@article{nunes_gowda_sailsbery_xue_chen_brown_oh_mitchell_dean_2011, title={Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae}, volume={12}, DOI={10.1186/1471-2164-12-288}, abstractNote={Abstract}, journal={BMC Genomics}, author={Nunes, C. C. and Gowda, M. and Sailsbery, J. and Xue, M. F. and Chen, F. and Brown, D. E. and Oh, Y. and Mitchell, T. K. and Dean, Ralph}, year={2011} }
 @misc{meng_brown_ebbole_torto-alalibo_oh_deng_mitchell_dean_2009, title={Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s8}, abstractNote={Abstract}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Brown, Douglas E. and Ebbole, Daniel J. and Torto-Alalibo, Trudy and Oh, Yeon Yee and Deng, Jixin and Mitchell, Thomas K. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @misc{oh_donofrio_pan_coughlan_brown_meng_mitchell_dean_2008, title={Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae}, volume={9}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2008-9-5-r85}, abstractNote={Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection. We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.}, number={5}, journal={GENOME BIOLOGY}, author={Oh, Yeonyee and Donofrio, Nicole and Pan, Huaqin and Coughlan, Sean and Brown, Douglas E. and Meng, Shaowu and Mitchell, Thomas and Dean, Ralph A.}, year={2008} }
 @article{meng_patel_heist_betts_tucker_galadima_donofrio_brown_mitchell_li_et al._2007, title={A systematic analysis of T-DNA insertion events in Magnaporthe oryzae}, volume={44}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2007.04.002}, abstractNote={We describe here the analysis of random T-DNA insertions that were generated as part of a large-scale insertional mutagenesis project for Magnaporthe oryzae. Chromosomal regions flanking T-DNA insertions were rescued by inverse PCR, sequenced and used to search the M. oryzae genome assembly. Among the 175 insertions for which at least one flank was rescued, 137 had integrated in single-copy regions of the genome, 17 were in repeated sequences, one had no match to the genome, and the remainder were unassigned due to illegitimate T-DNA integration events. These included in order of abundance: head-to-tail tandem insertions, right border excision failures, left border excision failures and insertion of one T-DNA into another. The left borders of the T-DNA were frequently truncated and inserted in sequences with micro-homology to the left terminus. By contrast the right borders were less prone to degradation and appeared to have been integrated in a homology-independent manner. Gross genome rearrangements rarely occurred when the T-DNAs integrated in single-copy regions, although most insertions did cause small deletions at the target site. Significant insertion bias was detected, with promoters receiving two times more T-DNA hits than expected, and open reading frames receiving three times fewer. In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Meng, Yan and Patel, Gayatri and Heist, Melanie and Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Donofrio, Nicole M. and Brown, Doug and Mitchell, Thomas K. and Li, Lei and et al.}, year={2007}, month={Oct}, pages={1050–1064} }
 @article{betts_tucker_galadima_meng_patel_li_donofrio_floyd_nolin_brown_et al._2007, title={Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae}, volume={44}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2007.05.001}, abstractNote={Towards the goal of disrupting all genes in the genome of Magnaporthe oryzae and identifying their function, a collection of >55,000 random insertion lines of M. oryzae strain 70-15 were generated. All strains were screened to identify genes involved in growth rate, conidiation, pigmentation, auxotrophy, and pathogenicity. Here, we provide a description of the high throughput transformation and analysis pipeline used to create our library. Transformed lines were generated either by CaCl2/PEG treatment of protoplasts with DNA or by Agrobacterium tumefaciens-mediated transformation (ATMT). We describe the optimization of both approaches and compare their efficiency. ATMT was found to be a more reproducible method, resulting in predominantly single copy insertions, and its efficiency was high with up to 0.3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Meng, Yan and Patel, Gayatri and Li, Lei and Donofrio, Nicole and Floyd, Anna and Nolin, Shelly and Brown, Doug and et al.}, year={2007}, month={Oct}, pages={1035–1049} }
 @article{donofrio_oh_lundy_pan_brown_jeong_coughlan_mitchell_dean_2006, title={Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea}, volume={43}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2006.03.005}, abstractNote={Efficient regulation of nitrogen metabolism likely plays a role in the ability of fungi to exploit ecological niches. To learn about regulation of nitrogen metabolism in the rice blast pathogen Magnaporthe grisea, we undertook a genome-wide analysis of gene expression under nitrogen-limiting conditions. Five hundred and twenty genes showed increased transcript levels at 12 and 48 h after shifting the fungus to media lacking nitrate as a nitrogen source. Thirty-nine of these genes have putative functions in amino acid metabolism and uptake, and include the global nitrogen regulator in M. grisea, NUT1. Evaluation of seven nitrogen starvation-induced genes revealed that all were expressed during rice infection. Targeted gene replacement on one such gene, the vacuolar serine protease, SPM1, resulted in decreased sporulation and appressorial development as well as a greatly attenuated ability to cause disease. Data are discussed in the context of nitrogen metabolism under starvation conditions, as well as conditions potentially encountered during invasive growth in planta.}, number={9}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Donofrio, N. M. and Oh, Y. and Lundy, R. and Pan, H. and Brown, D. E. and Jeong, J. S. and Coughlan, S. and Mitchell, T. K. and Dean, R. A.}, year={2006}, month={Sep}, pages={605–617} }
 @article{soderlund_haller_pampanwar_ebbole_farman_orbach_wang_wing_xu_brown_et al._2006, title={MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions}, volume={19}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI-19-1055}, abstractNote={ The MGOS (Magnaporthe grisea Oryza sativa) web-based database contains data from Oryza sativa and Magnaporthe grisea interaction experiments in which M. grisea is the fungal pathogen that causes the rice blast disease. In order to study the interactions, a consortium of fungal and rice geneticists was formed to construct a comprehensive set of experiments that would elucidate information about the gene expression of both rice and M. grisea during the infection cycle. These experiments included constructing and sequencing cDNA and robust long-serial analysis gene expression libraries from both host and pathogen during different stages of infection in both resistant and susceptible interactions, generating >50,000 M. grisea mutants and applying them to susceptible rice strains to test for pathogenicity, and constructing a dual O. sativa-M. grisea microarray. MGOS was developed as a central web-based repository for all the experimental data along with the rice and M. grisea genomic sequence. Community-based annotation is available for the M. grisea genes to aid in the study of the interactions. }, number={10}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Soderlund, Carol and Haller, Karl and Pampanwar, Vishal and Ebbole, Daniel and Farman, Mark and Orbach, Marc J. and Wang, Guo-Liang and Wing, Rod and Xu, Jin-Rong and Brown, Doug and et al.}, year={2006}, month={Oct}, pages={1055–1061} }
 @misc{rehmeyer_li_kusaba_kim_brown_staben_dean_farman_2006, title={Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae}, volume={34}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkl588}, abstractNote={Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the ∼2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions—out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.}, number={17}, journal={NUCLEIC ACIDS RESEARCH}, author={Rehmeyer, Cathryn and Li, Weixi and Kusaba, Motoaki and Kim, Yun-Sik and Brown, Doug and Staben, Chuck and Dean, Ralph and Farman, Mark}, year={2006}, month={Oct}, pages={4685–4701} }
 @article{payne_nierman_wortman_pritchard_brown_dean_bhatnagar_cleveland_machida_yu_2006, title={Whole genome comparison of Aspergillus flavus and A-oryzae}, volume={44}, ISSN={["1369-3786"]}, DOI={10.1080/13693780600835716}, abstractNote={Aspergillus flavus is a plant and animal pathogen that also produces the potent carcinogen aflatoxin. Aspergillus oryzae is a closely related species that has been used for centuries in the food fermentation industry and is Generally Regarded As Safe (GRAS). Whole genome sequences for these two fungi are now complete, providing us with the opportunity to examine any genomic differences that may explain the different ecological niches of these two fungi, and perhaps to identify pathogenicity factors in A. flavus. These two fungi are very similar in genome size and number of predicted genes. The estimated genome size (36·8 Mb) and predicted number of genes (12 197) for A. flavus is similar to that of A. oryzae (36·7 Mb and 12 079, respectively). These two fungi have significantly larger genomes than Aspergillus nidulans (30·1) and Aspergillus fumigatus (29·4). The A. flavus and A. oryzae genomes are enriched in genes for secondary metabolism, but do not differ greatly from one another in the predicted number of polyketide synthases, nonribosomal peptide synthases or the number of genes coding for cytochrome P450 enzymes. A micro-scale analysis of the two fungi did show differences in DNA correspondence between the two species and in the number of transposable elements. Each species has approximately 350 unique genes. The high degree of sequence similarity between the two fungi suggests that they may be ecotypes of the same species and that A. oryzae has resulted from the domestication of A. flavus.}, journal={MEDICAL MYCOLOGY}, author={Payne, G. A. and Nierman, W. C. and Wortman, J. R. and Pritchard, B. L. and Brown, D. and Dean, R. A. and Bhatnagar, D. and Cleveland, T. E. and Machida, Masayuki and Yu, J.}, year={2006}, month={Sep}, pages={S9–S11} }
 @article{cannon_crow_heuer_wang_cannon_dwan_lamblin_vasdewani_mudge_cook_et al._2005, title={Databases and information integration for the Medicago truncatula genome and transcriptome}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.104.059204}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Cannon, SB and Crow, JA and Heuer, ML and Wang, XH and Cannon, EKS and Dwan, C and Lamblin, AF and Vasdewani, J and Mudge, J and Cook, A and et al.}, year={2005}, month={May}, pages={38–46} }
 @article{donofrio_rajagopalon_brown_diener_windham_nolin_floyd_mitchell_galadima_tucker_et al._2005, title={PACLIMS: A component LIM system for high-throughput functional genomic analysis}, volume={6}, journal={BMC Bioinformatics}, author={Donofrio, N. and Rajagopalon, R. and Brown, D. and Diener, S. and Windham, D. and Nolin, S. and Floyd, A. and Mitchell, T. and Galadima, N. and Tucker, S. and et al.}, year={2005} }
 @article{dean_talbot_ebbole_farman_mitchell_orbach_thon_kulkarni_xu_pan_et al._2005, title={The genome sequence of the rice blast fungus Magnaporthe grisea}, volume={434}, ISSN={["1476-4687"]}, DOI={10.1038/nature03449}, abstractNote={Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.}, number={7036}, journal={NATURE}, author={Dean, RA and Talbot, NJ and Ebbole, DJ and Farman, ML and Mitchell, TK and Orbach, MJ and Thon, M and Kulkarni, R and Xu, JR and Pan, HQ and et al.}, year={2005}, month={Apr}, pages={980–986} }
 @inbook{altunay_brown_byrd_dean_2005, series={Lecture Notes in Computer Science}, title={Trust-Based Secure Workflow Path Construction}, volume={3826}, ISBN={9783540749738 9783540749745}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11596141_29}, DOI={10.1007/11596141_29}, abstractNote={Security and trust relationships between services significantly govern their willingness to collaborate and participate in a workflow. Existing workflow tools do not consider such relationships as an integral part of their planning logic: rather, they approach security as a run-time issue. We present a workflow management framework that fully integrates trust and security into the workflow planning logic. It considers not only trust relationships between the workflow requestor and individual services, but also trust relationships among the services themselves. It allows each service owner to define an upper layer of collaboration policies (rules that specify the terms under which participation in a workflow is allowed) and integrates them into the planning logic. Services that are unfit for collaboration due to security violations are replaced at the planning stage. This approach increases the services owners’ control over the workflow path, their willingness for collaboration, and avoids run-time security failures.}, booktitle={Service-Oriented Computing – ICSOC 2007}, publisher={Springer Berlin Heidelberg}, author={Altunay, M. and Brown, D. and Byrd, G. and Dean, R.}, editor={Benatallah, B. and Casati, F. and Traverso, P.Editors}, year={2005}, pages={382–395}, collection={Lecture Notes in Computer Science} }
 @misc{mitchell_thon_jeong_brown_deng_dean_2003, title={The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens}, volume={159}, ISSN={["0028-646X"]}, DOI={10.1046/j.1469-8137.2003.00787.x}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Mitchell, TK and Thon, MR and Jeong, JS and Brown, D and Deng, JX and Dean, RA}, year={2003}, month={Jul}, pages={53–61} }
 @article{foreman_brown_dankmeyer_dean_diener_dunn-coleman_goedegebuur_houfek_england_kelley_et al._2003, title={Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei}, volume={278}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M304750200}, abstractNote={The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.}, number={34}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Foreman, PK and Brown, D and Dankmeyer, L and Dean, R and Diener, S and Dunn-Coleman, NS and Goedegebuur, F and Houfek, TD and England, GJ and Kelley, AS and et al.}, year={2003}, month={Aug}, pages={31988–31997} }
 @article{martin_blackmon_rajagopalan_houfek_sceeles_denn_mitchell_brown_wing_dean_2002, title={MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea}, volume={30}, ISSN={["0305-1048"]}, DOI={10.1093/nar/30.1.121}, abstractNote={We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Martin, SL and Blackmon, BP and Rajagopalan, R and Houfek, TD and Sceeles, RG and Denn, SO and Mitchell, TK and Brown, DE and Wing, RA and Dean, RA}, year={2002}, month={Jan}, pages={121–124} }