Recent Publications

  • Huiqin Chen, Dihua Zhang, Guoping Zhang, Xiaofeng Li, Ying Liang, Mohan Vamsi Kasukurthi, Glen M. Borchert, and Jingshan Huang. A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia. BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):57. doi: 10.1186/s12911-018-0637-3. PMID: 30066657

  • Justin T. Roberts, Dillon G. Patterson, Valeria M. King, Shivam V. Amin, Caroline J. Polska, Dominika Houserova, Aline Crucello, Emmaline C. Barnhill, Molly M. Miller, Timothy D. Sherman, and Glen M. Borchert. ADAR mediated RNA editing modulates microRNA targeting in human breast cancer. Processes. April 2018, 6(5) 42; doi.org/10.3390/pr6050042
  • Dillon G. Patterson, Justin T. Roberts, Valeria M. King, Dominika Houserova, Emmaline C. Barnhill, Aline Crucello, Caroline J. Polska, Alex Coley, Melody Zeidan, Lucas W. Brantley, Garrett C. Kaufman, Michael Nguyen, Megann W. Santana, Ian A. Schiller, Julius S. Spicciani, Anastasia K. Zapata, Molly M. Miller, Timothy D. Sherman, Ruixia Ma, Hongyou Zhao, Ritu Arora, Ming Tan, Yaguang Xi, and Glen M. Borchert. Human snoRNA-93 is processed into a microRNA-like RNA. Nature NPJ Breast Cancer. 2017; 3:25 (2017). doi:10.1038/s41523-017-0032-8. PMID: 28702505.
  • Huiqin Chen, Dihua Zhang, Guoping Zhang, Xiaofeng Li, Ying Liang, Mohan Vamsi Kasukurthi, Glen M. Borchert, and Jingshan Huang, “A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia,” Proc. 2017 IEEE Intl’ Conference on Bioinformatics & Biomedicine (BIBM-17), IEEE Computer Society Press, Kansas City, MO, Nov. (2017).
  • Huawei Jin, Zhenhua Yu, Xiaodan Wang, Weian Chen, Shaolei Guo, Mohan Vamsi Kaukurthi, Glen M. Borchert, and Jingshan Huang, “Combining the analysis of Gene Expression Omnibus datasets with OmniSearch semantics-driven search and analysis to computationally discover microRNA-related biomarkers in glioblastoma,” Proc. 2017 IEEE Intl’ Conference on Bioinformatics & Biomedicine (BIBM-17), IEEE Computer Society Press, Kansas City, MO, Nov. (2017).
  • Jingshan Huang, Dejing Dou, Ming Tan, Glen M. Borchert, Karen Eilbeck, Alan Ruttenberg, Ping Yang. "Semantics-oriented Data Science and Computational Life Sciences: innovative application of semantic technologies in microRNA and lncRNA research." Proc. 2017 IEEE Intl’ Conference on Computational Advances in Bio and medical Sciences (ICCABS-2017), IEEE Computer Society Press, Orlando, FL, Oct. (2017).
  • Valeria M. King  and Glen M. Borchert. Protein Participants in MicroRNA Expression and Function. Bioinformatics in MicroRNA Research. Methods Mol Biol. 2017;1617:109-122. doi: 10.1007/978-1-4939-7046-9_2. PMID: 28540674

  • Justin T. Roberts and Glen M. Borchert. Computational Prediction of microRNAs’ Targets, MicroRNA Target Prediction Databases and Websites. Bioinformatics in MicroRNA Research. Methods Mol Biol. 2017;1617:109-122. doi: 10.1007/978-1-4939-7046-9_8. PMID: 28540680

  • David Chevalier and Glen M. Borchert. Genome-wide Analysis of microRNA-regulated Transcripts. Bioinformatics in MicroRNA Research. Methods Mol Biol. 2017;1617:109-122. doi: 10.1007/978-1-4939-7046-9_7. PMID: 28540679

  • Sara E. Cardin and Glen M. Borchert. Viral microRNAs, Host microRNAs Regulating Viruses, and Bacterial microRNA-like RNAs. Bioinformatics in MicroRNA Research. Methods Mol Biol. 2017;1617:109-122. doi: 10.1007/978-1-4939-7046-9_3. PMID: 28540675

  • Jingshan Huang, Fernando Gutierrez, Harrison Strachan, Dejing Dou, Weili Huang, Nisansa de Silva, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Bin Wu, Xiaowei Wang, Zixing Liu, Glen M Borchert, Ming Tan and Alan Ruttenberg. A semantic search system for knowledge capture of microRNA-target gene interactions based on the Ontology for MIcroRNA Target (OMIT). Int Journal of Data Mining and Bioinformatics. 2016. 15:3, 214-232.

  • Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva N, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. BMC Journal of Biomedical Semantics. 2016 May 10;7:25. eCollection 2016. PMID: 27175225

  • Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. BMC Journal of Biomedical Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016. PMID: 27152146

  • Shivam V. Amin, Dillon G. Patterson, Justin T. Roberts, Sara E. Cardin, Alexander B. Coley, Jonathan A. Allred, Jason M. Denner, Justin P. Johnson, Genevieve E. Mullen, Trenton K. O'Neal, Jason T. Smith, Hank T. Carr, Stacie L. Carr, Holly E. Cowart, David H. DaCosta, Brendon R. Herring, Valeria M. King, Caroline J. Polska, Erin E. Ward, Alice A. Wise, Kathleen N. Strunk, David Chevalier, Michael P. Spector, and Glen M. Borchert. Novel Small RNA (sRNA) Landscape of the Starvation-Stress Response Transcriptome of Salmonella enterica serovar Typhimurium. RNA Biology. 2016 Mar 3;13(3):331-42. doi: 10.1080/15476286.2016.1144010. PMID: 26853797
  • Chevalier, David, Roberts, Justin T, and Borchert, Glen M. Evolutionary Origin of MicroRNAs. eLS. (Nov 2015). http://www.els.net [doi: 10.1002/9780470015902.a0026316]
  • Viktor Pastukh, Justin Roberts, David Clark, Gina Bardwell, Mita Patel, Abu-Bakr Al-Mehdi, Glen Borchert, and Mark Gillespie. An Oxidative DNA "Damage" and Repair Mechanism Localized in the VEGF Promoter is Important for Hypoxia-induced VEGF mRNA Expression". American Journal of Physiology - Lung Cellular and Molecular Physiology. 2015 Oct 2:ajplung.00236.2015. PMID: 26432868
  • Sara-Elizabeth Cardin and Tabitha J. Perry, Caroline J. Polska, Laura Valverde, Alyson N. Askew, Dillon G. Patterson, Glen M. Borchert. MicroRNA Sponge Production using PCR-based Concatemerization of Short DNA Oligonucleotides. MOJ Cell Sci Rep. May 2015, 2(2): 00025.

  • Maurice D. Dale, Erin M. Mortimer, Santharam Kolli, Erik Achramowicz, Glen M. Borchert, Steven A. Juliano, Scott Halkyard, Nick Sietz, Craig Gatto, Patricia Y. Hester and David A. Rubin. Bone-Remodeling Transcript Levels Are Independent of Perching in End-of-Lay White Leghorn Chickens. Int. J. Mol. Sci. January 2015. 16(2), 2663-2677.
  • Jason T. Smith and Justine C. Harris, Oscar J. Lopez, Laura Valverde, Glen M. Borchert. “On the Job” Learning: A Bioinformatics Course Integrating Undergraduates into Actual Research Projects and Manuscript Submissions. Biochem Mol Biol Educ. January 2015. doi: 10.1002/bmb.20848.
  • Justin T. Roberts, Sara E. Cardin, Glen M. Borchert. Article highlight. MicroRNAs were initially formed from transposable element sequences. RNA Biology 11:7, 791-792; July 2014.

  • Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M. OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain. PLoS One. Jul 2014 15;9(7):e100855. doi: 10.1371/journal.pone.0100855.
  • Justin T Roberts, Sara E Cardin, Glen M. Borchert. Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences. Mobile Genetic Elements. 3:e29255. May 2014. http://dx.doi.org/10.4161/mge.29255\
  • Justin T. Roberts, Elvera A. Cooper, Connor J. Favreau, Jacob S. Howell, Lee G. Lane, James E. Mills, Derrick C. Newman, Tabitha J. Perry, Meaghan E. Russell, Brittany M. Wallace, Glen M. Borchert. Continuing Analysis of MicroRNA Origins: Formation from Transposable Element Insertions and Noncoding RNA Mutations. Mobile Genetic Elements. Nov/Dec 2013. 3:e27755; http://dx.doi.org/10.4161/mge.27755
  • Abramyan J, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, et al. The Western Painted Turtle genome: the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 2013 Mar 28;14(3):R28.

  • Teresa J. Filshtein, Craig O. Mackenzie, Maurice D. Dale, Paul S. Dela-Cruz, Dale M. Ernst, Edward A. Frankenberger, Chunyan He, Kaylee L. Heath, Andria S. Jones, Daniel K. Jones, Edward R. King, Maggie B. Maher, Travis J. Mitchell, Rachel R. Morgan, Sirisha Sirobhushanam, Scott D. Halkyard, Kiran B. Tiwari, David A. Rubin, Glen M. Borchert and Erik D. Larson. Article highlight. A new method to identify microRNA targets: OrbID. RNA Biology 9:10, 1209–1209; October 2012.
  • Edward A. Ehrat, Bradley R. Johnson, Jonathan D. Williams, Glen M. Borchert, Erik D Larson. G-quadruplex recognition activities of E. coli MutS. BMC Molecular Biology. 2012, 13:23.

  • Teresa J. Filshtein and Craig O. Mackenzie, Maurice D. Dale, Paul S. Dela-Cruz, Dale M. Ernst, Edward A Frankenberger, Chunyan He, Kaylee L. Heath, Andria S. Jones, Daniel K. Jones, Edward R. King, Maggie B. Maher, Travis J. Mitchell, Rachel R. Morgan, Sirisha Sirobhushanam, Scott D. Halkyard, Kiran B. Tiwari, David Rubin, Erik D Larson, Glen M. Borchert. OrbID: MicroRNA Origin Based microRNA target identification. Mobile Genetic Elements. May/June 2012, 2:3, 1-9.

  • Glen M. Borchert, Nathaniel W. Holton, Jonathan D. Williams, William L. Hernan, Ian P. Bishop, Joel A. Dembosky, James E. Elste, Nathaniel S. Gregoire, Jee-Ah Kim, Wesley W. Koehler, Joe C. Lengerich, Arianna A. Medema, Marilyn A. Nguyen, Geoffrey D. Ower, Michelle A. Rarick, Brooke N. Strong, Nicholas J. Tardi, Nathan M. Tasker, Darren J. Wozniak, Craig Gatto and Erik D. Larson. Article highlight. Genetic element model for genomic establishment of functional miRs. RNA Biology 8:4, 549-551; July/August 2011.
  • Glen M. Borchert, Nathaniel W Holton, Erik D Larson. Repression of human Activation Induced cytidine Deaminase by miR-93 and miR-155. BMC Cancer. 2011 Aug 11:347.

  • Glen M. Borchert, Nathaniel W. Holton, Jonathan D. Williams, William L. Hernan, Ian P. Bishop, Joel A. Dembosky, James E. Elste, Nathaniel S. Gregoire, Jee-Ah Kim, Wesley W. Koehler, Joe C. Lengerich, Arianna A. Medema, Marilyn A. Nguyen, Geoffrey D. Ower, Michelle A. Rarick, Brooke N. Strong, Nicholas J. Tardi, Nathan M. Tasker, Darren J. Wozniak, Craig Gatto and Erik D. Larson.  Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins. Mobile Genetic Elements. 2011 May/June: 1(1): 8-17.

  • GM Borchert, Holden NW, Vogel LA, Edwards KA, ED Larson. Histone H2A and H2B are monoubiquitinated at AID-targeted loci. PLoS One. 2010 Jul 16;5(7):e11641.

  • GM Borchert, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, Davidson BL. Adenosine deamination in human transcripts generates novel microRNA binding sites. Human Molecular Genetics. 2009 18(24):4801-4807.

  • GM Borchert, W Lanier and BL Davidson. RNA polymerase III transcribes human microRNAs. Nature Structural & Molecular Biology. 2006 Dec;13(12):1097-101.