Scholars@Duke

• Research
• 

  Selected Grants

  • CIVICS Component C - Option 13A awarded by National Institutes of Health 2019 - 2025
  • Rapid, point-of-care, host gene expression test for presymptomatic viral infection and to distinguish bacterial from viral illness awarded by Department of Defense 2021 - 2023
  • Preparing for prospective cohort study of acute febrile illness and sepsis in Madagascar (Madagascar Research Site Implementation) awarded by Henry M. Jackson Foundation 2022 - 2023
  • COVID Survivors Long Term Follow Up Study--WMD ECHO Detector awarded by Icahn School of Medicine at Mount Sinai 2021 - 2023
  • VTEU 18-0010.B1C1.0120_Task C Option 1 awarded by National Institutes of Health 2019 - 2022
  • Duke RDS2 (Respondent-Driven Sampling, Respiratory Disease Surveillance) the SNOWBALL Sampling Study awarded by Centers for Disease Control and Prevention 2020 - 2022
  • Mapping Epigenetic Memory of Exposure New To Observe (MEMENTO) awarded by Defense Advanced Research Projects Agency 2019 - 2022
  • Resilience Prediction to RSV Infection awarded by Sanofi US 2018 - 2021
  • Human-Based Sensor System for Presymptomatic Biological Exposure Detection awarded by Research Triangle Institute International 2019 - 2021
  • PREdicting contagion using Systems And GEnomic analysis (PRESAGE) awarded by Defense Advanced Research Projects Agency 2017 - 2020
  • Novel host-based diagnostics of febrile illness in the warfighter awarded by Department of Defense 2016 - 2020
  • MicroRNA Profiling to Characterize and Predict Posttraumatic Epilepsy following Traumatic Brain Injury awarded by Department of Defense 2018 - 2020
  • Predigen Research Program awarded by Predigen, Inc. 2019 - 2020
  • VTEU 18-0010.B1C1.0120_Task B Base awarded by National Institutes of Health 2019
  • DEVELOPMENT OF PLATELET RNA BIOMARKERS FOR THE RESPONSE TO TICAGRELOR awarded by AstraZeneca Healthcare Foundation 2015 - 2018
  • Feasibility for Predicting Warfighter Health Using Transcriptional Markers on the MAP Platform awarded by Ibis Biosciences, Inc. 2016
  • Baseline Bio-molecular Models to Predict Infectious Disease Susceptibility awarded by Defense Advanced Research Projects Agency 2015 - 2016
  • Validation of the host transcription diagnostic for prediction of incipient respiratory viral infection awarded by Defense Advanced Research Projects Agency 2014 - 2016
  • CTSA UL awarded by National Institutes of Health 2006 - 2012
  • Integrated instrument systems for maintenance and delivery of RNAi libraries awarded by National Institutes of Health 2008 - 2009
• 

  External Relationships

  • Biomeme, Inc.
• Publications & Artistic Works
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  Selected Publications

  • Academic Articles

    • Tsalik, Ephraim L., Ricardo Henao, Jesse L. Montgomery, Jeff W. Nawrocki, Mert Aydin, Emily C. Lydon, Emily R. Ko, et al. “Discriminating Bacterial and Viral Infection Using a Rapid Host Gene Expression Test.” Crit Care Med 49, no. 10 (October 1, 2021): 1651–63. https://doi.org/10.1097/CCM.0000000000005085.
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    • Mahle, Rachael E., Sunil Suchindran, Ricardo Henao, Julie M. Steinbrink, Thomas W. Burke, Micah T. McClain, Geoffrey S. Ginsburg, Christopher W. Woods, and Ephraim L. Tsalik. “Validation of a Host Gene Expression Test for Bacterial/Viral Discrimination in Immunocompromised Hosts.” Clin Infect Dis 73, no. 4 (August 16, 2021): 605–13. https://doi.org/10.1093/cid/ciab043.
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    • Yu, Chen, Sejiro Littleton, Nicholas S. Giroux, Rose Mathew, Shengli Ding, Joan Kalnitsky, Yuchen Yang, et al. “Mucosal-associated invariant T cell responses differ by sex in COVID-19.” Med (N Y) 2, no. 6 (June 11, 2021): 755-772.e5. https://doi.org/10.1016/j.medj.2021.04.008.
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    • Heggestad, Jacob T., David S. Kinnamon, Lyra B. Olson, Jason Liu, Garrett Kelly, Simone A. Wall, Solomon Oshabaheebwa, et al. “Multiplexed, quantitative serological profiling of COVID-19 from blood by a point-of-care test.” Sci Adv 7, no. 26 (June 2021). https://doi.org/10.1126/sciadv.abg4901.
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    • Wang, Liuyang, Thomas J. Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, et al. “An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility.” Genome Med 13, no. 1 (May 17, 2021): 83. https://doi.org/10.1186/s13073-021-00904-z.
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    • Garrido, Carolina, Jillian H. Hurst, Cynthia G. Lorang, Jhoanna N. Aquino, Javier Rodriguez, Trevor S. Pfeiffer, Tulika Singh, et al. “Asymptomatic or mild symptomatic SARS-CoV-2 infection elicits durable neutralizing antibody responses in children and adolescents.” Medrxiv, April 20, 2021. https://doi.org/10.1101/2021.04.17.21255663.
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    • McClain, Micah T., Florica J. Constantine, Bradly P. Nicholson, Marshall Nichols, Thomas W. Burke, Ricardo Henao, Daphne C. Jones, et al. “A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study.” Lancet Infect Dis 21, no. 3 (March 2021): 396–404. https://doi.org/10.1016/S1473-3099(20)30486-2.
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    • McClain, Micah T., Florica J. Constantine, Ricardo Henao, Yiling Liu, Ephraim L. Tsalik, Thomas W. Burke, Julie M. Steinbrink, et al. “Dysregulated transcriptional responses to SARS-CoV-2 in the periphery.” Nat Commun 12, no. 1 (February 17, 2021): 1079. https://doi.org/10.1038/s41467-021-21289-y.
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    • McClain, Micah T., Florica J. Constantine, Ricardo Henao, Yiling Liu, Ephraim L. Tsalik, Thomas W. Burke, Julie M. Steinbrink, et al. “Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches.” Medrxiv, July 26, 2020. https://doi.org/10.1101/2020.07.20.20155507.
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    • Tillekeratne, L Gayani, Sunil Suchindran, Emily R. Ko, Elizabeth A. Petzold, Champica K. Bodinayake, Ajith Nagahawatte, Vasantha Devasiri, et al. “Previously Derived Host Gene Expression Classifiers Identify Bacterial and Viral Etiologies of Acute Febrile Respiratory Illness in a South Asian Population.” Open Forum Infect Dis 7, no. 6 (June 2020): ofaa194. https://doi.org/10.1093/ofid/ofaa194.
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    • Nimmagadda, Sai N., Firas S. Midani, Heather Durand, Aspen T. Reese, Caitlin C. Murdoch, Bradley P. Nicholson, Timothy Veldman, et al. “Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection,” April 17, 2020. https://doi.org/10.1101/2020.04.11.20061911.
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    • Tsalik, Ephraim L., Ayeaye Khine, Abdossamad Talebpour, Alaleh Samiei, Vilcy Parmar, Thomas W. Burke, Micah T. Mcclain, et al. “Rapid, Sample-to-Answer Host Gene Expression Test to Diagnose Viral Infection.” Open Forum Infect Dis 6, no. 11 (November 2019): ofz466. https://doi.org/10.1093/ofid/ofz466.
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    • Ko, Emily R., Casandra W. Philipson, Thomas W. Burke, Regina Z. Cer, Kimberly A. Bishop-Lilly, Logan J. Voegtly, Ephraim L. Tsalik, Christopher W. Woods, Danielle V. Clark, and Kevin L. Schully. “Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever.” Bmc Infect Dis 19, no. 1 (October 28, 2019): 905. https://doi.org/10.1186/s12879-019-4462-9.
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    • Lydon, Emily C., Ricardo Henao, Thomas W. Burke, Mert Aydin, Bradly P. Nicholson, Seth W. Glickman, Vance G. Fowler, et al. “Validation of a host response test to distinguish bacterial and viral respiratory infection.” Ebiomedicine 48 (October 2019): 453–61. https://doi.org/10.1016/j.ebiom.2019.09.040.
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    • Lydon, Emily C., Charles Bullard, Mert Aydin, Olga M. Better, Anna Mazur, Bradly P. Nicholson, Emily R. Ko, et al. “A host gene expression approach for identifying triggers of asthma exacerbations.” Plos One 14, no. 4 (2019): e0214871. https://doi.org/10.1371/journal.pone.0214871.
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    • Poore, Gregory D., Emily R. Ko, Ashlee Valente, Ricardo Henao, Kelsey Sumner, Christopher Hong, Thomas W. Burke, et al. “A miRNA Host Response Signature Accurately Discriminates Acute Respiratory Infection Etiologies.” Front Microbiol 9 (2018): 2957. https://doi.org/10.3389/fmicb.2018.02957.
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    • Burke, Thomas W., Ricardo Henao, Erik Soderblom, Ephraim L. Tsalik, J Will Thompson, Micah T. McClain, Marshall Nichols, et al. “Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.” Ebiomedicine 17 (March 2017): 172–81. https://doi.org/10.1016/j.ebiom.2017.02.015.
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    • Yang, William E., Sunil Suchindran, Bradly P. Nicholson, Micah T. McClain, Thomas Burke, Geoffrey S. Ginsburg, Clayton D. Harro, et al. “Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans.” J Infect Dis 213, no. 9 (May 1, 2016): 1495–1504. https://doi.org/10.1093/infdis/jiv593.
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    • Liu, Tzu-Yu, Thomas Burke, Lawrence P. Park, Christopher W. Woods, Aimee K. Zaas, Geoffrey S. Ginsburg, and Alfred O. Hero. “An individualized predictor of health and disease using paired reference and target samples.” Bmc Bioinformatics 17 (January 22, 2016): 47. https://doi.org/10.1186/s12859-016-0889-9.
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    • Tsalik, Ephraim L., Ricardo Henao, Marshall Nichols, Thomas Burke, Emily R. Ko, Micah T. McClain, Lori L. Hudson, et al. “Host gene expression classifiers diagnose acute respiratory illness etiology.” Sci Transl Med 8, no. 322 (January 20, 2016): 322ra11. https://doi.org/10.1126/scitranslmed.aad6873.
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    • McClain, Micah T., Bradly P. Nicholson, Lawrence P. Park, Tzu-Yu Liu, Alfred O. Hero, Ephraim L. Tsalik, Aimee K. Zaas, et al. “A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses.” Open Forum Infect Dis 3, no. 1 (January 2016): ofw007. https://doi.org/10.1093/ofid/ofw007.
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    • Zaas, Aimee K., Bronwen H. Garner, Ephraim L. Tsalik, Thomas Burke, Christopher W. Woods, and Geoffrey S. Ginsburg. “The current epidemiology and clinical decisions surrounding acute respiratory infections.” Trends Mol Med 20, no. 10 (October 2014): 579–88. https://doi.org/10.1016/j.molmed.2014.08.001.
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    • Benjamin, Ashlee M., Marshall Nichols, Thomas W. Burke, Geoffrey S. Ginsburg, and Joseph E. Lucas. “Comparing reference-based RNA-Seq mapping methods for non-human primate data.” Bmc Genomics 15, no. 1 (July 7, 2014): 570. https://doi.org/10.1186/1471-2164-15-570.
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    • Ngo, Hoan T., Hsin-Neng Wang, Thomas Burke, Geoffrey S. Ginsburg, and Tuan Vo-Dinh. “Multiplex detection of disease biomarkers using SERS molecular sentinel-on-chip.” Anal Bioanal Chem 406, no. 14 (May 2014): 3335–44. https://doi.org/10.1007/s00216-014-7648-4.
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    • Zaas, Aimee K., Thomas Burke, Minhua Chen, Micah McClain, Bradly Nicholson, Timothy Veldman, Ephraim L. Tsalik, et al. “A host-based RT-PCR gene expression signature to identify acute respiratory viral infection.” Sci Transl Med 5, no. 203 (September 18, 2013): 203ra126. https://doi.org/10.1126/scitranslmed.3006280.
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    • Wang, Hsin-Neng, Andrew M. Fales, Aimee K. Zaas, Christopher W. Woods, Thomas Burke, Geoffrey S. Ginsburg, and Tuan Vo-Dinh. “Surface-enhanced Raman scattering molecular sentinel nanoprobes for viral infection diagnostics.” Anal Chim Acta 786 (July 5, 2013): 153–58. https://doi.org/10.1016/j.aca.2013.05.017.
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    • Betsou, Fotini, Rebecca Barnes, Thomas Burke, Domenico Coppola, Yvonne Desouza, James Eliason, Barbara Glazer, et al. “Human biospecimen research: experimental protocol and quality control tools.” Cancer Epidemiology, Biomarkers & Prevention : A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology 18, no. 4 (April 2009): 1017–25. https://doi.org/10.1158/1055-9965.epi-08-1231.
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    • Ginsburg, Geoffrey S., Thomas W. Burke, and Phillip Febbo. “Centralized biorepositories for genetic and genomic research.” Jama 299, no. 11 (March 19, 2008): 1359–61. https://doi.org/10.1001/jama.299.11.1359.
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    • Cook, Jeanette Gowen, Chi-Hyun Park, Thomas W. Burke, Gustavo Leone, James DeGregori, Amber Engel, and Joseph R. Nevins. “Analysis of Cdc6 function in the assembly of mammalian prereplication complexes.” Proceedings of the National Academy of Sciences of the United States of America 99, no. 3 (February 2002): 1347–52. https://doi.org/10.1073/pnas.032677499.
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    • Burke, T. W., J. G. Cook, M. Asano, and J. R. Nevins. “Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1.” The Journal of Biological Chemistry 276, no. 18 (May 2001): 15397–408. https://doi.org/10.1074/jbc.m011556200.
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    • Emami, K. H., T. W. Burke, and S. T. Smale. “Sp1 activation of a TATA-less promoter requires a species-specific interaction involving transcription factor IID.” Nucleic Acids Research 26, no. 3 (February 1998): 839–46. https://doi.org/10.1093/nar/26.3.839.
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    • Burke, T. W., and J. T. Kadonaga. “The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila.” Genes & Development 11, no. 22 (November 1997): 3020–31. https://doi.org/10.1101/gad.11.22.3020.
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    • Burke, T. W., and J. T. Kadonaga. “Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters.” Genes & Development 10, no. 6 (March 1996): 711–24. https://doi.org/10.1101/gad.10.6.711.
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    • Lira-DeVito, L. M., T. W. Burke, and J. T. Kadonaga. “Structure of the genes encoding transcription factor IIB and TATA box-binding protein from Drosophila melanogaster.” Gene 153, no. 2 (February 1995): 203–7. https://doi.org/10.1016/0378-1119(94)00764-j.
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    • BURKE, T. W., and S. VUKPAVLOVIC. “INSULIN-LIKE GROWTH FACTOR-I IS A SERUM COMPONENT STIMULATING GROWTH OF HUMAN NEUROBLASTOMA.” In Vitro Cellular & Developmental Biology Animal 29A, no. 5 (May 1, 1993): 391–94.
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    • Burke, T. W., and S. Vuk-Pavlović. “Insulin-like growth factor-I is a serum component stimulating growth of human neuroblastoma.” In Vitro Cellular & Developmental Biology. Animal 29A, no. 5 (May 1993): 391–94. https://doi.org/10.1007/bf02633987.
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  • Conference Papers

    • Ngo, H. T., H. N. Wang, T. Burke, C. Woods, G. S. Ginsburg, and T. Vo-Dinh. “Multiplex DNA biosensor for viral infection diagnosis using SERS molecular sentinel-on-chip.” In Ifmbe Proceedings, 46:15–20, 2015. https://doi.org/10.1007/978-3-319-11776-8_4.
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    • Burke, T. W., P. J. Willy, A. K. Kutach, J. E. Butler, and J. T. Kadonaga. “The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box.” In Cold Spring Harbor Symposia on Quantitative Biology, 63:75–82, 1998. https://doi.org/10.1101/sqb.1998.63.75.
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