A5025857432- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Advanced biosensing and bioanalysis techniques
- Chromosomal and Genetic Variations
- Asthma and respiratory diseases
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- RNA regulation and disease
- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Cancer, Hypoxia, and Metabolism
- Cancer Genomics and Diagnostics
- Therapeutic Uses of Natural Elements
- Total Knee Arthroplasty Outcomes
- Respiratory and Cough-Related Research
- Peripheral Nerve Disorders
- Genetic Mapping and Diversity in Plants and Animals
- Neuropeptides and Animal Physiology
National Institute of Advanced Industrial Science and Technology
2016-2025
Waseda University
2016-2025
Nippon Medical School
2017-2025
Okayama University Hospital
2003-2025
Hitachi (Japan)
2024
Okayama University
1993-2024
The University of Tokyo
2008-2022
Nippon Medical School Hospital
2022
Osaka University
2014
Information and Mathematical Science and Bioinformatics (Japan)
2012
Abstract Motivation: PacBio sequencers produce two types of characteristic reads (continuous long reads: and high error rate circular consensus sequencing: short low rate), both which could be useful for de novo assembly genomes. Currently, there is no available simulator that targets the specific generation libraries. Results: Our analysis 13 datasets showed features (e.g. read length follows a log-normal distribution). We have developed simulator, PBSIM, captures these using either...
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...
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...
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...
Genome sequence alignments form the basis of much research. alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters use. Surprisingly, there has been no large-scale assessment these choices using real genomic data. Moreover, rigorous procedures control rate spurious have not employed. We assessed 495 combinations for animal, plant, fungal genomes. As our gold-standard accuracy, we used genome implied by multiple proteins structural...
N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As type of post-transcriptional methylation, m6A plays an important role diverse activities such as alternative splicing, interplay with microRNAs translation efficiency. Although existing tools can predict at single-base resolution, it still challenging to extract the biological information surrounding sites.We implemented deep learning framework, named DeepM6ASeq, m6A-containing...
Recent advances in high-throughput long-read sequencers, such as PacBio and Oxford Nanopore produce longer reads with more errors than short-read sequencers. In addition to the high error rates of reads, non-uniformity leads difficulties various downstream analyses using long reads. Many useful simulators, which characterize patterns simulate them, have been developed. However, there is still room for improvement simulation errors.To capture characteristics here, we introduce a generative...
Long non-coding RNAs (lncRNAs) play critical roles in various biological processes, but the function of majority lncRNAs is still unclear. One approach for estimating a lncRNA identification its interaction target because functions are expressed through with other biomolecules quite few cases. In this paper, we developed "LncRRIsearch," which web server comprehensive prediction human and mouse lncRNA-lncRNA lncRNA-mRNA interaction. The was conducted using RIblast, fast accurate RNA-RNA tool....
LncRNAs play important roles in various biological processes. Although more than 58 000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterized. One approach to understanding the functions of is detection interacting RNA target each lncRNA. Because experimental detections comprehensive lncRNA-RNA interactions difficult, computational prediction an indispensable technique. However, high costs existing RNA-RNA interaction tools prevent their application...
Abstract Nucleic acid aptamers are generated by an in vitro molecular evolution method known as systematic of ligands exponential enrichment (SELEX). Various candidates limited actual sequencing data from experiment. Here we developed RaptGen, which is a variational autoencoder for silico aptamer generation. RaptGen exploits profile hidden Markov model decoder to represent motif sequences effectively. We showed that embedded simulation sequence into low-dimensional latent space on the basis...
Long-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have improved their read length accuracy, thereby opening up unprecedented research. Many tools algorithms been developed to analyze long reads, rapid progress in PacBio ONT has further accelerated development. Together with the development of high-throughput sequencing technologies analysis tools, many simulators effectively utilized. PBSIM is one popular long-read simulators. In this study, we...
The accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult interpret require additional information sequences. Bidirectional encoder representations from transformer (BERT) is a language-based deep model that highly interpretable. Therefore, based on BERT architecture can potentially overcome such limitations.
Idiopathic pulmonary fibrosis (IPF) causes remodeling of the distal lung. Pulmonary is histologically characterized by fibrosis, as well appearance basal cells; however, involvement cells in IPF remains unclear. Here, we focus on long noncoding RNA MIR205HG, which highly expressed cells, using sequencing. Through sequencing genetic manipulations primary and organoids, discovered that MIR205HG regulates IL-33 expression. Mechanistically, AluJb element plays a key role Additionally, identified...
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,...
LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent PacBio RS, we show reduces reference bias for Oxford Nanopore reads.the source code is freely available at http://last.cbrc.jp/.mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp.Supplementary data are Bioinformatics online.
Although the number of discovered long non-coding RNAs (lncRNAs) has increased dramatically, their biological roles have not been established. Many recent studies used ribosome profiling data to assess protein-coding capacity lncRNAs. However, very little work done identify ribosome-associated lncRNAs, here defined as lncRNAs interacting with ribosomes related protein synthesis well other unclear functions. On average, 39.17% expressed were observed interact in human and 48.16% mouse. We...
Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few them been identified with their functions. Identification the interaction target is an important step predicting The current experimental methods to identify RNA–RNA interactions, however, not fast enough apply whole human transcriptome. Therefore, computational predictions interactions desirable, this challenging task due huge costs involved. Here, we report comprehensive targets...
It has been recently suggested that transposable elements (TEs) are re-used as functional of long non-coding RNAs (lncRNAs). This is supported by some examples such the human endogenous retrovirus subfamily H (HERVH) contained within lncRNAs and expressed specifically in embryonic stem cells (hESCs), required to maintain hESC identity. There at least two unanswered questions about all lncRNAs. How many TEs lncRNAs? Are there any other affect tissue specificity lncRNA expression? To answer...
Emerging evidence supports the hypothesis that multicellular tumor clusters invade and seed metastasis. However, whether tumor-associated stroma induces epithelial–mesenchymal plasticity in cell clusters, to promote invasion metastasis, remains unknown. We demonstrate herein carcinoma-associated fibroblasts (CAFs) frequently present drive formation of composed two distinct cancer populations, one a highly epithelial (E-cadherin hi ZEB1 lo/neg : E ) state another hybrid epithelial/mesenchymal...