1. Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity.

    Nature 523(7559):231 (2015) PMID 25970248

    Melanoma treatment is being revolutionized by the development of effective immunotherapeutic approaches. These strategies include blockade of immune-inhibitory receptors on activated T cells; for example, using monoclonal antibodies against CTLA-4, PD-1, and PD-L1 (refs 3-5). However, only a sub...
  2. 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...
  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 mechanisms th...
  4. 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. ...
  5. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.

    Cancer Informatics 13(Suppl 2):67 (2014) PMID 25288881 PMCID PMC4179624

    The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-eff...
  6. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.

    Cancer Informatics 13(Suppl 2):67 (2014) PMID 25288881 PMCID PMC4179624

    The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-eff...
  7. Analysis and correction of crosstalk effects in pathway analysis.

    Genome Research 23(11):1885 (2013) PMID 23934932 PMCID PMC3814888

    Identifying the pathways that are significantly impacted in a given condition is a crucial step in understanding the underlying biological phenomena. All approaches currently available for this purpose calculate a P-value that aims to quantify the significance of the involvement of each pathway ...
  8. Analysis and correction of crosstalk effects in pathway analysis.

    Genome Research 23(11):1885 (2013) PMID 23934932 PMCID PMC3814888

    Identifying the pathways that are significantly impacted in a given condition is a crucial step in understanding the underlying biological phenomena. All approaches currently available for this purpose calculate a P-value that aims to quantify the significance of the involvement of each pathway ...
  9. Parallel duplication and partial subfunctionalization of β-catenin/armadillo during insect evolution.

    Molecular Biology and Evolution 29(2):647 (2012) PMID 21890476 PMCID PMC3283115

    β-Catenin is a multifunctional scaffolding protein with roles in Wnt signaling, cell adhesion, and centrosome separation. Here, we report on independent duplications of the insect β-Catenin ortholog armadillo (arm) in the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum...
  10. Parallel duplication and partial subfunctionalization of β-catenin/armadillo during insect evolution.

    Molecular Biology and Evolution 29(2):647 (2012) PMID 21890476 PMCID PMC3283115

    β-Catenin is a multifunctional scaffolding protein with roles in Wnt signaling, cell adhesion, and centrosome separation. Here, we report on independent duplications of the insect β-Catenin ortholog armadillo (arm) in the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum...
  11. Detecting phenotype-specific interactions between biological processes from microarray data and annotations.

    Computational Biology and Bioinformatics, IEEE/... 9(5):1399 (2012) PMID 22547431 PMCID PMC3748606

    High throughput technologies enable researchers to measure expression levels on a genomic scale. However, the correct and efficient biological interpretation of such voluminous data remains a challenging problem. Many tools have been developed for the analysis of GO terms that are over- or under...
  12. Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave.

    Journal of Experimental Biology 214(Pt 21):3532 (2011) PMID 21993781

    Obligatory cave species exhibit dramatic trait modifications such as eye reduction, loss of pigmentation and an increase in touch receptors. As molecular studies of cave adaptation have largely concentrated on vertebrate models, it is not yet possible to probe for genetic universalities underlyi...
  13. Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave.

    Journal of Experimental Biology 214(Pt 21):3532 (2011) PMID 21993781

    Obligatory cave species exhibit dramatic trait modifications such as eye reduction, loss of pigmentation and an increase in touch receptors. As molecular studies of cave adaptation have largely concentrated on vertebrate models, it is not yet possible to probe for genetic universalities underlyi...
  14. The Pax gene eyegone facilitates repression of eye development in Tribolium.

    EvoDevo 2(1):8 (2011) PMID 21463500 PMCID PMC3082225

    The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes,...
  15. The Pax gene eyegone facilitates repression of eye development in Tribolium.

    EvoDevo 2(1):8 (2011) PMID 21463500 PMCID PMC3082225

    The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes,...
  16. Probing the Drosophila retinal determination gene network in Tribolium (I): The early retinal genes dachshund, eyes absent and sine oculis.

    Developmental Biology 333(1):202 (2009) PMID 19324029

    The early retinal genes dachshund (dac), eyes absent (eya) and sine oculis (so) are key regulators of adult eye development in Drosophila. Expression data implicate homologs of all three transcription factor genes in vertebrate eye development. However, functional confirmation has thus far only ...
  17. Probing the Drosophila retinal determination gene network in Tribolium (I): The early retinal genes dachshund, eyes absent and sine oculis.

    Developmental Biology 333(1):202 (2009) PMID 19324029

    The early retinal genes dachshund (dac), eyes absent (eya) and sine oculis (so) are key regulators of adult eye development in Drosophila. Expression data implicate homologs of all three transcription factor genes in vertebrate eye development. However, functional confirmation has thus far only ...
  18. Molecular evolution of the Drosophila retinome: exceptional gene gain in the higher Diptera.

    Molecular Biology and Evolution 26(6):1273 (2009) PMID 19252076

    Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene s...
  19. Molecular evolution of the Drosophila retinome: exceptional gene gain in the higher Diptera.

    Molecular Biology and Evolution 26(6):1273 (2009) PMID 19252076

    Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene s...
  20. Probing theDrosophilaretinal determination gene network inTribolium(I): The early retinal genesdachshund,eyes absentandsine oculis

    Developmental Biology 333(1):202 (2009)

    The early retinal genes dachshund ( dac), eyes absent ( eya) and sine oculis ( so) are key regulators of adult eye development in Drosophila. Expression data implicate homologs of all three transcription factor genes in vertebrate eye developmen...