Recent Publications

  • Dominika Houserova, Donavon J. Dahmer, Shivam V. Amin, Aline Crucello, Valeria M. King, Emmaline C. Barnhill, Yulong Huang, Mike E. Zambrano, Meghan A. Dean, Kevin M. Aria, Michael P. Spector, Glen M. Borchert. Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starved Salmonella enterica serovar Typhimurium. bioRxiv 2021.01.11.426214; doi: https://doi.org/10.1101/2021.01.11.426214

  • Dinesh Devadoss, Grant Daly, Marko Manevski, Dominika Houserova, Shah Hussain, Nathalie Baumlin, Matthias Salathe, Glen M. Borchert, Raymond J. Langley, Hitendra S. Chand A Long Noncoding RNA Antisense to ICAM-1 is Involved in Allergic Asthma Associated Hyperreactive Response of Airway Epithelial Cells. Mucosal Immunology (Nature NPJ), 2020 Oct 29. doi.org/10.1038/s41385-020-00352-9 PMID: 33122732
  • Jonathan D Williams, Dominika Houserova, Bradley R Johnson, Brad Dyniewski, Alexandra Berroyer, Hannah French, Addison A Barchie, Dakota D Bilbrey, Jeffrey D Demeis, Kanesha R Ghee, Alexandra G Hughes, Naden W Kreitz, Cameron H McInnis, Susanna C Pudner, Monica N Reeves, Ashlyn N Stahly, Ana Turcu, Brianna C Watters, Raymond J Langley, Mark N Gillespie, Aishwarya Prakash, Erik D Larson, Sue Jinks-Robertson, and Glen M. Borchert. G4-rich regions of the human genome are associated with increased genomic variation and form higher order, composite G4 structures via a novel loop:loop kissing interaction in vitro. Nucleic Acids Research, 2020 April 27. doi.org/10.1093/nar/gkaa357 PMID: 32383760
  • Ma B, Wu Z, Li S, Benton R, Li D, Huang Y, Kasukurthi MV, Lin J, Borchert GM, Tan S, Li G, Yang M, Huang J.. Development of a support vector machine learning and smart phone Internet of Things-based architecture for real-time sleep apnea diagnosis. BMC Med Inform Decis Mak 20, 298 (2020). https://doi.org/10.1186/s12911-020-01329-1 PMID: 33323112; PMCID: PMC7739462.

  • Li J, Zhang Z, Li S, Benton R, Huang Y, Kasukurthi MV, Li D, Lin J, Borchert GM, Tan S, Li G, Ma B, Yang M, Huang J. A partial encryption algorithm for medical images based on quick response code and reversible data hiding technology. BMC Med Inform Decis Mak. 2020 Dec 15;20(Suppl 14):297. doi: 10.1186/s12911-020-01328-2. PubMed PMID: 33323108; PubMed Central PMCID: PMC7739464.

  • Glen M. Borchert, Dominika Houserova, Raymond J. Langley, Mark N. Gillespie, Jonathan D. Williams. Long G4‐rich Regions in the Human Genome Primarily Function as Enhancers and Form Higher Order, Composite G4 Structures via a Novel Loop:Loop Kissing Interaction. The FASEB Journal. 2020. 34. 1-1. 10.1096/fasebj.2020.34.s1.04316.
  • Emmaline C. Barnhill,  Aline Crucello Dominika Houserova, Valeria M. King, Shivam V. Amin, Justin T. Roberts, Michael E. Zambrano, Jeffrey D. DeMeis, Donovan J. Dahmer Zara Ijaz, Addison A. Barchie, Brianna C. Watters, James E. Prusak, Meghan A. Dean, Nathaniel W. Holton, Jaire A. Ferreira-Filho, Anderson S. Sant’Ana, Michael P. Spector, and Glen M. Borchert. Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium. RNA Biology. Epub August 8 2019. PMID: 31390935
  • R. Renner, S. Li, Y. Huang, A. van der Zijp-Tan, S. Tan, D. Li, M.V. Kasukurthi, R. Benton, G.M. Borchert, J. Huang, and G. Jiang. Using an Artificial Neural Network to Map Cancer Common Data Elements to the Biomedical Research Integrated Domain Group Model in a Semi-automated Manner. BMC Medical Informatics and Decision Making. 2019, 19(Suppl 7):276. https://doi.org/10.1186/s12911-019-0979-5. PMID: 31865899
  • B. Ma, C. Li, Z. Wu, Y. Huang, A. van der Zijp-Tan, S. Tan, D. Li, A. Fong, C. Basetty, G.M. Borchert, R. Benton, B. Wu, and J. Huang. Muscle Fatigue Detection and Treatment System Driven by Internet of Things.BMC Medical Informatics and Decision Making. 2019, 19(S7):275.doi.org/10.1186/s12911-019-0982 PMID: 31865898
  • Long Noncoding Transcriptome in Chronic Obstructive Pulmonary Disease Dinesh Devadoss, Christopher Long, Raymond J. Langley, Marko Manevsk, Madhavan Nair, Michael A. Campos, Glen M. Borchert, Irfan Rahman, Hitendra S. Chand. Long Noncoding Transcriptome in Chronic Obstructive Pulmonary Disease. AJRCMB American Journal of Respiratory Cell and Molecular Biology. 2019 Sept 5. doi.org/10.1165/rcmb.2019-0184TR. PMID: 31486667
  • Yushan Qiu, Yulong Huang, Shaobo Tan, Dongqi Li, Ada Chaeli van der Zijp-Tan, Ada Fong, Glen M. Borchert, Jingshan Huang. Exploring Observability of Attractor Cycles in Boolean Networks for Biomarker Detection. IEEE access. August 2019. doi: 10.1109/ACCESS.2019.2937133. https://ieeexplore.ieee.org/document/8811490
  • Yaxin Guan, Jingshan Huang, Shengting Huang, Mohan Vamsi Kasukurthi, Yulong Huang, Dongqi Li, Shaobo Tan, Sida Wang, Xin Nian, Jingwei Lin, Glen M. Borchert, and Bin Wu. FGF21 mediates corticosteroid-related bone mass loss through PPAR-γ. Nov 2019. IEEE Bioinformatics & Biomedicine (BIBM-19), IEEE Computer Society Press, San Diego, CA. (2019). Conference Paper
  • Guanyi Yang, Xiuyu Leng, Fangwan Huang, Mohan Vamsi Kasukurthi, Yulong Huang, Dongqi Li, Jingwei Lin, Shaobo Tan, Guiying Lu, Ryan Benton, Glen M. Borchert, Bin Ma, and Jingshan Huang. Use CPET data to predict the intervention effect of aerobic exercise on young hypertensive patients. Nov 2019. IEEE Bioinformatics & Biomedicine (BIBM-19), IEEE Computer Society Press, San Diego, CA. (2019). Conference Paper
  • Jian Li, Zelin Zhang, Shengyu Li, Ryan Benton, Yulong Huang, Dongqi Li, Jingwei Lin, Shaobo Tan, Mohan Vamsi Kasukurthi, Glen M. Borchert, Bin Ma, and Jingshan Huang. Use Reversible Data Hiding to Protect Key Regions in Medical Images. Nov 2019. IEEE Bioinformatics & Biomedicine (BIBM-19), IEEE Computer Society Press, San Diego, CA. (2019). Conference Paper
  • Mohan Vamsi Kasukurthi, Dihua Zhang, Mika Housevera, Yulong Huang, Dongqi Li, Jingwei Lin, Shaobo Tan, Bin Ma, Ryan Benton, Shengyu Li, Glen M. Borchert, and Jingshan Huang. SURFr: Algorithm for identification and analysis of ncRNA-derived RNAs. Nov 2019. IEEE Bioinformatics & Biomedicine (BIBM-19), IEEE Computer Society Press, San Diego, CA. (2019). Conference Paper
  • Bin Ma, Zhaolong Wu, Shengyu Li, Ryan Benton, Yulong Huang, Dongqi Li, Jingwei Lin, Shaobo Tan, Mohan Vamsi Kasukurthi, Glen M. Borchert, and Jingshan Huang. A SVM-Based Algorithm to Diagnose Sleep Apnea. Nov 2019. IEEE Bioinformatics & Biomedicine (BIBM-19), IEEE Computer Society Press, San Diego, CA. (2019). Conference Paper

  • 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. PMID: 30197877

  • Robinette Renner, Shengyu Li, Yulong Huang, Shaobo Tan, Dongqi Li, Ada Chaeli van der Zijp-Tan, Ryan Benton, Glen M. Borchert, Jingshan Huang, and Guoqian Jiang. Mapping Common Data Elements to a Domain Model Using an Artificial Neural Network. Oct 2018 IEEE Bioinformatics & Biomedicine (BIBM-18), IEEE Computer Society Press, Madrid, Spain. (2018). Conference Paper, https://ieeexplore.ieee.org/document/8621535

  • Bin Ma, Chunxiao Li, Zhaolong Wu, Yulong Huang, Ada Chaeli van der Zijp-Tan, Shaobo Tan, Dongqi Li, Ada Fong, Chandan Basetty, Glen M. Borchert, and Jingshan Huang. A PWM-Based Muscle Fatigue Detection and Recovery System. Oct 2018 IEEE Bioinformatics & Biomedicine (BIBM-18), IEEE Computer Society Press, Madrid, Spain. (2018). Conference Paper, https://ieeexplore.ieee.org/document/8621418

  • Yushan Qiu, Yulong Huang, Shaobo Tan, Dongqi Li, Ada Chaeli van der Zijp-Tan, Ada Fong, Glen M. Borchert, Jingshan Huang. Novel Method for Singleton and Cyclic Attractor Observability in Boolean Networks. Oct 2018 IEEE Bioinformatics & Biomedicine (BIBM-18), IEEE Computer Society Press, Madrid, Spain. (2018). Conference Paper, https://ieeexplore.ieee.org/document/8621334

  • Jingshan Huang, Keisuke Fukuo, Gen Yoshino, Tsutomu Kazumi, Chandan Basetty, Yulong Huang, Shaobo Tan, Dongqi Li, Ada Chaeli van der Zijp-Tan, Ada Fong, Glen M. Borchert, Bin Wu. Body Composition and Biochemical Characteristics of Normal Weight Obesity in Japanese Young Women with Different Physical Activities. Oct 2018 IEEE Bioinformatics & Biomedicine (BIBM-18), IEEE Computer Society Press, Madrid, Spain. (2018). Conference Paper, https://ieeexplore.ieee.org/document/8621153

  • 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, “MeSH term-based semantic analysis of 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). Conference Paper, https://ieeexplore.ieee.org/document/8217837
  • Huawei Jin, Zhenhua Yu, Xiaodan Wang, Weian Chen, Shaolei Guo, Mohan Vamsi Kaukurthi, Glen M. Borchert, and Jingshan Huang, “Computational analysis to discover microRNA biomarkers in glioblastoma,” Proc. 2017 IEEE Intl’ Conference on Bioinformatics & Biomedicine (BIBM-17), IEEE Computer Society Press, Kansas City, MO, Nov. (2017). Conference Paper, https://ieeexplore.ieee.org/document/8217841
  • 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). Conference Paper, https://ieeexplore.ieee.org/document/8114284
  • 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.