I have a strong interdisciplinary background based on six years of experience in the field of Bioinformatics, on an academic and industrial basis, and 25+ years of expertise in the computer field. I have actively participated in the generation, annotation, and analysis of genome information, via high throughput large-scale computational techniques, for five biological systems. My current research interests are in the areas of systems biology for the manipulation of biological systems, graph theoretic data mining, and workflows in distributed computing environments.
Framingham State College, Individualized Major, B.S.,1993
A multidisciplinary custom degree focused on the applications of Artificial Intelligence to computer based educational systems, that encompassed the equivalent of minors in mathematics, communications, psychology, and a one-year research project producing a prototype system.
Professional Positions
2001–present, Bioinformatics lead - Fungal Genomics Laboratory, North Carolina State University
Provided leadership in determining the direction for the development and technical support team of a genomic research laboratory and center. Supported the research objectives of more than 20 active wet lab research scientists. Research activities spanned full range of computational genomics including multiple whole genome DNA sequence projects, genome annotation, evolutionary analyses, coding and non-coding models,RNA, biochemical pathway analysis, etc. Collaborated with researchers on a national, international, and local level. Senior personnel and/or collaborator on multiple multi-institution research grants. Responsible for writing research grant proposals, training and supervising computing systems support personnel, providing training on the use and manipulation of databases and related systems, directing and collaborating extensively with other personnel to design and execute research efforts, written and verbal communication on project progress and status to local and national agencies, software and hardware purchases and upgrades, mentoring and oversight of graduate students and post-doctoral researchers. Implemented a grid oriented multiple whole genome comparative analysis system, multiple high-throughput bioinformatics tools, genomic databases, web applications, and other support tools. Integrated and manipulated various types of data from different software packages into a comprehensive matrix.
1987 – present, Consulting software engineer - Small System Solutions
Industrial consulting for multiple companies. Activities and projects include: corporate representative in international standards; client-server systems’ management solutions, B2 level operating system security validation; Unix and VMS kernel coding and validation; WWW interfaces; operating system fault analysis; multi-thread parallel programming; cluster computing; high volume RDB development and optimization; network development and administration; user interface/human factors; and Project management.
1980 – 1987, Software engineer - Digital equipment Corp.
Multiple positions involving: advanced research and development in educational computing technologies; development of Computer Aided Instructional systems; Computer Automated Manufacturing for factory floor control; and general MIS programming.
1979 – 1979, Computer science instructor - Newton C.E.T.A.
Instruction of students in the fundamentals of computer science with emphasis on business applications using Basic Plus and Cobol. Determined and implemented class and lab structure.
Senior Personnel –Whole Genome Sequencing of the soil fungus Rhizoctonia solani anastomosis group 3 (AG-3). Co-sponsored U.S. Department of Agriculture/National Science Foundation, Microbial Genome Sequencing Program. Awarded 2007.
Collaborator – Plant Associated Microbes Gene Ontology (PAMGO), U.S. Department of Agriculture, Microbial Genome Sequencing Program. Awarded 2005.
Collaborator – Wheat stem rust fungus genome sequencing project, U.S. Department of Agriculture, Microbial Genome Sequencing Program. Awarded 2004.
Collaborator - Finishing the draft genome of Magnaporthe grisea, Co-Sponsored National Science Foundation / U.S. Department of Agriculture, Microbial Genome Sequencing Program. Awarded 2003.
Collaborator – Whole Genome Sequence and Assembly of Aspergillus flavus, U.S. Department of Agriculture Initiative. Awarded 2003.
Senior Personnel - High Throughput Comparative Genomic Analysis Using Grids, University of North Carolina, Office of the President. Awarded 2002.
Senior Personnel - Whole genome analysis of pathogen-host recognition and subsequent responses in the rice blast patho system, National Science Foundation Plant Genome Research Program. Awarded 2001.
Collaborator – Genome Sequence of Magnaporthe grisea, U.S. Department of Agriculture. Awarded 2001.
Collaborator - Gene discovery in the rice blast fungus: ESTs and the sequence of chromosome 7, U.S. Department of Agriculture Initiative for Future Agriculture and Food Systems Program. Awarded 2000.
Collaborator - Durable resources for discovery and development of new gene products from Trichoderma reesei and Aspergillus niger, Contract with Genecor International. Awarded 2000.
Publications
Meng S, Brown D, Ebbole D, Torto-Alalibo T, Oh Y, Deng J,
Mitchell T, Dean R. GeneOntology annotation ofthe rice blast fungus.
Magnaporthe oryzae. BMC Microbiology (in press).
Brown D, Powell A, Carbone I, Dean R. GT-Miner: a
graph-theoretic data miner, viewer, and model processor. Bioinformation
2008, V3(5), p235-237.
Smith CA, Robertson D, Yates B, Nielsen DM, Brown D, Dean RA, Payne GA. The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Curr Genet. 2008 V54(5):241-69
Betts MF, Tucker SL, Galadima N, Meng Y, Patel G, Li L, Donofrio N, Floyd A, Nolin S, Brown D, Mandel MA, Mitchell TK, Xu JR, Dean RA, Farman ML, Orbach MJ. Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae. Fungal Genet Biol. 2007; May 18;
Meng Y, Patel G, Heist M, Betts MF, Tucker SL, Galadima N, Donofrio NM, Brown D, Mitchell TK, Li L, Xu JR, Orbach M, Thon M, Dean RA, Farman ML. A systematic analysis of T-DNA insertion events in Magnaporthe oryzae. Fungal Genet Biol. 2007; Apr 13.
Soderlund C, Haller K, Pampanwar V, Ebbole D, Farman M, Orbach MJ, Wang GL, Wing R, Xu JR, Brown D, Mitchell T, Dean R. MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions. Mol Plant Microbe Interact. 2006; Oct;19(10):1055-61.
Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, Dean RA, Bhatnagar D, Cleveland TE, Machida M, Yu J. Whole genome comparison of Aspergillus flavus and A. oryzae. Medical Mycology 2006; 44:1-3.
Altunay M, Brown DE, Byrd GT, Dean RA. Collaboration Policies: Access Control Management in Decentralized Heterogeneous Workflows. Journal of Software 2006;V1(1).
Altunay M, Brown D, Byrd G, Dean R. Trust-Based Secure Workflow Path Construction. ICSOC 2005;382-395.
Donofrio N, Oh Y, Lundy R, Pan H, Brown D, Jeong J, Coughlan S, Mitchell T, Dean R. Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea. Fungal genetics and biology 2006;43 (9):605-617.
Rehmeyer C, Li W, Kusaba M, Kim YS, Brown D, Staben C, Dean R, Farman M. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Research 2006;34(17):4685-4701.
Donofrio N, Rajagopalon R, Brown D, Diener S, Windham D, Nolin S, Floyd A, Mitchell T, Galadima N, Tucker S, Orbach MJ, Patel G, Farman M, Pampanwar V, Soderlund C, Lee YH, Dean RA, PACLIMS: A component LIM system for high-throughput functional genomic analysis. BMC Bioinformatics 2005;6:94.
Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun MH, Bohnert H, CoughlanS, Butler J, Calvo S, Ma LJ, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 2005;434:980-986.
Altunay M, Brown DE, Byrd G. Encapsulation of Grid Information Services to Assess Secure Client Access. GlobusWorld 2005; Boston.
Altunay M, Brown DE, Dean RA, Byrd G. Evaluation of Mutual Trust during Matchmaking. IEEE Peer to Peer conference 2005; Zurich.
Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, CookA, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF. Databases and Information Integration for the Medicago truncatula Genome and Transcriptome. Plant Physiology 2005;138:38-46.
Mitchell TK, Thon MR, Jeong JS, Brown DE, Deng J, Dean RA. The rice blast patho system as a case study for the development of new tools and raw materials for genome analysis of fungal pathogens. New Phytologist 2003;159:53-61.
Foreman PK, Brown D, Dankmeyer L, Dean R, Diener S, Dunn-Coleman NS, Goedegebuur F, Houfek TD, England GJ, Kelley A, Meerman HJ, Mitchell T, Mitchinson C, Olivares HA, Teunissen P, Yao J, Ward M. Synthesis and Regulation of Biomass-degrading Enzymes in the Filamentous Fungus Trichoderma reesei. J Biol Chem. 2003;Aug 22;278(34):31988-97.
Martin SL, Blackmon B, Rajagopalan R, Houfek TD, Sceeles RG, Denn SO, Mitchell TK, Brown DE, Wing RA, Dean RA. MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea. Nucleic Acids Research, 2002;30:121-124.
Carbone I, Ramirez-Prado JH, Jakobek JL, Horn BW. Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC Evolutionary Biology 2007; 7:111.
Price EW, Carbone I. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics, 2005;21(3):402-404.
Altunay M, Colonnese D, Warade C. Web services for bioinformatics, IBM Developer Works, 2004.Altunay M, Colonnese D, and Warade, C. High throughput Web services for life sciences. International Conference on Information Technology: Coding and Computing, ITCC 2005;1(4-6) 329-334.
Meng S, Brown DE, Tyler B, Mitchell TK, and Dean RA. A GO annotation database for the rice blast fungus Magnaporthe grisea, Phytopathology 2007;97:S75, APS Annual Meeting Poster.
Selvadurai SB, Brown DE, Byrd GT. Lightweight Web-Service Wrapper for Command-Line Programs. International Conference on the Virtual Computing Initiative 2007.
Powell AJ, Conant GC, Carbone I, Evangelisti AM, Brown DE, Dean RA.
Gene duplication in fungal pathogenesis. APS/MSA Joint Meeting, 2006.
Payne GA, Pritchard BL, Brown D, Yu J, Nierman WC, Dean RA, Bhatnagar D, Cleveland TE, Machida M. Whole genome comparison of A. flavus and A. oryzae. Athens, Greece. February 22 – 25, 2006.
Pritchard BL, Yu JJ, Wortman J, Fedorova N, Machida M, Gomi K, Abe K, Dean RA, Bhatnagar D, Cleveland TE, Nierman W, Brown DE, Payne GA. Genome comparisons between A. flavus and A. oryzae reveal unique genes. 8th European Congress on Fungal Genetic. April 8-11, 2006.
Payne GA, Yu JJ, Woloshuk CP, Wortman JR, Fedorova N, Machida M, Brown DE, Dean RA, Bhatnagar D, Cleveland TE, Nierman WC. Comparative Genomics of Aspergillus flavus. World Mycotoxin Forum. Cleveland, OH. November 5-8, 2006.
Lamblin AF, Dwan CM, Brown DE, Freeman JL, Roe BA, Cook DR, Young ND, VandenBosch KA, Retzel EF. Automated annotation and display of Medicago truncatula genome sequence data using ensemble. Plant & Animal Genomes XI Conference 2004;
Brown D, Thon M, Byrd G, Rajagopalan R, Dean RA. DECIFR: a high throughput, grid based, comparative genomic analysis system. Plant & Animal Genomes XI Conference, 2003.