1. Missed Hospital Appointments of Patients Receiving Ranibizumab Therapy for Neovascular Age-Related Macular Degeneration.

    Ophthalmology and Therapy 4(1):43 (2015) PMID 25769782 PMCID PMC4470979

    The aim of this study was to investigate the frequency and duration of missed hospital appointments (MHAs) in a consecutive cohort of patients treated with ranibizumab for neovascular age-related macular degeneration (nAMD) and to assess their impact on outcomes of therapy in a real-world clinic...
  2. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.

    PNAS 112(11):3451 (2015) PMID 25733908 PMCID PMC4371944

    Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely ...
  3. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

    Current Biology 25(5):613 (2015) PMID 25660540

    Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mec...
  4. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor.

    Current Biology 25(5):613 (2015) PMID 25660540

    Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms th...
  5. Irinophore C™, a lipid nanoparticulate formulation of irinotecan, improves vascular function, increases the delivery of sequentially administered 5-FU in HT-29 tumors, and controls tumor growth in patient derived xenografts of colon cancer.

    Journal of Controlled Release 199:72 (2015) PMID 25497312

    A liposomal formulation of irinotecan, Irinophore C™ (IrC™) is efficacious in a panel of tumor models, normalizes tumor vasculature, and increases the accumulation of a second drug in the same tumor. We now show that Irinophore C™ is also effective against patient derived xenografts (PDX) of col...
  6. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

    Current Biology (2014)

    • The plant galling Mayetiola destructor genome is replete with effector genes • The SSGP-71 effector gene family is the largest known arthropod gene family. ...
  7. The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola.

    BMC Genomics 15(1):1132 (2014) PMID 25519841

    In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determini...
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  8. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.

    Biology 3(2):295 (2014) PMID 24833511 PMCID PMC4085609

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs ...
  9. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.

    Biology 3(2):295 (2014) PMID 24833511 PMCID PMC4085609

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs ...
  10. Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease.

    International Journal of Systematic and Evoluti... 63(Pt 6):2146 (2013) PMID 23104363

    Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99% sequence similarity) to Corynebacterium pseudodiphtheriticum. The two species are very similar biochemically, commonly dif...
  11. Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease.

    International Journal of Systematic and Evoluti... 63(Pt 6):2146 (2013) PMID 23104363

    Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99% sequence similarity) to Corynebacterium pseudodiphtheriticum. The two species are very similar biochemically, commonly dif...
  12. The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.

    BMC Genomics 14:686 (2013) PMID 24093210 PMCID PMC3852528

    Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium...
  13. Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

    BMC Genomics 14:502 (2013) PMID 23883295 PMCID PMC3726317

    Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characteriz...
  14. The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.

    BMC Genomics 14:686 (2013) PMID 24093210 PMCID PMC3852528

    Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium...
  15. Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

    BMC Genomics 14:502 (2013) PMID 23883295 PMCID PMC3726317

    Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characteriz...
  16. Functional and structural divergence of an unusual LTR retrotransposon family in plants.

    PLoS ONE 7(10):e48595 (2012) PMID 23119066 PMCID PMC3485330

    Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to O...
  17. Functional and structural divergence of an unusual LTR retrotransposon family in plants.

    PLoS ONE 7(10):e48595 (2012) PMID 23119066 PMCID PMC3485330

    Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to O...
  18. Genome sequence of the palaeopolyploid soybean.

    Nature 463(7278):178 (2010) PMID 20075913

    Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physi...
  19. Genome sequence of the palaeopolyploid soybean.

    Nature 463(7278):178 (2010) PMID 20075913

    Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physi...
  20. A lineage-specific centromere retrotransposon in Oryza brachyantha.

    Plant Journal 60(5):820 (2009) PMID 19702667

    Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elem...