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Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
TLDR
The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus and revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. Expand
Genome sequencing and analysis of Aspergillus oryzae
TLDR
Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. Expand
A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
TLDR
In gonadal somatic cells, tj gives rise simultaneously to two different molecules: the TJ protein, which activates Piwi expression, and piRNAs, which define the Piwi targets for silencing. Expand
Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells
TLDR
These findings indicate that different types of small RNAs and Argonautes are used to repress retrotransposons in germline and somatic cells in Drosophila. Expand
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
TLDR
The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution, and a comparative study with Aspergillus fumigatus and As pergillus oryzae, used in the production of sake, miso and soy sauce, provides new insight into eukaryotic genome evolution and gene regulation. Expand
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
TLDR
IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers Pseudoknots, leading to the capability of modeling a wide class of pseudOKnots and running quite fast. Expand
PBSIM: PacBio reads simulator - toward accurate genome assembly
TLDR
A read simulator, PBSIM, is developed that captures characteristic features of PacBio reads using either a model-based or sampling-based method, suggesting that a continuous long reads coverage depth of at least 15 in combination with a circular consensus sequencing coveragedepth of at at least 30 achieved extensive assembly results. Expand
CentroidFold: a web server for RNA secondary structure prediction
TLDR
The CentroidFold web server is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine which scores the best accuracy in the authors' benchmark results. Expand
Marginalized kernels for biological sequences
TLDR
This work proposes a reasonable way of designing a kernel when objects are generated from latent variable models (e.g., HMM), and derives several marginalized kernels useful for biological sequences. Expand
Prediction of RNA secondary structure using generalized centroid estimators
TLDR
Novel estimators are proposed which improve the accuracy of secondary structure prediction of RNAs and represent extensions of the centroid estimators proposed in Ding et al. and Carvalho and Lawrence, and are applicable to a wide variety of problems in bioinformatics. Expand
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