Publications

For current publications please visit The National Center for Biotechnology Information’s PubMed website at KEYoder Bibliography

Yoder, K.E., A.J. Rabe, R. Fishel, and R.C. Larue. 2021. Strategies for targeting retroviral integration for safer gene therapy: advances and challenges. Frontiers in Molecular Biosciences. 8:662331.

Kotlar, R.M., N.D. Jones, G. Senavirathne, A.M. Gardner, R.K. Messer, Y.Y. Tan, A.J. Rabe, R. Fishel, and K.E. Yoder. 2021. Retroviral prototype foamy virus intasome binding to a nucleosome target does not determine integration efficiency. Journal of Biological Chemistry. 296:100550.

Panfil, A.R., P.L. Green, and K.E. Yoder. 2020. CRISPR genome editing applied to the pathogenic retrovirus HTLV-1. Frontiers in Cellular and Infection Microbiology. 10:580371.

Messer, R.K., M.A. Lopez, G. Senavirathne, and K.E. Yoder. 2019. Expression and purification of nuclease-free oxygen scavenger protocatechuate 3,4-dioxygenase. Journal of Visualized Experiments. 153:e59599.

Yoder, K.E. 2019. A CRISPR/Cas9 library to map the HIV-1 provirus genetic fitness. Acta Virologica. 63:128-138.

Yoder, K.E. 2019. Absence of LEDGF/p75 expression in astrocytes may affect HIV-1 integration efficiency. Molecular Genetics, Microbiology, and Virology. 34:81-83.

Mackler, R.M., N.D. Jones, A.M. Gardner, M.A. Lopez Jr., C.J. Howard, R. Fishel, and K.E. Yoder. 2019. Nucleosome DNA unwrapping does not affect prototype foamy virus integration efficiency or site selection. Plos One. 14:e0212764.

Jones, N.D., R.M. Mackler, M.A. Lopez, L. Baltierra Jasso, M.P. Altman, G. Senavirathne, and K.E. Yoder. 2019. Prototype foamy virus intasome aggregation is mediated by outer protein domains and prevented by protocatechuic acid. Scientific Reports. 9:132.

Panfil, A.R., J.A. London, P.L. Green, and K.E. Yoder. 2018. CRISPR/Cas9 genome editing to disable the latent HIV-1 provirus. Frontiers in Microbiology. 9:3107.

Mackler, R.M., M.A. Lopez, M.J. Osterhage, and K.E. Yoder. 2018. Prototype foamy virus integrase is promiscuous for target choice. Biochemical and Biophysical Research Communications. 503(3):1241-1246.

Senavirathne, G., M.A. Lopez, R. Messer, R. Fishel, and K.E. Yoder. 2018. Expression and purification of nuclease-free protocatechuate 3,4-dioxygenase for prolonged single-molecule flourescence imaging. Analytical Biochemistry. 556:78-84.

Mackler, R.M., M.A. Lopez, and K.E. Yoder. 2018. Assembly and purification of prototype foamy virus intasomes. Journal of Visualized Experiments. 133:e57453

Lopez, M.A., R.M. Mackler, M.P. Altman, and K.E. Yoder. 2017 Detection and removal of nuclease contamination during purification of recombinant prototype foamy virus integrase. Journal of Visualized Experiments. 130:e56605.

Pi, F., Z. Zhao, V. Chelikani, K. Yoder, M. Kvaratskhelia, and P. Guo. 2016. Development of potent antiviral drugs inspired by viral DNA packaging motors with revolution mechanism. Journal of Virology. 90:8036.

Yoder, K.E. and R. Bundschuh. 2016. Host double strand break repair generates HIV-1 strains resistant to CRISPR/Cas9. Scientific Reports. 6:29530.

Lopez, M., R. Mackler, and K.E. Yoder. 2016. Removal of nuclease contamination during purification of recombinant Prototype Foamy Virus integrase. Journal of Virological Methods. 235:134-138.

Jones, N.D., M.A. Lopez Jr., J. Hanne, M.B. Peake, J-B. Lee, R. Fishel, and K.E. Yoder. 2016. Retroviral intasomes search a target DNA by 1D-diffusion. Nature Communications. 7:11409.

Senavirathne G., J. Liu, M.A. Lopez, J. Hanne, J. Martin-Lopez, J.B. Lee, K.E. Yoder, and R. Fishel. 2015 Widespread nuclease contamination in commonly used oxygen-scavenging systems. Nature Methods. 12:901-902.

Bennett, G, R. Peters, X. Wang, J. Hanne, R.W. Sobol, R. Bundschuh, R. Fishel, and K.E. Yoder. 2014 Repair of oxidative DNA base damage in the host genome influences the HIV integration site sequence preference. PLoS ONE. 9:e103164.

Yoder, K.E., A. Espeseth, X. Wang, Q. Fang, M.T. Russo, R.S. Lloyd, D. Hazuda, R.W. Sobol, and R. Fishel. 2011 The Base Excision Repair Pathway Is Required for Efficient Lentivirus Integration. PLoS ONE. 6:e17862.

Yoder, K.E., W. Roddick, P. Hoellerbauer, and R. Fishel. 2011. XPB mediated retroviral cDNA degradation coincides with entry to the nucleus. Virology. 410:291-298.

Espeseth, A.S., R. Fishel, D. Hazuda, Q. Huang, M. Xu, K. Yoder, and H. Zhou. 2011 siRNA Screening of a Targeted Library of DNA Repair Factors in HIV Infection Reveals a Role for Base Excision Repair in HIV Integration. PLoS ONE. 6:e17612.

Charbonneau, N., R. Amunugama, C. Schmutte, K. Yoder, and R. Fishel. 2009. Evidence that hMLH3 functions primarily in meiosis and in hMSH2-hMSH3 mismatch repair. Cancer Biology & Therapy. 8:1411-1420.

Yoder, K.E., and R. Fishel. 2008. Real-time quantitative PCR and fast QPCR have similar sensitivity and accuracy with HIV cDNA late reverse transcripts and 2-LTR circles. Journal of Virological Methods. 153:253-256.

Ikura, T., S. Tashiro, A. Kakino, H. Shima, N. Jacob, R. Amunugarna, K. Yoder, S. Izumi, I. Kuraoka, K. Tanaka, H. Kimura, M. Tkura, S. Nishikubo, T. Ito, A. Muto, K. Miyagawa, S. Takeda, R. Fishel, K. Igarashi, and K. Kamiya. 2007 DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics. Molecular and Cellular Biology. 27:7028-7040.

Shim, K-S., C. Schmutte, K. Yoder, and R. Fishel. 2006. Defining the salt effect on human RAD51 activities. DNA Repair. 5:718-730.

Yoder, K., A. Sarasin, K. Kraemer, M. McIlhatton, F. Bushman, and R. Fishel. 2006. The DNA repair genes XPB and XPD defend cells from retroviral infection. Proceedings of the National Academy of Sciences of the United States of America. 103:4622-4627.

Yoder, K.E., and R. Fishel. 2006. PCR-based detection is unable to consistently distinguish HIV 1LTR circles. Journal of Virological Methods. 138:201-206.

Picchio, M.C., E.S. Martin, R. Cesari, G.A. Calin, S. Yendamuri, T. Kuroki, F. Pentimalli, M. Sarti, K. Yoder, L.R. Kaiser, R. Fishel, and C.M. Croce. 2004. Alterations of the tumor suppressor gene Parkin in non-small cell lung cancer. Clinical Cancer Research. 10:2720-2724.

Martin, E.S., R. Cesari, F. Pentimalli, K. Yoder, R. Fishel, A.L. Himelstein, S.E. Martin, A.K. Godwin, M. Negrini, and C.M. Croce. 2003. The BCSC-1 locus at chromosome 11q23-q24 is a candidate tumor suppressor gene. Proceedings of the National Academy of Sciences of the United States of America. 100:11517-11522.

Olson, P.D., K. Yoder, L.F. Fajardo, A.M. Marty, S. van de Pas, C. Olivier, and D.A. Relman. 2003. Lethal invasive cestodiasis in immunosuppressed patients. Journal of Infectious Diseases. 187:1962-1966.

Olivier, C., S. van de Pas, P.W. Lepp, K. Yoder, and D.A. Relman. 2001. Sequence variability in the first internal transcribed spacer region within and among Cyclospora species is consistent with polyparasitism. International Journal for Parasitology. 31:1475-1487.

Li, L., J.M. Olvera, K.E. Yoder, R.S. Mitchell, S.L. Butler, M. Lieber, S.L. Martin, and F.D. Bushman. 2001. “Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection.” EMBO Journal. 20:3272-3281.

Yoder, K.E., and F.D. Bushman. 2000. Repair of gaps in retroviral DNA integration intermediates. Journal of Virology. 74:11191-11200.

Li, L., K. Yoder, M.S.T. Hansen, J. Olvera, M.D. Miller, and F.D. Bushman. 2000. Retroviral cDNA integration: Stimulation by HMG I family proteins. Journal of Virology. 74:10965-10974.

Relman, D.A., D.N. Fredericks, K.E. Yoder, G. Mirowski, T. Berger, and J.E. Koehler. 1999. Absence of Kaposi’s sarcoma-associated herpesvirus DNA in bacillary angiomatosis-peliosis lesions. Journal of Infectious Diseases. 180:1386-1389.

Fortunato, E.A., M.H. Sommer, K. Yoder, D.H. Spector. 1997. Identification of domains within the human cytomegalovirus major immediate-early 86-kilodalton protein and the retinoblastoma protein required for physical and functional interaction with each other. Journal of Virology. 71:8176-8185.

Relman, D.A., T.M. Schmidt, A. Gajadhar, M. Sogin, J. Cross, K. Yoder, O. Sethabutr, P. Echeverria. 1996. Molecular phylogenetic analysis of Cyclospora, the human intestinal pathogen, suggests that it is closely related to Eimeria species. Journal of Infectious Diseases. 173:440-445.

Book Chapter:

Yoder, KE, Sethabutr, O, and Relman, DA. “PCR-based detection of the intestinal pathogen Cyclospora.” In PCR Protocols for Emerging Infectious Diseases. Edited by Persing, DH. -. Washington, DC, US|USA: ASM Press, January 1996.