Bio

I am a plant biologist who studies the "dark side" of the genome that scientists don't think about on a regular basis. Specifically, I want to more about the portion of the genome that is transcribed - but not producing proteins. These non-coding transcripts come in a variety of sizes, but can have an out-sized effect on plant development and stress responses. We happen to know quite a bit about the smaller non-coding RNAs (e.g. micro and small interfering RNAs), but very little about the long non-coding class of RNAs (lncRNAs).

As a research associate at the University of Arizona in the School of Plant Sciences, I use a combination of bioinformatic, genomic, molecular, and evolutionary tools to identify and functionally characterize lncRNAs that help plants respond to environmental stresses like heat and drought.

Research Areas:
Biochemistry, Computational Biology, Evolution, Genomics

Publications

20. Castillo AI, Nelson AD, Lyons E. A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model. Database. 

19. Nelson AD, Haug-Baltzell AK, Davey S, Gregory BD, and Lyons E. EPIC-CoGe: Managing and Analyzing Genomic Data, Bioinformatics, 2018. February 20, DOI: 10.1093/bioinformatics/bty106 

18. Nelson AD*c, Devisetty Upendra*, Palos Kyle, Haug-Baltzell Asher, Lyons Eric, Beilstein, Markc. Evolinc: a tool for the identification and evolutionary comparison of long intergenic non-coding RNAs. Frontiers in Genetics, 2017. DOI: 10.3389/fgene.2017.00052 *1st co-first author, cco-corresponding author

 17. Nelson AD*, Forsythe ES, Devisetty UK, Haug-Baltzell AK, Meldrum AMR, Frank MR, Lyons E, Beilstein MA*. A genomic and transcriptomic analysis of factors driving lincRNA diversification: lessons from plants. G3. 2016 July 20, DOI: 10.1534/g3.116.030338.

* Co-corresponding author

 16. Park S, Moon JC, Kim N, Kim E, Jeong J, Nelson AD, Jo B, Jang M, Lee JR. Algicidal effect of hybrid peptides as potential inhibitors of harmful algal blooms. Biotechnology Letters. 2016 May 1, DOI: 10.1007/s10529-016-2052-0. 

 15. Nelson AD* and Shippen DE* Evolution of TERT-interacting lncRNAs: expanding the regulatory landscape of telomerase. Frontiers in Genetics-The Evolving Telomeres. 2015 Sept 10, 6(277). DOI: 10.3389/fgene.2015.00277

* Co-corresponding author

 14. Xu H, Nelson AD, Shippen DE.

A Transposable Element within the Non-canonical Telomerase RNA of Arabidopsis thaliana Modulates Telomerase in Response to DNA Damage. PLoS Genetics. 2015 Jun 15;11(6).  DOI: 10.1371/journal.pgen.1005281

 13. González-García M, Pavelescu I, Canela A, Sevillano J, Leehy KA, Nelson AD, Shippen DE, Blasco M, Caño-Delgado A. Single-cell telomere-length quantification couples telomere length to meristem activity and stem cell development in Arabidopsis. Cell Reports. 2015 May 12; 11(6):977-89. Selected for the paper of the month at TAIR (www.arabidopsis.org), June 2, 2015. DOI: 10.1016/j.celrep.2015.04.013

 12. Gosai SJ, Foley SW, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory B. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Molecular Cell. 2015 Jan 22;57(2):376-88. DOI: 10.1016/j.molcel.2014.12.004

 11. Nelson AD, Beilstein MA, Shippen DE.

Nucleus and Genome: Telomeres (Book Chapter). The Plant Sciences - Molecular Biology, Springer Science. 2014:25-49.

 10. Nelson AD, Forsythe ES, Gan X, Tsiantis M, Beilstein MA.

Extending the model of Arabidopsis telomere length and composition across Brassicaceae. Chromosome Res. 2014 Jun;22(2):153-66. DOI: 10.1007/s10577-014-9423-y

 9. Nelson AD, Shippen DE.

Surprises from the Chromosome Front: Lessons from Arabidopsis on Telomeres and Telomerase. Cold Spring Harb Symp Quant Biol. 2012;77:7-15. DOI: 10.1101/sqb.2013.77.017053

 8. Cifuentes-Rojas C, Nelson AD, Boltz KA, Kannan K, She X, Shippen DE.

An alternative telomerase RNA in Arabidopsis modulates enzyme activity in response to DNA damage. Genes Dev. 2012 Nov 15;26 (22):2512-23. DOI: 10.1101/gad.202960.112

 7. Nelson AD, Shippen DE.

Blunt-ended telomeres: an alternative ending to the replication and end protection stories.

Genes Dev. 2012 Aug 1;26(15):1648-52. DOI: 10.1101/gad.199059.112

 6. Boltz KA, Song X, Leehy K, Nelson AD, Shippen DE.

ATR cooperates with CTC1 and STN1 to maintain telomeres and genome integrity in Arabidopsis. MBoC, 2012, Apr;23(8): 1558-68 DOI: 10.1091/mbc.E11-12-1002

 5. Nelson AD, Lamb JC, Kobrossly PS, Shippen DE.

Parameters affecting telomere-mediated chromosomal truncation in Arabidopsis. Plant Cell, 2011, Jun;23(6):2263-72. Recommended by F1000:

Schmidt R: "This article describes a clever strategy which is highly suitable to study the mechanism and..." Evaluation of: [Nelson AD et al. Parameters affecting telomere-mediated chromosomal truncation in Arabidopsis. Plant Cell.  2011 Jun; 23(6):2263-72; doi: 10.1105/tpc.111.086017]. Faculty of 1000, 30 Jun 2011.

Highlighted author and article in same issue. DOI: 10.1105/tpc.111.086017

 4. Shakirov EV, Perroud PF, Nelson AD, Cannell ME, Quatrano RS, Shippen DE.

Protection of Telomeres 1 is required for telomere integrity in the moss Physcomitrella patens. Plant Cell, 2010 Jun;22(6):1838-48. DOI: 10.1105/tpc.110.075846

 3. Kannan K, Nelson AD, Shippen DE.

Dyskerin is a component of the Arabidopsis telomerase RNP required for telomere maintenance. MCB, 2008 Apr;28(7):2332-41. DOI: 10.1128/MCB.01490-07

 2. Johnson JL, West JK, Nelson AD, Reinhart GD.

Resolving the Fluorescence Response of Escherichia coli Carbamoyl Phosphate Synthetase: Mapping Intra- and Intersubunit Conformational Changes. Biochemistry. 2007 Jan 16;46(2):387-97. DOI: 10.1021/bi061642n

 1. McClain JM (II), Maples DL, Maples RD, Matz DL, Harris SM, Nelson AD, Silversides JD, Archibald SJ, Hubin TJ. Dichloro(4,10-dimethyl-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane)iron (III) hexafluorophosphate. Acta Crystallogr C. 2006 Nov;62(Pt 11):m553-5. Epub 2006 Oct 31. DOI: 10.1107/S0108270106040765

Volunteer Activities

Director of the Climbing Association of Southern Arizona (www.theclimbershome.org)

Mendeley Advisor (www.mendeley.com)

Co-founder/Instructor of LIVE-for-Plants (lincRNA identification and validation exercise), a wet-bench/bioinformatic exercise aimed at primarily undergraduate institutions.

Moderator for Big Data and Cyberinfrastructure network on Plantae

Interests
Current Affiliations
Experience & Education