Mailing Address:
Neil Moore
321 E Maxwell St
Lexington, KY 40508-2701
Phone: 859-317-9772
Email: neil@s-z.org
Ph.D. in Computer Science, University of Kentucky, 2003–2012. Dissertation Multihierarchical Documents and Fine-Grained Access Control.
Undergraduate, University of Kentucky, 1997–2002. Majored in computer science and mathematics. College of Engineering Dean's List Fall 1997, Spring 1998, Fall 1998, Spring 1999, Fall 1999, Spring 2000, and Spring 2001. Graduated December 2002, receiving a B.S. Cum Laude in Computer Science and a B.S. Cum Laude in Mathematics with departmental honors.
April 2007. Excellence in Contribution to the Computer Science Enrichment Programs award, University of Kentucky Department of Computer Science.
April 2004. Awarded First Place Graduate Student Talk at Eastern Kentucky University's 18th Annual Symposium in Mathematics, Statistical, and Computer Sciences, for "A Geometric Approach to Efficient Implementation of Concurrent XML Markup".
March 2001: Member of the University of Kentucky Programming Team, which advanced to the world finals of the 25th annual ACM International Collegiate Programming Contest, Vancouver, BC, Canada.
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September 2009– |
IS technical support specialist IV (research support in bioinformatics), University of Kentucky. Worked as lead developer and system administrator/database administrator for the Epichloë festucae Genome Project. Developed, maintained, and enhanced web-based tools and databases for viewing, managing, and annotating many gigabytes of bioinformatic data covering ten strains and nine species of fungal endophytes in the family Clavicipitaceae. Worked extensively with GBrowse, MAKER, BioPerl and other bioinformatics tools and libraries. Administered GNU/Linux and Mac OS X Server systems, including Apache, MySQL, RAID/NAS/NFS backups, and LDAP user management. Assisted in research, including co-authoring scholarly papers. |
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January 2008– |
Research assistant, University of Kentucky. Worked as lead developer and system administrator/database administrator for the Epichloë festucae Genome Project. Coordinated a small team of developers (3–4 members) to develop, maintain, and enhance web-based tools and databases for viewing, managing, and annotating over 5 GiB of bioinformatic data. Worked extensively with GBrowse, BioPerl and other bioinformatics tools and libraries. Administered GNU/Linux and Mac OS X Server systems, including Apache, MySQL, RAID/NAS/NFS backups, LDAP user management. Assisted in research, including co-authoring scholarly papers. |
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January– |
Teaching assistant, University of Kentucky. Primary lecturer for the evening section of CS 215, "Introduction to Program Design, Abstraction, and Problem Solving", Spring 2007. Responsible for delivering lectures, guiding student laboratory work, preparing examinations, and grading. Primary lecturer for the summer section of CS 115, "Introduction to Computer Programming", Second Summer Session 2007. Responsible for preparing and delivering lectures, designing programming and laboratory assignments, guiding student laboratory work, preparing examinations, and grading. Primary lecturer for the evening section, and teaching assistant for a day section, of CS 215, Fall 2007. Responsible for delivering lectures (night section only), guiding student laboratory work, preparing examinations, and grading. Teaching assistant for two day sections of CS 215, Spring 2008. Responsible for guiding student laboratory work, preparing examinations, and grading. |
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July 2003– |
Research assistant, University of Kentucky. Worked in a team environment to develop infrastructure for producing image-based electronic editions of manuscripts. Designed and implemented a library for storing, modifying, and querying multi-hierarchical XML. Participated in the design of a framework to facilitate the sharing of markup and other data among a number of independently-developed modules. Participated in the implementation, testing, and integration of these modules as plugins for the Eclipse application framework. Assisted in research, including authoring scholarly papers. |
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September 2001– |
Lead developer, BigTrends.com (Headley Investment Analysis). Designed and implemented a distributed application for financial charting and analysis, using Java, Perl, and MySQL. Developed a number of web-based applications for financial charting and analysis, using Perl and MySQL. Co-maintained three GNU/Linux servers to provide database and web services for these applications. |
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November 1998– |
Undergraduate research, University of Kentucky CS department. Logic programming and nonmonotonic reasoning systems; distributed computing. Translation and conversion of logic programs to default theories. Analysis of logic programs, including stratification, well-founded semantics, and stable model semantics. Wrote a number of logic programs, many encoding graph-theoretical problems. Developed and optimized a distributed implementation of the stable model semantics using PVM (Parallel Virtual Machine). |
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June 1998– |
Teaching assistant, Institute for the Academic Advancement of Youth (IAAY), Johns Hopkins University. Served as a teaching assistant for two three-week sessions of IAAY's Center for Talented Youth (CTY) program. Assisted the instructor of a Digital Logic class for talented and gifted middle school and high school students. Prepared classroom materials, graded papers and exams, and supervised electronics laboratory assignments for approximately 30 students ranging in age from 13 to 16. |
I have performed volunteer work for the ACM International Collegiate Programming Contest (Mid-Central region, University of Kentucky Satellite site) for the past seven years now (since 2005). Tasks have included configuring and preparing the contest server, administering the PC^2 contest software, developing and preparing bootable live CDs providing a uniform and secure environment for contestants, and leading the troubleshooting and technical support team.
In addition to the core technical competencies listed above, I have wide-ranging experience with other technologies. I am eager to widen my experience, and am capable of learning programming languages, operating systems, and other software with minimal guidance.
R. A. Finkel, V. W. Marek, N. Moore and M. Truszczyński. Computing Stable Models in Parallel. In Answer Set Programming: Towards Efficient and Scalable Knowledge Representation and Reasoning. AAAI Press, Palo Alto, CA, pp. 72–76, 2001.
J. W. Jaromczyk and N. Moore. Geometric data structures for multihierarchical XML tagging of manuscripts. In Proc. 20th European Workshop on Computational Geometry. Seville, Spain, March 2004.
N. Moore. A Geometric Approach to Efficient Implementation of Concurrent XML Markup. Eastern Kentucky University 18th Annual Symposium in Mathematics, Statistical, and Computer Sciences. Richmond, KY, April 2004.
A. Dekhtyar, I. E. Iacob, J. W. Jaromczyk, K. Kiernan, N. Moore, and D. C. Porter. Database Support for Image-based Electronic Editions. Proc. Int'l Workshop on Multimedia Information Systems (MIS 2004). College Park, MD, August 2004.
J. W. Jaromczyk, M. Kowaluk, N. Moore. On Visualization of Complex Image-Based Markup. In Proc. Int'l Conf. on Computer Vision and Geometry. Warsaw, Poland, September 2004.
J. W. Jaromczyk, M. Kowaluk, N. Moore. A Web Interface to Image-Based Concurrent Markup Using Image Maps. In Proc. 6th ACM Int'l Workshop on Web Information and Data Management (WIDM 2004). Washington, DC, November 2004.
A. Dekhtyar, I. E. Iacob, J. W. Jaromczyk, K. Kiernan, N. Moore, D. C. Porter. Support for XML Markup of Image-based Electronic Editions. Int'l Journal on Digital Libraries 6(1): 55–69, 2006.
K. Kiernan, D. Porter, A. Dekhtyar, I. E. Iacob, J. W. Jaromczyk, N. Moore. The Edition Production Technology (EPT) and the ARCHway and Electronic Boethius Projects. 17th Joint International Conference of the Association for Computers and the Humanities and the Association for Literary and Linguistic Computing (ACH/ALLC). Victoria, BC, June 2005.
J. W. Jaromczyk, N. Moore. The ARCHway Software Infrastructure: a Demo of a Platform and Utilities for Building Applications for Electronic Editions. Demo at 17th Joint International Conference of the Association for Computers and the Humanities and the Association for Literary and Linguistic Computing (ACH/ALLC). Victoria, BC, June 2005.
A. Dekhtyar, I. E. Iacob, J. Jaromczyk, K. Kiernan, N. Moore, D. C. Porter. Building Image-based Electronic Editions using the Edition Production Technology. Poster at ACM/IEEE Joint Conference on Digital Libraries (JCDL 2005). Denver, CO, June 2005.
E. G. Arnaoudova, P. J. Bowens, R. G. Chui, R. D. Dinkins, U. Hesse, J. W. Jaromczyk, M. Martin, P. Maynard, N. Moore, C. L. Schardl. Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports. BMC Bioinformatics 10(S-7), 2009.
N. Moore. The Halting Problem and Undecidability of Document Generation under Access Control for Tree Updates. 3rd Int'l Conference on Language and Automata Theory and Applications (LATA 2009). Tarragona, Spain, April 2009.
E. G. Arnaoudova, J. W. Jaromczyk, N. Moore, C. L. Schardl, R. Yoshida. Phylotree—a toolkit for computing experiments with distance-based methods for genome coevolution. BMC Bioinformatics 11(S-4): P6, 2010.
E. G. Arnaoudova, D. C. Haws, P. Huggins, J. W. Jaromczyk, N. Moore, C. L. Schardl, R. Yoshida. Statistical phylogenetic tree analysis using differences of means. Frontiers in Neuroscience 4:47, 2010.
N. Moore. Reconciling two models of multihierarchical markup. 13th Int'l Workshop on the Web and Databases (WebDB 2010). Indianapolis, IN, June 2010.
N. Moore. Computational complexity of the problem of tree generation under fine-grained access control policies. J. Information and Computation 209(3): 548–567, 2011.
N. Moore, J.W. Jaromczyk. Finding a longest open reading frame of an alternatively spliced gene. In Proc. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Workshops, November 2011.
J.W. Jaromczyk, N. Moore, C.L. Schardl. A linear-time algorithm for finding a maximum-length ORF in a splice graph. Int'l J. of Computational Biology and Drug Design 5(3/4): 284–297, 2012.
R. J. O'Connell, M. R. Thon, S. Hacquard, S. G. Amyotte, J. Kleeman, M. F. Torres, U. Damm, E. A. Buiate, L. Eppstein, N. Alkan, J. Altmüller, L. Alvarado-Balderrama, C. A. Bauser, C. Becker, B. W. Birren, Z. Chen, J. Choi, J. A. Crouch, J. P. Duvick, M. A. Farman, P. Gan, D. Heiman, B. Henrissat, R. J. Howard, M. Kabbage, C. Koch, B. Kracher, Y. Kubo, A. D. Law, M.-H. Lebrun, Y.-H. Lee, I. Miyara, N. Moore, U. Neumann, K. Nordström, D. G. Panaccione, R. Panstruga, M. Place, R. H. Proctor, D. Prusky, G. Reich, R. Reinhardt, J. A. Rollins, S. Rounsley, C. L. Schardl, D. C. Schwartz, N. Shenoy, K. Shirasu, U. R. Sikhakolli, K. Stüber, S. A. Sukno, J. A. Sweigard, Y. Takano, H. Takahara, F. Trail, H. C. van der Does, L. M. Voll, I. Will, S. Young, Q. Zeng, J. Zhang, S. Zhou, M. B. Dickman, P. Schulze-Lefert, E. V. L. van Themaat, L.-J. Ma, L. J. Vaillancourt. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics 44(9):1060–5, 2012.
C. L. Schardl, C. A. Young, U. Hesse, S. G. Amyotte, K. Andreeva, P. J. Calie, D. J. Fleetwood, D. C. Haws, N. Moore, B. Oeser, D. G. Panaccione, K. K. Schweri, C. R. Voisey, M. L. Farman, J. W. Jaromczyk, B. A. Roe, D. M. O'Sullivan, B. Scott, P. Tudzynski, Z. An, E. G. Arnaoudova, C. T. Bullock, N. D. Charlton, L. Chen, M. Cox, R. D. Dinkins, S. Florea, A. E. Glenn, A. Gordon, U. Güldener, D. R. Harris, W. Hollin, J. Jaromczyk, R. D. Johnson, A. K. Khan, E. Leistner, A. Leuchtmann, C. Li, J. Liu, J. Liu, M. Liu, W. Mace, C. Machado, P. Nagabhyru, J. Pan, J. Schmid, K. Sugawara, U. Steiner, J. E. Takach, E. Tanaka, J. S. Webb, E. V. Wilson, J. L. Wiseman, R. Yoshida, Z. Zeng. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genetics 9(2), 2013.
C. L. Schardl, C.A. Young, N. Moore, N. Krom, P.-Y. Dupont, J. Pan, S. Florea, J. S. Webb, J. Jaromczyk, J. W. Jaromczyk, M. P. Cox, M. L. Farman. Genomes of plant-associated Clavicipitaceae. Advances in Botanical Research 70:291–327, 2014.
C. A. Young, C. L. Schardl, D. G. Panaccione, S. Florea, J. E. Takach, N. D. Charlton, N. Moore, J. S. Webb, J. Jaromczyk. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity. Toxins 7(4):1273–1302, 2015.
M. F. Torres, N. Ghaffari, E. A. S. Buiate, N. Moore, S. Schwartz, C. D. Johnson, L. J. Vaillancourt. A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction. BMC Genomics 8:17(1):202.Epub, 2016.