@article{opperman_bird_williamson_rokhsar_burke_cohn_cromer_diener_gajan_graham_et al._2008, title={Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism}, volume={105}, ISSN={["1091-6490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54149092490&partnerID=MN8TOARS}, DOI={10.1073/pnas.0805946105}, abstractNote={
            We have established
            Meloidogyne hapla
            as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp,
            M. hapla
            represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The
            M. hapla
            genome encodes significantly fewer genes than does the free-living nematode
            Caenorhabditis elegans
            (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although
            M. hapla
            and
            C. elegans
            diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Opperman, Charles H. and Bird, David M. and Williamson, Valerie M. and Rokhsar, Dan S. and Burke, Mark and Cohn, Jonathan and Cromer, John and Diener, Steve and Gajan, Jim and Graham, Steve and et al.}, year={2008}, month={Sep}, pages={14802–14807} }
 @article{thon_pan_diener_papalas_taro_mitchell_dean_2006, title={The  role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae}, volume={7}, number={2}, journal={Genome Biology}, author={Thon, M. R. and Pan, H. Q. and Diener, S. and Papalas, J. and Taro, A. and Mitchell, T. K. and Dean, R. A.}, year={2006} }
 @article{diener_houfek_kalat_windham_burke_opperman_dean_2005, title={Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system}, volume={6}, journal={BMC Bioinformatics}, author={Diener, S. E. and Houfek, T. D. and Kalat, S. E. and Windham, D. E. and Burke, M. and Opperman, C. and Dean, R. A.}, year={2005} }
 @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{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei}, volume={230}, ISSN={["1574-6968"]}, DOI={10.1016/S0378-1097(03)00916-9}, abstractNote={Trichoderma reesei is a filamentous fungus widely used as an efficient protein producer and known to secrete large quantities of biomass degrading enzymes. Much work has been done aimed at improving the secretion efficiency of this fungus. It is generally accepted that the major bottlenecks in secretion are protein folding and ornamentation steps in this pathway. In an attempt to identify genes involved in these steps, the 5' ends of 21888 cDNA clones were sequenced from which a unique set of over 5000 were also 3' sequenced. Using annotation tools Gene Ontology terms were assigned to 2732 of the sequences. Homologs to the majority of Aspergillus niger's Srg genes as well as a number of homologs to genes involved in protein folding and ornamentation pathways were identified.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Diener, SE and Dunn-Coleman, N and Foreman, P and Houfek, TD and Teunissen, PJM and Solingen, P and Dankmeyer, L and Mitchell, TK and Ward, M and Dean, RA}, year={2004}, month={Jan}, pages={275–282} }
 @article{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei (vol 230, pg 275, 2004)}, volume={235}, DOI={10.1111/j.1574-6968.2004.tb09588.x}, number={1}, journal={FEMS Microbiology Letters}, author={Diener, S. E. and Dunn-Coleman, N. and Foreman, P. and Houfek, T. D. and Teunissen, P. J. M. and Solingen, P. Van and Dankmeyer, L. and Mitchell, T. K. and Ward, M. and Dean, Ralph}, year={2004}, pages={209} }
 @article{diener_chellappan_mitchell_dunn-coleman_ward_dean_2004, title={Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization}, volume={41}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2004.08.007}, abstractNote={Trichoderma reesei is an important industrial fungus known for its ability to efficiently secrete large quantities of protein as well as its wide variety of biomass degrading enzymes. Past research on this fungus has primarily focused on extending its protein production capabilities, leaving the structure of its 33 Mb genome essentially a mystery. To begin to address these deficiencies and further our knowledge of T. reesei's secretion and cellulolytic potential, we have created a genomic framework for this fungus. We constructed a BAC library containing 9216 clones with an average insert size of 125 kb which provides a coverage of 28 genome equivalents. BAC ends were sequenced and annotated using publicly available software which identified a number of genes not seen in previously sequenced EST datasets. Little evidence was found for repetitive sequence in T. reesei with the exception of several copies of an element with similarity to the Podospora anserina transposon, PAT. Hybridization of 34 genes involved in biomass degradation revealed five groups of co-located genes in the genome. BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results.}, number={12}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Diener, SE and Chellappan, MK and Mitchell, TK and Dunn-Coleman, N and Ward, M and Dean, RA}, year={2004}, month={Dec}, pages={1077–1087} }
 @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} }