of hibernation as a new approach to protection against acute organ injury awarded by Society of Cardiovascular Anesthesiologists 2015 - 2017
- Adjuvant Discovery Program awarded by National Institutes of Health 2014 - 2017
- Longitudinal assessment of CMV and BK virus immunity in renal transplant patients awarded by National Institutes of Health 2013 - 2016
- Multiscale Systems Immunology awarded by National Institutes of Health 2010 - 2015
- Novel Cellular Immune Profiles to Predict Lung Disease Outcomes awarded by National Institutes of Health 2011 - 2013
- Immune profiling of multi-parameter flow cytometry using computational statistics awarded by National Institutes of Health 2009 - 2012
- Multiscale Integrative Immunology for Adjuvant Development awarded by National Institutes of Health 2005 - 2010
- Microsimulation of anthracis-immune system interaction awarded by National Institutes of Health 2004 - 2007
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External Relationships
- Singapore General Hospital
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Fang, Jiyuan, Cliburn Chan, Kouros Owzar, Liuyang Wang, Diyuan Qin, Qi-Jing Li, and Jichun Xie. “Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering.” Genome Biol 23, no. 1 (December 27, 2022): 269. https://doi.org/10.1186/s13059-022-02825-5.Full Text Link to Item
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Sass, Julian, Achal Awasthi, Veronica Obregon-Perko, Janice McCarthy, Alun L. Lloyd, Ann Chahroudi, Sallie Permar, and Cliburn Chan. “A simple model for viral decay dynamics and the distribution of infected cell life spans in SHIV-infected infant rhesus macaques.” Math Biosci 356 (December 22, 2022): 108958. https://doi.org/10.1016/j.mbs.2022.108958.Full Text Link to Item
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Murdoch, David M., Richard Barfield, Cliburn Chan, Sheri L. Towe, Ryan P. Bell, Alicia Volkheimer, Joyce Choe, et al. “Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV.” J Neurovirol, November 8, 2022. https://doi.org/10.1007/s13365-022-01102-2.Full Text Link to Item
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Harnois, Melissa J., Maria Dennis, Dagmar Stöhr, Sarah M. Valencia, Nicole Rodgers, Eleanor C. Semmes, Helen S. Webster, et al. “Characterization of Plasma Immunoglobulin G Responses in Elite Neutralizers of Human Cytomegalovirus.” J Infect Dis 226, no. 9 (November 1, 2022): 1667–77. https://doi.org/10.1093/infdis/jiac341.Full Text Link to Item
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Chen, Jui-Lin, Chelsea N. Fries, Stella J. Berendam, Nicole S. Rodgers, Emily F. Roe, Yaoying Wu, Shuk Hang Li, et al. “Self-assembling peptide nanofiber HIV vaccine elicits robust vaccine-induced antibody functions and modulates Fc glycosylation.” Sci Adv 8, no. 38 (September 23, 2022): eabq0273. https://doi.org/10.1126/sciadv.abq0273.Full Text Link to Item
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SoRelle, Elliott D., Joanne Dai, Nicolás M. Reinoso-Vizcaino, Ashley P. Barry, Cliburn Chan, and Micah A. Luftig. “Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection.” Cell Rep 40, no. 9 (August 30, 2022): 111286. https://doi.org/10.1016/j.celrep.2022.111286.Full Text Link to Item
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SoRelle, Elliott D., Joanne Dai, Emmanuela N. Bonglack, Emma M. Heckenberg, Jeffrey Y. Zhou, Stephanie N. Giamberardino, Jeffrey A. Bailey, Simon G. Gregory, Cliburn Chan, and Micah A. Luftig. “Correction: Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines.” Elife 10 (November 11, 2021). https://doi.org/10.7554/eLife.75422.Full Text Link to Item
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Telzrow, Calla L., Paul J. Zwack, Shannon Esher Righi, Fred S. Dietrich, Cliburn Chan, Kouros Owzar, J Andrew Alspaugh, and Joshua A. Granek. “Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries.” G3 (Bethesda) 11, no. 11 (October 19, 2021). https://doi.org/10.1093/g3journal/jkab301.Full Text Link to Item
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Shaw, Brian I., Alejandro Ochoa, Cliburn Chan, Chloe Nobuhara, Rasheed Gbadegesin, Annette M. Jackson, and Eileen T. Chambers. “HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation.” Transplant Direct 7, no. 10 (October 2021): e748. https://doi.org/10.1097/TXD.0000000000001201.Full Text Open Access Copy Link to Item
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Webster, Helen, Sarah Valencia, Amit Kumar, Cliburn Chan, Maria Dennis, Hunter Roark, Angela Woods, Shinu John, Andrea Carfi, and Sallie R. Permar. “Pre-existing immunity to cytomegalovirus in macaques influences human CMV vaccine responses in preclinical models.” Vaccine 39, no. 38 (September 2021): 5358–67. https://doi.org/10.1016/j.vaccine.2021.08.011.Full Text
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Fries, Chelsea N., Jui-Lin Chen, Maria L. Dennis, Nicole L. Votaw, Joshua Eudailey, Brian E. Watts, Kelly M. Hainline, et al. “HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth.” Sci Rep 11, no. 1 (July 14, 2021): 14494. https://doi.org/10.1038/s41598-021-93702-x.Full Text Link to Item
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Klus, Jonathan, Vo Trieu Ly, Cliburn Chan, and Thuy Le. “Prognosis and treatment effects of HIV-associated talaromycosis in a real-world patient cohort.” Med Mycol 59, no. 4 (April 6, 2021): 392–99. https://doi.org/10.1093/mmy/myab005.Full Text Open Access Copy Link to Item
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Guptill, Jeffrey T., Richard Barfield, Cliburn Chan, Melissa A. Russo, Doug Emmett, Shruti Raja, Janice M. Massey, et al. “Reduced plasmablast frequency is associated with seronegative myasthenia gravis.” Muscle Nerve 63, no. 4 (April 2021): 577–85. https://doi.org/10.1002/mus.27140.Full Text Link to Item
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Masci, Anna Maria, Scott White, Ben Neely, Maryanne Ardini-Polaske, Carol B. Hill, Ravi S. Misra, Bruce Aronow, et al. “Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images.” Bmc Bioinformatics 22, no. 1 (February 23, 2021): 82. https://doi.org/10.1186/s12859-021-04008-8.Full Text Link to Item
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Terrando, Niccolò, John J. Park, Michael Devinney, Cliburn Chan, Mary Cooter, Pallavi Avasarala, Joseph P. Mathew, et al. “Immunomodulatory lipid mediator profiling of cerebrospinal fluid following surgery in older adults.” Sci Rep 11, no. 1 (February 4, 2021): 3047. https://doi.org/10.1038/s41598-021-82606-5.Full Text Open Access Copy Link to Item
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Shaw, Brian I., Hui-Jie Lee, Cliburn Chan, Robert Ettenger, Paul Grimm, Meghan Pearl, Elaine F. Reed, et al. “Relationship between antithymocyte globulin, T cell phenotypes, and clinical outcomes in pediatric kidney transplantation.” Am J Transplant 21, no. 2 (February 2021): 766–75. https://doi.org/10.1111/ajt.16263.Full Text Link to Item
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Xu, Yunan, Yizi Lin, Ryan P. Bell, Sheri L. Towe, John M. Pearson, Tauseef Nadeem, Cliburn Chan, and Christina S. Meade. “Machine learning prediction of neurocognitive impairment among people with HIV using clinical and multimodal magnetic resonance imaging data.” J Neurovirol 27, no. 1 (February 2021): 1–11. https://doi.org/10.1007/s13365-020-00930-4.Full Text Link to Item
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SoRelle, Elliott D., Joanne Dai, Emmanuela N. Bonglack, Emma M. Heckenberg, Jeffrey Y. Zhou, Stephanie N. Giamberardino, Jeffrey A. Bailey, Simon G. Gregory, Cliburn Chan, and Micah A. Luftig. “Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines.” Elife 10 (January 27, 2021). https://doi.org/10.7554/eLife.62586.Full Text Link to Item
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Johnson-Weaver, Brandi T., Hae Woong Choi, Hang Yang, Josh A. Granek, Cliburn Chan, Soman N. Abraham, and Herman F. Staats. “Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens.” Front Immunol 12 (2021): 730346. https://doi.org/10.3389/fimmu.2021.730346.Full Text Link to Item
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White, Scott, John Quinn, Jennifer Enzor, Janet Staats, Sarah M. Mosier, James Almarode, Thomas N. Denny, Kent J. Weinhold, Guido Ferrari, and Cliburn Chan. “FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.” Front Immunol 12 (2021): 768541. https://doi.org/10.3389/fimmu.2021.768541.Full Text Open Access Copy Link to Item
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Obregon-Perko, Veronica, Katherine M. Bricker, Gloria Mensah, Ferzan Uddin, Mithra R. Kumar, Emily J. Fray, Robert F. Siliciano, et al. “Simian-Human Immunodeficiency Virus SHIV.C.CH505 Persistence in ART-Suppressed Infant Macaques Is Characterized by Elevated SHIV RNA in the Gut and a High Abundance of Intact SHIV DNA in Naive CD4+ T Cells.” J Virol 95, no. 2 (December 22, 2020). https://doi.org/10.1128/JVI.01669-20.Full Text Link to Item
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Jenks, Jennifer A., Cody S. Nelson, Hunter K. Roark, Matthew L. Goodwin, Robert F. Pass, David I. Bernstein, Emmanuel B. Walter, et al. “Antibody binding to native cytomegalovirus glycoprotein B predicts efficacy of the gB/MF59 vaccine in humans.” Sci Transl Med 12, no. 568 (November 4, 2020). https://doi.org/10.1126/scitranslmed.abb3611.Full Text Link to Item
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Zhang, Tian, Michael R. Harrison, Peter H. O’Donnell, Ajjai S. Alva, Noah M. Hahn, Leonard J. Appleman, Jeremy Cetnar, et al. “A randomized phase 2 trial of pembrolizumab versus pembrolizumab and acalabrutinib in patients with platinum-resistant metastatic urothelial cancer.” Cancer 126, no. 20 (October 15, 2020): 4485–97. https://doi.org/10.1002/cncr.33067.Full Text Open Access Copy Link to Item
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Sung, Anthony D., Shekeab Jauhari, Sharareh Siamakpour-Reihani, Arati V. Rao, Janet Staats, Cliburn Chan, Everett Meyer, et al. “Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects.” Am J Hematol 95, no. 6 (June 2020): 662–71. https://doi.org/10.1002/ajh.25781.Full Text Link to Item
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Berger, Miles, David M. Murdoch, Janet S. Staats, Cliburn Chan, Jake P. Thomas, Grant E. Garrigues, Jeffrey N. Browndyke, et al. “Flow Cytometry Characterization of Cerebrospinal Fluid Monocytes in Patients With Postoperative Cognitive Dysfunction: A Pilot Study.” Anesth Analg 129, no. 5 (November 2019): e150–54. https://doi.org/10.1213/ANE.0000000000004179.Full Text Open Access Copy Link to Item
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Goswami, Ria, Ashley N. Nelson, Joshua J. Tu, Maria Dennis, Liqi Feng, Amit Kumar, Jesse Mangold, et al. “Analytical Treatment Interruption after Short-Term Antiretroviral Therapy in a Postnatally Simian-Human Immunodeficiency Virus-Infected Infant Rhesus Macaque Model.” Mbio 10, no. 5 (September 5, 2019). https://doi.org/10.1128/mBio.01971-19.Full Text Link to Item
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Kim-Chang, Julie J., Lorena Wilson, Cliburn Chan, Bernard Fischer, Guglielmo Venturi, Maureen M. Goodenow, Grace Aldrovandi, Thomas J. Weber, John W. Sleasman, and John W. Adolescent Medicine Trials Network for HIV/AIDS Interventions. “Tenofovir Has Minimal Effect on Biomarkers of Bone Health in Youth with HIV Receiving Initial Antiretroviral Therapy.” Aids Res Hum Retroviruses 35, no. 8 (August 2019): 746–54. https://doi.org/10.1089/AID.2018.0270.Full Text Link to Item
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Choi, Hae Woong, Cliburn Chan, Ivo D. Shterev, Heather E. Lynch, Taylor J. Robinette, Brandi T. Johnson-Weaver, Jianling Shi, et al. “Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening.” Slas Discov 24, no. 6 (July 2019): 628–40. https://doi.org/10.1177/2472555219834699.Full Text Link to Item
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Lin, Jiaxing, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan, and Kouros Owzar. “fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies.” Bmc Bioinformatics 20, no. 1 (June 13, 2019): 333. https://doi.org/10.1186/s12859-019-2869-3.Full Text Link to Item
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Berger, Miles, Deborah Oyeyemi, Mobolaji O. Olurinde, Heather E. Whitson, Kent J. Weinhold, Marty G. Woldorff, Lewis A. Lipsitz, et al. “The INTUIT Study: Investigating Neuroinflammation Underlying Postoperative Cognitive Dysfunction.” J Am Geriatr Soc 67, no. 4 (April 2019): 794–98. https://doi.org/10.1111/jgs.15770.Full Text Open Access Copy Link to Item
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Yi, John S., Marilyn Rosa-Bray, Janet Staats, Pearl Zakroysky, Cliburn Chan, Melissa A. Russo, Chelsae Dumbauld, et al. “Establishment of normative ranges of the healthy human immune system with comprehensive polychromatic flow cytometry profiling.” Plos One 14, no. 12 (2019): e0225512. https://doi.org/10.1371/journal.pone.0225512.Full Text Open Access Copy Link to Item
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Lin, Jiaxing, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S. Damrauer, Scott Floyd, et al. “bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.” Bioinformatics 34, no. 20 (October 15, 2018): 3581–83. https://doi.org/10.1093/bioinformatics/bty402.Full Text Link to Item
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Shterev, Ivo D., David B. Dunson, Cliburn Chan, and Gregory D. Sempowski. “Bayesian Multi-Plate High-Throughput Screening of Compounds.” Sci Rep 8, no. 1 (June 22, 2018): 9551. https://doi.org/10.1038/s41598-018-27531-w.Full Text Link to Item
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Johnson-Weaver, Brandi T., Susan McRitchie, Kelly A. Mercier, Wimal Pathmasiri, Susan J. Sumner, Cliburn Chan, Dori Germolec, Michael Kulis, A Wesley Burks, and Herman F. Staats. “Effect of endotoxin and alum adjuvant vaccine on peanut allergy.” J Allergy Clin Immunol 141, no. 2 (February 2018): 791-794.e8. https://doi.org/10.1016/j.jaci.2017.07.043.Full Text Link to Item
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Sibley, Alexander, Zhiguo Li, Yu Jiang, Yi-Ju Li, Cliburn Chan, Andrew Allen, and Kouros Owzar. “Facilitating the Calculation of the Efficient Score Using Symbolic Computing.” Am Stat 72, no. 2 (2018): 199–205. https://doi.org/10.1080/00031305.2017.1392361.Full Text Link to Item
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Ardini-Poleske, Maryanne E., Robert F. Clark, Charles Ansong, James P. Carson, Richard A. Corley, Gail H. Deutsch, James S. Hagood, et al. “LungMAP: The Molecular Atlas of Lung Development Program.” Am J Physiol Lung Cell Mol Physiol 313, no. 5 (November 1, 2017): L733–40. https://doi.org/10.1152/ajplung.00139.2017.Full Text Link to Item
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Norton, John N., Randall P. Reynolds, Cliburn Chan, Raphael H. Valdivia, and Herman F. Staats. “Assessing the satisfaction and burden within an academic animal care and use program.” Faseb J 31, no. 9 (September 2017): 3913–21. https://doi.org/10.1096/fj.201700072RR.Full Text Link to Item
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Pedersen, Natasja Wulff, P Anoop Chandran, Yu Qian, Jonathan Rebhahn, Nadia Viborg Petersen, Mathilde Dalsgaard Hoff, Scott White, et al. “Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.” Front Immunol 8 (2017): 858. https://doi.org/10.3389/fimmu.2017.00858.Full Text Link to Item
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Himes, Jonathon E., Carrie Ho, Quang N. Nguyen, Joshua D. Amos, Haolin Xu, Cliburn Chan, Shein-Chung Chow, et al. “Characterization of Simian Immunodeficiency Virus Variants Anatomically Compartmentalized in Plasma and Milk in Chronically Infected African Green Monkeys.” J Virol 90, no. 19 (October 1, 2016): 8795–8808. https://doi.org/10.1128/JVI.00701-16.Full Text Link to Item
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Zidar, David A., Joseph C. Mudd, Steven Juchnowski, Joao P. Lopes, Sara Sparks, Samantha S. Park, Masakazu Ishikawa, et al. “Altered Maturation Status and Possible Immune Exhaustion of CD8 T Lymphocytes in the Peripheral Blood of Patients Presenting With Acute Coronary Syndromes.” Arterioscler Thromb Vasc Biol 36, no. 2 (February 2016): 389–97. https://doi.org/10.1161/ATVBAHA.115.306112.Full Text Link to Item
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Lin, Lin, Cliburn Chan, and Mike West. “Discriminative variable subsets in Bayesian classification with mixture models, with application in flow cytometry studies.” Biostatistics 17, no. 1 (January 2016): 40–53. https://doi.org/10.1093/biostatistics/kxv021.Full Text Link to Item
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Snyder, Laurie D., Cliburn Chan, Darongsae Kwon, John S. Yi, Jessica A. Martissa, C Ashley Finlen Copeland, Robyn J. Osborne, Sara D. Sparks, Scott M. Palmer, and Kent J. Weinhold. “Polyfunctional T-Cell Signatures to Predict Protection from Cytomegalovirus after Lung Transplantation.” Am J Respir Crit Care Med 193, no. 1 (January 1, 2016): 78–85. https://doi.org/10.1164/rccm.201504-0733OC.Full Text Link to Item
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Lai, Weihong, Li Huang, Lei Zhu, Guido Ferrari, Cliburn Chan, Wei Li, Kuo-Hsiung Lee, and Chin-Ho Chen. “Gnidimacrin, a Potent Anti-HIV Diterpene, Can Eliminate Latent HIV-1 Ex Vivo by Activation of Protein Kinase C β.” J Med Chem 58, no. 21 (November 12, 2015): 8638–46. https://doi.org/10.1021/acs.jmedchem.5b01233.Full Text Link to Item
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Gouttefangeas, Cécile, Cliburn Chan, Sebastian Attig, Tania T. Køllgaard, Hans-Georg Rammensee, Stefan Stevanović, Dorothee Wernet, et al. “Data analysis as a source of variability of the HLA-peptide multimer assay: from manual gating to automated recognition of cell clusters.” Cancer Immunol Immunother 64, no. 5 (May 2015): 585–98. https://doi.org/10.1007/s00262-014-1649-1.Full Text Link to Item
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Gouttefangeas, C., S. Walter, M. J. P. Welters, C. Ottensmeier, S. H. Van Der Burg, C. M. Britten, and C. Chan. “Flow cytometry in cancer immunotherapy: Applications, quality assurance, and future,” January 1, 2015, 471–90. https://doi.org/10.1007/978-3-662-44006-3_25.Full Text
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Richards, Adam J., Janet Staats, Jennifer Enzor, Katherine McKinnon, Jacob Frelinger, Thomas N. Denny, Kent J. Weinhold, and Cliburn Chan. “Setting objective thresholds for rare event detection in flow cytometry.” J Immunol Methods 409 (July 2014): 54–61. https://doi.org/10.1016/j.jim.2014.04.002.Full Text Open Access Copy Link to Item
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Staats, Janet S., Jennifer H. Enzor, Ana M. Sanchez, Wes Rountree, Cliburn Chan, Maria Jaimes, Ray Chun-Fai Chan, Amitabh Gaur, Thomas N. Denny, and Kent J. Weinhold. “Toward development of a comprehensive external quality assurance program for polyfunctional intracellular cytokine staining assays.” J Immunol Methods 409 (July 2014): 44–53. https://doi.org/10.1016/j.jim.2014.05.021.Full Text Open Access Copy Link to Item
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Nair, Smita K., Georgia D. Tomaras, Ana Paula Sales, David Boczkowski, Cliburn Chan, Kelly Plonk, Yongting Cai, et al. “High-throughput identification and dendritic cell-based functional validation of MHC class I-restricted Mycobacterium tuberculosis epitopes.” Sci Rep 4 (April 23, 2014): 4632. https://doi.org/10.1038/srep04632.Full Text Link to Item
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White, Scott, Karoline Laske, Marij Jp Welters, Nicole Bidmon, Sjoerd H. van der Burg, Cedrik M. Britten, Jennifer Enzor, et al. “Managing Multi-center Flow Cytometry Data for Immune Monitoring.” Cancer Inform 13, no. Suppl 7 (2014): 111–22. https://doi.org/10.4137/CIN.S16346.Full Text Link to Item
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Lin, Lin, Cliburn Chan, Sine R. Hadrup, Thomas M. Froesig, Quanli Wang, and Mike West. “Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies.” Stat Appl Genet Mol Biol 12, no. 3 (June 2013): 309–31. https://doi.org/10.1515/sagmb-2012-0001.Full Text Link to Item
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Shetty, Gina, Georgia M. Beasley, Sara Sparks, Michael Barfield, Melanie Masoud, Paul J. Mosca, Scott K. Pruitt, et al. “Plasma cytokine analysis in patients with advanced extremity melanoma undergoing isolated limb infusion.” Ann Surg Oncol 20, no. 4 (April 2013): 1128–35. https://doi.org/10.1245/s10434-012-2785-5.Full Text Link to Item
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Aghaeepour, Nima, Greg Finak, Greg FlowCAP Consortium, Greg DREAM Consortium, Holger Hoos, Tim R. Mosmann, Ryan Brinkman, Raphael Gottardo, and Richard H. Scheuermann. “Critical assessment of automated flow cytometry data analysis techniques.” Nat Methods 10, no. 3 (March 2013): 228–38. https://doi.org/10.1038/nmeth.2365.Full Text Link to Item
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Chan, C., M. Billard, S. A. Ramirez, H. Schmidl, E. Monson, and T. B. Kepler. “A Model for Migratory B Cell Oscillations from Receptor Down-Regulation Induced by External Chemokine Fields.” Bulletin of Mathematical Biology 75, no. 1 (2013): 185–205. https://doi.org/10.1007/s11538-012-9799-9.Full Text
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Chan, Cliburn, Matthew Billard, Samuel A. Ramirez, Harald Schmidl, Eric Monson, and Thomas B. Kepler. “A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields.” Bull Math Biol 75, no. 1 (January 2013): 185–205. https://doi.org/10.1007/s11538-012-9799-9.Full Text Link to Item
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Cron, Andrew, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder K. Singh, Cedrik M. Britten, Marij J. P. Welters, Sjoerd H. van der Burg, Mike West, and Cliburn Chan. “Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples.” Plos Comput Biol 9, no. 7 (2013): e1003130. https://doi.org/10.1371/journal.pcbi.1003130.Full Text Link to Item
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Snyder, L. D., R. Medinas, C. Chan, S. Sparks, W. A. Davis, S. M. Palmer, and K. J. Weinhold. “Polyfunctional cytomegalovirus-specific immunity in lung transplant recipients receiving valganciclovir prophylaxis.” Am J Transplant 11, no. 3 (March 2011): 553–60. https://doi.org/10.1111/j.1600-6143.2010.03405.x.Full Text Link to Item
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Chan, Cliburn, Lin Lin, Jacob Frelinger, Valérie Hérbert, Dominic Gagnon, Claire Landry, Rafick-Pierre Sékaly, et al. “Optimization of a highly standardized carboxyfluorescein succinimidyl ester flow cytometry panel and gating strategy design using discriminative information measure evaluation.” Cytometry A 77, no. 12 (December 2010): 1126–36. https://doi.org/10.1002/cyto.a.20987.Full Text Link to Item
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Manolopoulou, I., C. Chan, and M. West. “Rejoinder.” Bayesian Analysis 5, no. 3 (December 1, 2010): 461–64. https://doi.org/10.1214/10-BA517REJ.Full Text
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Frelinger, Jacob, Janet Ottinger, Cécile Gouttefangeas, and Cliburn Chan. “Modeling flow cytometry data for cancer vaccine immune monitoring.” Cancer Immunol Immunother 59, no. 9 (September 2010): 1435–41. https://doi.org/10.1007/s00262-010-0883-4.Full Text Link to Item
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Suchard, Marc A., Quanli Wang, Cliburn Chan, Jacob Frelinger, Andrew Cron, and Mike West. “Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.” J Comput Graph Stat 19, no. 2 (June 1, 2010): 419–38. https://doi.org/10.1198/jcgs.2010.10016.Full Text Open Access Copy Link to Item
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Manolopoulou, I., C. Chan, and M. West. “Selection sampling from large data sets for targeted inference in mixture modeling.” Bayesian Analysis 5, no. 3 (2010): 429–50. https://doi.org/10.1214/10-BA517.Full Text
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Chan, Cliburn, Feng Feng, Janet Ottinger, David Foster, Mike West, and Thomas B. Kepler. “Statistical mixture modeling for cell subtype identification in flow cytometry.” Cytometry A 73, no. 8 (August 2008): 693–701. https://doi.org/10.1002/cyto.a.20583.Full Text Link to Item
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Frelinger, Jacob, Thomas B. Kepler, and Cliburn Chan. “Flow: Statistics, visualization and informatics for flow cytometry.” Source Code Biol Med 3 (June 17, 2008): 10. https://doi.org/10.1186/1751-0473-3-10.Full Text Link to Item
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Mitha, Faheem, Timothy A. Lucas, Feng Feng, Thomas B. Kepler, and Cliburn Chan. “The Multiscale Systems Immunology project: software for cell-based immunological simulation.” Source Code Biol Med 3 (April 28, 2008): 6. https://doi.org/10.1186/1751-0473-3-6.Full Text Open Access Copy Link to Item
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Chan, C., A. J. T. George, and J. Stark. “Cytotoxic killing and immune evasion by repair.” Journal of Statistical Physics 128, no. 1–2 (July 1, 2007): 393–411. https://doi.org/10.1007/s10955-006-9242-4.Full Text
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Yates, Andrew, Cliburn Chan, Jessica Strid, Simon Moon, Robin Callard, Andrew J. T. George, and Jaroslav Stark. “Reconstruction of cell population dynamics using CFSE.” Bmc Bioinformatics 8 (June 12, 2007): 196. https://doi.org/10.1186/1471-2105-8-196.Full Text Link to Item
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Kepler, Thomas B., and Cliburn Chan. “Spatiotemporal programming of a simple inflammatory process.” Immunol Rev 216 (April 2007): 153–63. https://doi.org/10.1111/j.1600-065X.2007.00500.x.Full Text Link to Item
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Stark, Jaroslav, Cliburn Chan, and Andrew J. T. George. “Oscillations in the immune system.” Immunol Rev 216 (April 2007): 213–31. https://doi.org/10.1111/j.1600-065X.2007.00501.x.Full Text Link to Item
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Chan, Cliburn, and Thomas B. Kepler. “Computational immunology--from bench to virtual reality.” Ann Acad Med Singap 36, no. 2 (February 2007): 123–27.Link to Item
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Alam, AKM Shamsul, Oliver Florey, Michele Weber, Radhakrishna G. Pillai, Cliburn Chan, Peng H. Tan, Robert I. Lechler, Myra O. McClure, Dorian O. Haskard, and Andrew J. T. George. “Knockdown of mouse VCAM-1 by vector-based siRNA.” Transpl Immunol 16, no. 3–4 (November 2006): 185–93. https://doi.org/10.1016/j.trim.2006.08.004.Full Text Link to Item
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Chan, C., J. Stark, and A. J. T. George. “The impact of multiple T cell - APC encounters and the role of anergy.” Journal of Computational and Applied Mathematics 184, no. 1 (December 1, 2005): 101–20. https://doi.org/10.1016/j.cam.2004.07.036.Full Text
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George, Andrew J. T., Jaroslav Stark, and Cliburn Chan. “Understanding specificity and sensitivity of T-cell recognition.” Trends Immunol 26, no. 12 (December 2005): 653–59. https://doi.org/10.1016/j.it.2005.09.011.Full Text Link to Item
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Yates, A. J., C. C. T. Chan, and R. E. Callard. “16 Modelling T cell activation, proliferation, and homeostasis.” Studies in Multidisciplinarity 3, no. C (December 1, 2005): 281–308. https://doi.org/10.1016/S1571-0831(06)80020-1.Full Text
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Tan, P. H., C. L. H. Chan, C. Chan, and A. J. T. George. “The evolving role of gene-based treatment in surgery.” Br J Surg 92, no. 12 (December 2005): 1466–80. https://doi.org/10.1002/bjs.5181.Full Text Link to Item
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Tan, Peng H., John B. Yates, Shao-An Xue, Cliburn Chan, William J. Jordan, Jennifer E. Harper, Martin P. Watson, et al. “Creation of tolerogenic human dendritic cells via intracellular CTLA4: a novel strategy with potential in clinical immunosuppression.” Blood 106, no. 9 (November 1, 2005): 2936–43. https://doi.org/10.1182/blood-2005-05-1826.Full Text Link to Item
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Tan, Peng H., Pervinder Sagoo, Cliburn Chan, John B. Yates, Jamie Campbell, Sven C. Beutelspacher, Brian M. J. Foxwell, Giovanna Lombardi, and Andrew J. T. George. “Inhibition of NF-kappa B and oxidative pathways in human dendritic cells by antioxidative vitamins generates regulatory T cells.” J Immunol 174, no. 12 (June 15, 2005): 7633–44. https://doi.org/10.4049/jimmunol.174.12.7633.Full Text Link to Item
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Chan, Cliburn, Jaroslav Stark, and Andrew J. T. George. “Feedback control of T-cell receptor activation.” Proc Biol Sci 271, no. 1542 (May 7, 2004): 931–39. https://doi.org/10.1098/rspb.2003.2587.Full Text Link to Item
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Tan, P. H., C. Chan, S. A. Xue, R. Dong, B. Ananthesayanan, M. Manunta, C. Kerouedan, et al. “Phenotypic and functional differences between human saphenous vein (HSVEC) and umbilical vein (HUVEC) endothelial cells.” Atherosclerosis 173, no. 2 (April 2004): 171–83. https://doi.org/10.1016/j.atherosclerosis.2003.12.011.Full Text Link to Item
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Chan, C., R. I. Lechler, and A. J. T. George. “Tolerance mechanisms and recent progress.” Transplant Proc 36, no. 2 Suppl (March 2004): 561S-569S. https://doi.org/10.1016/j.transproceed.2004.01.019.Full Text Link to Item
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Chan, C., A. J. T. George, and J. Stark. “T cell sensitivity and specificity - Kinetic proofreading revisited.” Discrete and Continuous Dynamical Systems Series B 3, no. 3 (January 1, 2003): 343–60. https://doi.org/10.3934/dcdsb.2003.3.343.Full Text
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Yates, A., C. C. Chan, R. E. Callard, A. J. George, and J. Stark. “An approach to modelling in immunology.” Brief Bioinform 2, no. 3 (September 2001): 245–57. https://doi.org/10.1093/bib/2.3.245.Full Text Link to Item
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Chan, C., A. J. George, and J. Stark. “Cooperative enhancement of specificity in a lattice of T cell receptors.” Proc Natl Acad Sci U S A 98, no. 10 (May 8, 2001): 5758–63. https://doi.org/10.1073/pnas.101113698.Full Text Link to Item
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Chan, C. C., J. Stark, and A. J. George. “Analysis of cytokine dynamics in corneal allograft rejection.” Proc Biol Sci 266, no. 1434 (November 7, 1999): 2217–23. https://doi.org/10.1098/rspb.1999.0911.Full Text Link to Item
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Book Sections
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Gouttefangeas, C., S. Walter, M. J. P. Welters, C. Ottensmeier, S. H. Van der Burg, and C. Chan. “Flow cytometry in cancer immunotherapy: Applications, quality assurance, and future.” In Cancer Immunology: A Translational Medicine Context, Second Edition, 761–83, 2020. https://doi.org/10.1007/978-3-030-30845-2_33.Full Text
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Chan, C., M. G. Hudgens, and S. C. Chow. “Preface,” xi–xv, 2017. https://doi.org/10.1201/9781315120805.Full Text
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Lin, L., and C. Chan. “Quantitative methods and bayesian models for flow cytometry analysis in HIV/AIDS research.” In Quantitative Methods for HIV/AIDS Research, 135–56, 2017. https://doi.org/10.1201/9781315120805.Full Text
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Other Articles
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Kvistborg, Pia, Cécile Gouttefangeas, Nima Aghaeepour, Angelica Cazaly, Pratip K. Chattopadhyay, Cliburn Chan, Judith Eckl, et al. “Thinking outside the gate: single-cell assessments in multiple dimensions.” Immunity, April 21, 2015. https://doi.org/10.1016/j.immuni.2015.04.006.Full Text Link to Item
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Preprints
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Gong, Yishu, Matilda Moström, Claire Otero, Sarah Valencia, Amitinder Kaur, Sallie R. Permar, and Cliburn Chan. “Mathematical Modeling of Rhesus Cytomegalovirus (RhCMV) Placental Transmission in Seronegative Rhesus Macaques.” Cold Spring Harbor Laboratory, April 10, 2022. https://doi.org/10.1101/2022.04.07.487583.Full Text
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