@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{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{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} }