Search Results - "Kiryu, Hisanori"

Identification of oxidative stress-related genes differentially expressed in Alzheimer’s disease and construction of a hub gene-based diagnostic model by Zhang, Yanting, Kiryu, Hisanori

“…Alzheimer’s disease (AD) is the most prevalent dementia disorder globally, and there are still no effective interventions for slowing or stopping the…”
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SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation by Matsumoto, Hirotaka, Kiryu, Hisanori

“…Single-cell technologies make it possible to quantify the comprehensive states of individual cells, and have the power to shed light on cellular…”
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MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes by Zhang, Yanting, Kiryu, Hisanori

“…The identification of cancer subtypes can help researchers understand hidden genomic mechanisms, enhance diagnostic accuracy and improve clinical treatments…”
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SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation by Matsumoto, Hirotaka, Kiryu, Hisanori, Furusawa, Chikara, Ko, Minoru S H, Ko, Shigeru B H, Gouda, Norio, Hayashi, Tetsutaro, Nikaido, Itoshi

“…The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in…”
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Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome by Kawaguchi, Risa, Kiryu, Hisanori

“…RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural…”
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Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations by Kojima, Yasuhiro, Matsumoto, Hirotaka, Kiryu, Hisanori

“…Abstract Motivation Evolve and resequence (E&R) experiments show promise in capturing real-time evolution at genome-wide scales, enabling the assessment of…”
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Sufficient statistics and expectation maximization algorithms in phylogenetic tree models by KIRYU, Hisanori

“…Measuring evolutionary conservation is a routine step in the identification of functional elements in genome sequences. Although a number of studies have…”
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Prediction of RNA secondary structure using generalized centroid estimators by Hamada, Michiaki, Kiryu, Hisanori, Sato, Kengo, Mituyama, Toutai, Asai, Kiyoshi

“…Motivation: Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding of the base-pairing…”
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reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction by Kawaguchi, Risa, Kiryu, Hisanori, Iwakiri, Junichi, Sese, Jun

“…Recently, next-generation sequencing techniques have been applied for the detection of RNA secondary structures, which is referred to as high-throughput RNA…”
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A fast structural multiple alignment method for long RNA sequences by Tabei, Yasuo, Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi

“…Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm…”
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Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations by KIRYU, Hisanori, ASAI, Kiyoshi

“…Measuring the effects of base mutations is a powerful tool for functional and evolutionary analyses of RNA structures. To date, only a few methods have been…”
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Integrating dilution-based sequencing and population genotypes for single individual haplotyping by Matsumoto, Hirotaka, Kiryu, Hisanori

“…Haplotype information is useful for many genetic analyses and haplotypes are usually inferred using computational approaches. Among such approaches, the…”
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A detailed investigation of accessibilities around target sites of siRNAs and miRNAs by Kiryu, Hisanori, Terai, Goro, Imamura, Osamu, Yoneyama, Hiroyuki, Suzuki, Kenji, Asai, Kiyoshi

“…Motivation: The importance of RNA sequence analysis has been increasing since the discovery of various types of non-coding RNAs transcribed in animal cells…”
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TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column by Kiryu, Hisanori, Ichikawa, Yuto, Kojima, Yasuhiro

“…As the number of sequenced genomes grows, researchers have access to an increasingly rich source for discovering detailed evolutionary information. However,…”
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Murlet: a practical multiple alignment tool for structural RNA sequences by Kiryu, Hisanori, Tabei, Yasuo, Kin, Taishin, Asai, Kiyoshi

“…Motivation: Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken…”
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Rfold: an exact algorithm for computing local base pairing probabilities by Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi

“…Motivation: Base pairing probability matrices have been frequently used for the analyses of structural RNA sequences. Recently, there has been a growing need…”
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CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score by Hamada, Michiaki, Sato, Kengo, Kiryu, Hisanori, Mituyama, Toutai, Asai, Kiyoshi

“…Motivation: The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent findings about functional…”
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Predictions of RNA secondary structure by combining homologous sequence information by Hamada, Michiaki, Sato, Kengo, Kiryu, Hisanori, Mituyama, Toutai, Asai, Kiyoshi

“…Motivation: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction…”
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Generalized centroid estimators in bioinformatics by Hamada, Michiaki, Kiryu, Hisanori, Iwasaki, Wataru, Asai, Kiyoshi

“…In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that…”
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Robust prediction of consensus secondary structures using averaged base pairing probability matrices by Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi

“…Motivation: Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic…”
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