A5076175043- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA Research and Splicing
- Machine Learning in Bioinformatics
- Natural Language Processing Techniques
- Cancer-related molecular mechanisms research
- Topic Modeling
- Genetic diversity and population structure
- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- Computational Drug Discovery Methods
- Gene expression and cancer classification
- Advanced Steganography and Watermarking Techniques
- Evolution and Genetic Dynamics
- Metal Forming Simulation Techniques
- Viral Infections and Immunology Research
- Genomics and Chromatin Dynamics
- Speech and dialogue systems
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- Microbial Metabolic Engineering and Bioproduction
- High-Velocity Impact and Material Behavior
- Text and Document Classification Technologies
- Protein Structure and Dynamics
Jichi Medical University
2024
Tokyo Denki University
2022-2023
Keio University
2012-2021
Tokushima University
2013-2014
Nara Institute of Science and Technology
2011-2012
The University of Tokyo
1997-2012
National Institute of Advanced Industrial Science and Technology
2008-2012
Kyoto University
2010-2011
Genome Institute of Singapore
2011
Chiba Institute of Technology
2011
Szymon M. Kiełbasa1, Raymond Wan2, Kengo Sato3, Paul Horton2 and Martin C. Frith2,4 Department of Computational Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany; Biology Research Center, Tokyo 135-0064, Japan; Graduate School Frontier Sciences, University Tokyo, Chiba 277-8561, Japan
Pseudoknots found in secondary structures of a number functional RNAs play various roles biological processes. Recent methods for predicting RNA cover certain classes pseudoknotted structures, but only few them achieve satisfying predictions terms both speed and accuracy.We propose IPknot, novel computational method with pseudoknots based on maximizing expected accuracy predicted structure. IPknot decomposes structure into set pseudoknot-free substructures approximates base-pairing...
Abstract Accurate predictions of RNA secondary structures can help uncover the roles functional non-coding RNAs. Although machine learning-based models have achieved high performance in terms prediction accuracy, overfitting is a common risk for such highly parameterized models. Here we show that be minimized when folding scores learnt using deep neural network are integrated together with Turner’s nearest-neighbor free energy parameters. Training model thermodynamic regularization ensures...
The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a application for RNA secondary structure prediction powered by one of the most accurate engine. accepts two kinds sequence data: single and multiple alignment sequences. It responses with result shown as popular base-pair notation graph representation. PDF version representation also available. For sequence, predicts common structure. Usage quite simple. You can paste (FASTA or plain text) (CLUSTAL-W format) into textarea...
Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds new drugs. Several models been developed by addressing the use of various kinds fingerprints and graph convolution architectures. However, these methods are either advantageous or disadvantageous depending on whether they (1) can distinguish structural differences including chirality compounds, (2) automatically discover features.We another model compound classification. In this...
Abstract Motivation: Recent studies have shown that the methods for predicting secondary structures of RNAs on basis posterior decoding base-pairing probabilities has an advantage with respect to prediction accuracy over conventionally utilized minimum free energy methods. However, there is room improvement in objective functions presented previous studies, which are maximized measures structures. Results: We propose novel estimators improve structure RNAs. The proposed maximize function...
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome program (assembler) not capable resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet an extension the assembler Velvet. It has proved to generate assemblies with higher N50 scores and quality than such as Velvet SOAPdenovo when applied frequently used this research community. One important open problem its low...
Abstract RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model pseudoknots, prediction methods considering not yet widely available. We developed IPknot, which uses heuristics speed up computations, but has remained difficult apply long sequences, such as messenger and viral RNA, because requires cubic computational time with respect...
Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number computational studies have so far devoted joint secondary structures or binding sites under specific class interactions. In general, there trade-off between range type and efficiency prediction algorithm, thus efficient methods for comprehensive are still awaited.We present RactIP,...
Abstract Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled production of target-gene knock-out (KO) NHP models. Target-gene-KO/knock-in (KI) efficiency CRISPR/Cas9 has not been extensively investigated in marmosets. In this study, optimum conditions target gene modification efficacies CRISPR/mRNA and CRISPR/nuclease marmoset embryos were examined. was more effective than avoiding mosaic genetic alteration....
Abstract Motivation: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it essentially harder than gene-finding problems for protein-coding because sequences do not have strong statistical signals. Since comparative sequence analysis effective detection, efficient methods are expected structural alignment sequences. Several been proposed to accomplish tasks sequences, and we found that one most important points estimate an...
Motivation: Since the whole genome sequences of many species have been determined, computational prediction RNA secondary structures and identification those non-coding regions by comparative genomics become important. Therefore, more advanced alignment methods are required. Recently, an approach structural for has introduced to solve these problems. Pair hidden Markov models on tree (PHMMTSs) proposed Sakakibara efficient automata-theoretic structures, although PHMMTSs incapable handling...
Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only improving limiting accuracy of conventional prediction but also finding non-coding RNAs in genomic sequences. Although there exist many algorithms sequences, further improvement still awaited. In this article, toward accuracy, a theoretical classification state-of-the-art presented. The based viewpoint maximum expected (MEA), which successfully applied various...
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically most stable with minimum free energy (MFE). For further improvement, an alternative based on machine learning techniques has been developed. The learning-based can employ fine-grained includes much richer feature representations ability to fit training data. Although achieved extremely high performance in prediction accuracy, possibility of risk overfitting...
Bacillus subtilis is the main component in fermentation of soybeans. To investigate genetics soybean-fermenting B. strains and its relationship with productivity extracellular poly-γ-glutamic acid (γPGA), we sequenced whole genome eight stains isolated from non-salted fermented soybean foods Southeast Asia. Assembled nucleotide sequences were compared those a natto (fermented food) starter strain BEST195 laboratory standard 168 that incapable γPGA production. Detected variants investigated...
The importance of accurate and fast predictions multiple alignments for RNA sequences has increased due to recent findings about functional non-coding RNAs. Recent studies suggest that maximizing the expected accuracy will be useful many problems in bioinformatics.We designed a novel estimator structured RNAs, based on predictions. First, we define maximum (MEA) pairwise alignment sequences. This maximizes sum-of-pairs score (SPS) predicted under probability distribution given by...
Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy from sequence still limited. In many cases, however, homologous are available with target whose secondary to be predicted.In article, we propose a new method for predictions individual by taking information their into account without assuming common entire sequences. The proposed based on posterior decoding techniques, which consider all suboptimal structures and...
Abstract Motivation: It is well known that the accuracy of RNA secondary structure prediction from a single sequence limited, and thus comparative approach predicts common aligned sequences better choice if homologous with reliable alignments are available. However, correct information needed to produce sequences. To tackle this dilemma, we require fast accurate aligner takes structural into consideration yield alignments, which suitable for prediction. Results: We develop DAFS, novel...
De novo microbial genome sequencing reached a turning point with third-generation (TGS) platforms, and several genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. Marburg 168, it has function in production of traditional Japanese fermented food “natto.” The BEST195 was previously sequenced short reads, but included some incomplete regions. We resequenced using PacBio RS sequencer, we successfully obtained complete...
Abstract The first draft of the common marmoset ( Callithrix jacchus ) genome was published by Marmoset Genome Sequencing and Analysis Consortium. based on whole-genome shotgun sequencing current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions supercontigs relatively short contigs that are unmapped to chromosomes in genome. We performed resequencing deep with high-throughput technology. Several different sequence runs using Illumina...
We present a web-based tool set Rtips for fast and accurate prediction of RNA 2D complex structures. comprises two computational tools based on integer programming, IPknot predicting secondary structures with pseudoknots RactIP RNA-RNA interactions kissing hairpins. Both servers can run much faster than existing services the same purpose large data sets as well being at least comparable in accuracy. The web server along stand-alone programs is freely accessible http://rna.naist.jp/.
Abstract Background Prediction of biochemical (metabolic) pathways has a wide range applications, including the optimization drug candidates, and elucidation toxicity mechanisms. Recently, several methods have been developed for pathway prediction to derive goal compound from start compound. However, these require high computational costs, cannot perform comprehensive novel metabolic pathways. Our aim this study is develop de novo method reconstructions predictions unknown biosynthetic in...