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MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline
MitoFish contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses.
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods and has the potential to serve as an alternative tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families
A clade of open-ocean fishes containing Scombridae is named “Pelagia” in reference to the common habitat preference that links the 15 families, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm.
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data
- T. Fukunaga, Haruka Ozaki, G. Terai, K. Asai, W. Iwasaki, H. Kiryu
- BiologyGenome Biology
- 21 January 2014
Using CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context, it is demonstrated that several RBPs bind to their target RNA molecules under specific structural contexts.
MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding
- Yukuto Sato, M. Miya, T. Fukunaga, T. Sado, W. Iwasaki
- Environmental Science, BiologyMolecular biology and evolution
- 14 April 2018
Recent functional updates of MitoFish and implementation of MiFish pipeline for metabarcoding analysis of fish mitochondrial environmental DNA, which is a fast-emerging and powerful technology in fish studies are described.
RIblast: an ultrafast RNA–RNA interaction prediction system based on a seed-and-extension approach
RIblast is an ultrafast RNA‐RNA interaction prediction method based on the seed‐and‐extension approach that discovers seed regions using suffix arrays and subsequently extends seed regions based on an RNA secondary structure energy model.
LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data
“LncRRIsearch” is developed, which is a web server for comprehensive prediction of human and mouse lncRNA-lncRNA and lnc RNA-mRNA interaction and integrated tissue-specific expression and subcellular localization data for the lncRNAs with the web server.
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data
The results suggest that RAI can be used as an integrative and evidence-based tool for distinguishing between ribosome-associated and free lncRNAs, providing a valuable resource for the study of lncRNA functions.
GroupTracker: Video tracking system for multiple animals under severe occlusion
Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression
It is found TR4 nuclear receptor might alter the sunitinib resistance to RCC via altering the TR4/lncTASR/AXL signaling, and targeting this newly identified TR4-mediated signaling with small molecules, including tretinoin, metformin, orTR4-shRNAs, all led to increase the sun itinib sensitivity to better suppress the RCC progression.