Publications

Featured publications

Helping others enhances graduate student wellness and mental health

April 22, 2022

Hermanstyne TO, Johnson L, Wylie KM, Skeath JB. Helping others enhances graduate student wellness and mental health. Nat Biotechnol. 2022 Apr;40(4):618-619. doi: 10.1038/s41587-022-01275-5. PMID: 35418639; PMCID: PMC9074398.

Chronic villitis of unknown etiology: Investigations into viral pathogenesis

April 1, 2021

Ernst LM, Bockoven C, Freedman A, Wang V, Pellerite M, Wylie TN, Wylie KM. Chronic villitis of unknown etiology: Investigations into viral pathogenesis. Placenta. 2021 Apr;107:24-30. doi: 10.1016/j.placenta.2021.02.020. Epub 2021 Mar 1. PMID: 33730616; PMCID: PMC8101289.

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data

March 4, 2021

Wylie TN, Wylie KM. ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data. Microbiol Resour Announc. 2021 Mar 4;10(9):e01468-20. doi: 10.1128/MRA.01468-20. PMID: 33664143; PMCID: PMC7936641.

Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study

January 1, 2020

Eskew AM, Stout MJ, Bedrick BS, Riley JK, Omurtag KR, Jimenez PT, Odem RR, Ratts VS, Keller SL, Jungheim ES, Wylie KM. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study. BJOG. 2020 Jan;127(2):208-216. doi: 10.1111/1471-0528.15951. Epub 2019 Oct 20. PMID: 31529767; PMCID: PMC6910962.

The vaginal eukaryotic DNA virome and preterm birth

August 1, 2018

Wylie KM, Wylie TN, Cahill AG, Macones GA, Tuuli MG, Stout MJ. The vaginal eukaryotic DNA virome and preterm birth. Am J Obstet Gynecol. 2018 Aug;219(2):189.e1-189.e12. doi: 10.1016/j.ajog.2018.04.048. Epub 2018 May 5. PMID: 29738749; PMCID: PMC6066425.

Enhanced virome sequencing using targeted sequence capture

December 1, 2015

Wylie TN, Wylie KM, Herter BN, Storch GA. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015 Dec;25(12):1910-20. doi: 10.1101/gr.191049.115. Epub 2015 Sep 22. PMID: 26395152; PMCID: PMC4665012.

Metagenomic analysis of double-stranded DNA viruses in healthy adults

December 10, 2014

Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol. 2014 Sep 10;12:71. doi: 10.1186/s12915-014-0071-7. PMID: 25212266; PMCID: PMC4177058.

Recent publications

• The Post-transplant Lymphoproliferative Disorders – Metagenomic Shotgun Microbial Sequencing (PTLD-MSMS) Study Methods and Protocol
  October 28, 2024
  The Post-transplant Lymphoproliferative Disorders – Metagenomic Shotgun Microbial Sequencing (PTLD-MSMS) Study Methods and ProtocolDharnidharka, V. R., Wylie, K. M., Wylie, T. N., Ruzinova, M. B., Goss, C. W., Storch, G. A., Mehta-Shah, N., Byers, D., Walther, L., Jaza, L., Gu, H., Agarwal, M., Green, M., Moore, E., Swerdlow, S. H., Silveira, F., Marks, L. J., Gratzinger, D., Bagg, A. & Law, S. C. & 1 others, Gandhi, M., Oct 28 2024, In: Transplantation Direct. 10, 11, p. e1723Research output: Contribution to journal › Article › peer-review
• Molecular detection of bacteria, placental inflammation, and neonatal sepsis risk
  January 1, 2024
  Molecular detection of bacteria, placental inflammation, and neonatal sepsis riskFranklin, A. D., Freedman, A., Wylie, K., Mangold, K. A., Wang, V., Price, E. & Ernst, L. M., Jan 2024, In: Journal of Perinatology. 44, 1, p. 46-54 9 p.Research output: Contribution to journal › Article › peer-review
• Simplified methods for variance estimation in microbiome abundance count data analysis
  January 1, 2024
  Simplified methods for variance estimation in microbiome abundance count data analysisShi, Y., Liu, L., Chen, J., Wylie, K. M., Wylie, T. N., Stout, M. J., Wang, C., Zhang, H., Shih, Y. C. T., Xu, X., Zhang, A., Park, S. H., Jiang, H. & Liu, L., 2024, In: Frontiers in Genetics. 15, 1458851.Research output: Contribution to journal › Article › peer-review
• Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health Surveillance
  September 8, 2023
  Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health SurveillanceMcCall, C., Leo Elworth, R. A., Wylie, K. M., Wylie, T. N., Dyson, K., Doughty, R., Treangen, T. J., Hopkins, L., Ensor, K. & Stadler, L. B., Sep 8 2023, In: ACS ES and T Water. 3, 9, p. 2955-2965 11 p.Research output: Contribution to journal › Article › peer-review
• Analysis of Plasmablasts From Children With Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein Epitope
  August 15, 2023
  Analysis of Plasmablasts From Children With Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein EpitopeRowley, A. H., Arrollo, D., Shulman, S. T., Torres, A., O’Brien, A., Wylie, K., Kim, K. Y. A. & Baker, S. C., Aug 15 2023, In: Journal of Infectious Diseases. 228, 4, p. 412-421 10 p.Research output: Contribution to journal › Article › peer-review
• The Fungal Microbiome of the Upper Airway Is Associated With Future Loss of Asthma Control and Exacerbation Among Children With Asthma
  August 1, 2023
  The Fungal Microbiome of the Upper Airway Is Associated With Future Loss of Asthma Control and Exacerbation Among Children With AsthmaYuan, H., Liu, Z., Dong, J., Bacharier, L. B., Jackson, D., Mauger, D., Boushey, H., Castro, M., Durack, J., Huang, Y. J., Lemanske, R. F., Storch, G. A., Weinstock, G. M., Wylie, K., Covar, R., Fitzpatrick, A. M., Phipatanakul, W., Robison, R. G., Beigelman, A. & Zhou, Y., Aug 2023, In: CHEST. 164, 2, p. 302-313 12 p.Research output: Contribution to journal › Article › peer-review
• Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal Conjunctiva
  May 1, 2023
  Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal ConjunctivaSchaefer, E. A. F., Chu, S., Wylie, K. M., Wylie, T. N., Griffith, O. L., Pearce, J. W., Johnson, G. C., Bryan, J. N. & Flesner, B. K., May 2023, In: Microorganisms. 11, 5, 1163.Research output: Contribution to journal › Article › peer-review
• Pathogen and Antibody Identification in Children with Encephalitis in Myanmar
  March 1, 2023
  Pathogen and Antibody Identification in Children with Encephalitis in MyanmarGalardi, M. M., Sowa, G. M., Crockett, C. D., Rudock, R., Smith, A. E., Shwe, E. E., San, T., Linn, K., Aye, A. M. M., Ramachandran, P. S., Zia, M., Wapniarski, A. E., Hawes, I. A., Hlaing, C. S., Kyu, E. H., Thair, C., Mar, Y. Y., Nway, N., Storch, G. A. & Wylie, K. M. & 4 others, Wylie, T. N., Dalmau, J., Wilson, M. R. & Mar, S. S., Mar 2023, In: Annals of neurology. 93, 3, p. 615-628 14 p.Research output: Contribution to journal › Article › peer-review
• The plasma virome in longitudinal samples from pregnant patients
  February 9, 2023
  The plasma virome in longitudinal samples from pregnant patientsStout, M. J., Brar, A. K., Herter, B. N., Rankin, A. & Wylie, K. M., Feb 9 2023, In: Frontiers in cellular and infection microbiology. 13, 1061230.Research output: Contribution to journal › Article › peer-review
• Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart Disease
  February 1, 2023
  Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart DiseaseGarand, M., Huang, S. S. Y., Goessling, L. S., Wan, F., Santillan, D. A., Santillan, M. K., Brar, A., Wylie, T. N., Wylie, K. M. & Eghtesady, P., Feb 2023, In: Microorganisms. 11, 2, 262.Research output: Contribution to journal › Article › peer-review