1. A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly.

    Nature Genetics 47(4):405 (2015) PMID 25751626

    In Batesian mimicry, animals avoid predation by resembling distasteful models. In the swallowtail butterfly Papilio polytes, only mimetic-form females resemble the unpalatable butterfly Pachliopta aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry; h...
  2. Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation.

    BMC Genomics 16(1):80 (2015) PMID 25758444 PMCID PMC4334915

    Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dic...
  3. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

    Genome Research 24(8):1384 (2014) PMID 24755901 PMCID PMC4120091

    Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing d...
  4. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

    Genome Research 24(8):1384 (2014) PMID 24755901 PMCID PMC4120091

    Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing d...
  5. Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis.

    Development 141(14):2885 (2014) PMID 25005477

    Apoptosis is an important mechanism for sculpting morphology. However, the molecular cascades that control apoptosis in developing limb buds remain largely unclear. Here, we show that MafB was specifically expressed in apoptotic regions of chick limb buds, and MafB/cFos heterodimers repressed ap...
  6. Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis.

    Development 141(14):2885 (2014) PMID 25005477

    Apoptosis is an important mechanism for sculpting morphology. However, the molecular cascades that control apoptosis in developing limb buds remain largely unclear. Here, we show that MafB was specifically expressed in apoptotic regions of chick limb buds, and MafB/cFos heterodimers repressed ap...
  7. Sensory-neuron subtype-specific transcriptional programs controlling dendrite morphogenesis: genome-wide analysis of Abrupt and Knot/Collier.

    Developmental Cell 27(5):530 (2013) PMID 24290980

    The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of these isolated neurons. Their ...
  8. Sensory-Neuron Subtype-Specific Transcriptional Programs Controlling Dendrite Morphogenesis: Genome-wide Analysis of Abrupt and Knot/Collier

    Developmental Cell 27(5):530 (2013)

    The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of these isolated neuro...
  9. Sensory-Neuron Subtype-Specific Transcriptional Programs Controlling Dendrite Morphogenesis: Genome-wide Analysis of Abrupt and Knot/Collier

    Developmental Cell 27(5):530 (2013) PMID 24290980

    The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of these isolated neuro...
  10. Coelacanth genomes reveal signatures for evolutionary transition from water to land.

    Genome Research 23(10):1740 (2013) PMID 23878157 PMCID PMC3787270

    Coelacanths are known as "living fossils," as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish t...
  11. Coelacanth genomes reveal signatures for evolutionary transition from water to land.

    Genome Research 23(10):1740 (2013) PMID 23878157 PMCID PMC3787270

    Coelacanths are known as "living fossils," as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish t...
  12. Transcriptomic analysis of four developmental stages ofStrongyloides venezuelensis

    Parasitology International 62(1):57 (2013)

    Strongyloides venezuelensis is one of some 50 species of genus Strongyloides, obligate gastrointestinal parasites of vertebrates, responsible for strongyloidiasis in humans and other domestic/companion animals. Although S. venezuelensis has been widely used as a model species for study...
  13. Transcriptomic analysis of four developmental stages of Strongyloides venezuelensis.

    Parasitology International 62(1):57 (2013) PMID 23022620

    Strongyloides venezuelensis is one of some 50 species of genus Strongyloides, obligate gastrointestinal parasites of vertebrates, responsible for strongyloidiasis in humans and other domestic/companion animals. Although S. venezuelensis has been widely used as a model species for studying human/...
  14. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.

    Nature 489(7415):313 (2012) PMID 22885700 PMCID PMC3443318

    Cornelia de Lange syndrome (CdLS) is a dominantly inherited congenital malformation disorder, caused by mutations in the cohesin-loading protein NIPBL for nearly 60% of individuals with classical CdLS, and by mutations in the core cohesin components SMC1A (~5%) and SMC3 (<1%) for a smaller fract...
  15. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.

    Nature 489(7415):313 (2012) PMID 22885700 PMCID PMC3443318

    Cornelia de Lange syndrome (CdLS) is a dominantly inherited congenital malformation disorder, caused by mutations in the cohesin-loading protein NIPBL for nearly 60% of individuals with classical CdLS, and by mutations in the core cohesin components SMC1A (~5%) and SMC3 (<1%) for a smaller fract...
  16. Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases.

    Molecular Cell 45(5):696 (2012) PMID 22325992

    The S phase checkpoint pathway preserves genome stability by protecting defective DNA replication forks, but the underlying mechanisms are still understood poorly. Previous work with budding yeast suggested that the checkpoint kinases Mec1 and Rad53 might prevent collapse of the replisome when n...
  17. Replisome Stability at Defective DNA Replication Forks Is Independent of S Phase Checkpoint Kinases

    Molecular Cell 45(5):696 (2012)

    The S phase checkpoint pathway preserves genome stability by protecting defective DNA replication forks, but the underlying mechanisms are still understood poorly. Previous work with budding yeast suggested that the checkpoint kinases Mec1 and Rad53 might prevent collapse of the replis...
  18. Replisome Stability at Defective DNA Replication Forks Is Independent of S Phase Checkpoint Kinases

    Molecular Cell 45(5):696 (2012) PMID 22325992

    The S phase checkpoint pathway preserves genome stability by protecting defective DNA replication forks, but the underlying mechanisms are still understood poorly. Previous work with budding yeast suggested that the checkpoint kinases Mec1 and Rad53 might prevent collapse of the replis...
  19. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem.

    PLoS ONE 7(1):e30559 (2012) PMID 22303444 PMCID PMC3267732

    A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of prot...
  20. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem.

    PLoS ONE 7(1):e30559 (2012) PMID 22303444 PMCID PMC3267732

    A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of prot...