Search Results - "Frith, Martin C."

Adaptive seeds tame genomic sequence comparison by Kiełbasa, Szymon M, Wan, Raymond, Sato, Kengo, Horton, Paul, Frith, Martin C

“…The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern…”
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Significant non-existence of sequences in genomes and proteomes by Koulouras, Grigorios, Frith, Martin C

“…Abstract Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or proteome. Although some artificially synthesized MAWs have…”
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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads by Mitsuhashi, Satomi, Frith, Martin C, Mizuguchi, Takeshi, Miyatake, Satoko, Toyota, Tomoko, Adachi, Hiroaki, Oma, Yoko, Kino, Yoshihiro, Mitsuhashi, Hiroaki, Matsumoto, Naomichi

“…Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report…”
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Improved DNA-Versus-Protein Homology Search for Protein Fossils by Yao, Yin, Frith, Martin C.

“…Protein fossils, i.e., noncoding DNA descended from coding DNA, arise frequently from transposable elements (TEs), decayed genes, and viral integrations. They…”
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A survey of localized sequence rearrangements in human DNA by Frith, Martin C, Khan, Sofia

“…Abstract Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what…”
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Parameters for accurate genome alignment by Frith, Martin C, Hamada, Michiaki, Horton, Paul

“…Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and…”
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Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells by Mitsuhashi, Satomi, Nakagawa, So, Sasaki-Honda, Mitsuru, Sakurai, Hidetoshi, Frith, Martin C, Mitsuhashi, Hiroaki

“…Abstract Facioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle. DUX4 is a…”
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Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variants by Akamatsu, Shintaro, Mitsuhashi, Satomi, Soga, Kaima, Mizukami, Heisuke, Shiraishi, Makoto, Frith, Martin C, Yamano, Yoshihisa

“…Variants in mitochondrial genomes (mtDNA) can cause various neurological and mitochondrial diseases such as mitochondrial myopathy, encephalopathy, lactic…”
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A pipeline for complete characterization of complex germline rearrangements from long DNA reads by Mitsuhashi, Satomi, Ohori, Sachiko, Katoh, Kazutaka, Frith, Martin C, Matsumoto, Naomichi

“…Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number…”
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Inferring transcription factor complexes from ChIP-seq data by Whitington, Tom, Frith, Martin C, Johnson, James, Bailey, Timothy L

“…Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows researchers to determine the genome-wide binding locations of individual…”
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Long-read sequencing identifies the pathogenic nucleotide repeat expansion in RFC1 in a Japanese case of CANVAS by Nakamura, Haruko, Doi, Hiroshi, Mitsuhashi, Satomi, Miyatake, Satoko, Katoh, Kazutaka, Frith, Martin C, Asano, Tetsuya, Kudo, Yosuke, Ikeda, Takuya, Kubota, Shun, Kunii, Misako, Kitazawa, Yu, Tada, Mikiko, Okamoto, Mitsuo, Joki, Hideto, Takeuchi, Hideyuki, Matsumoto, Naomichi, Tanaka, Fumiaki

“…Recently, a recessively inherited intronic repeat expansion in replication factor C1 (RFC1) was identified in cerebellar ataxia with neuropathy and bilateral…”
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Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy by Mitsuhashi, Satomi, Nakagawa, So, Takahashi Ueda, Mahoko, Imanishi, Tadashi, Frith, Martin C., Mitsuhashi, Hiroaki

“…Subtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC…”
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Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population by Mitsuhashi, Satomi, Frith, Martin C, Matsumoto, Naomichi

“…Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. It is difficult to predict which tandem…”
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A code for transcription initiation in mammalian genomes by Frith, Martin C, Valen, Eivind, Krogh, Anders, Hayashizaki, Yoshihide, Carninci, Piero, Sandelin, Albin

“…Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian…”
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Evaluation and application of RNA-Seq by MinION by Seki, Masahide, Katsumata, Eri, Suzuki, Ayako, Sereewattanawoot, Sarun, Sakamoto, Yoshitaka, Mizushima-Sugano, Junko, Sugano, Sumio, Kohno, Takashi, Frith, Martin C, Tsuchihara, Katsuya, Suzuki, Yutaka

“…Abstract The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here,…”
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A mostly traditional approach improves alignment of bisulfite-converted DNA by Frith, Martin C, Mori, Ryota, Asai, Kiyoshi

“…Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use…”
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Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer by Suzuki, Ayako, Suzuki, Mizuto, Mizushima-Sugano, Junko, Frith, Martin C, Makalowski, Wojciech, Kohno, Takashi, Sugano, Sumio, Tsuchihara, Katsuya, Suzuki, Yutaka

“…Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes,…”
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Discovering sequence motifs with arbitrary insertions and deletions by Frith, Martin C, Saunders, Neil F W, Kobe, Bostjan, Bailey, Timothy L

“…BIOLOGY IS ENCODED IN MOLECULAR SEQUENCES: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein…”
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Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer-Giedion syndrome and Cornelia de Lange syndrome-4 by Lei, Ming, Liang, Desheng, Yang, Yifeng, Mitsuhashi, Satomi, Katoh, Kazutaka, Miyake, Noriko, Frith, Martin C, Wu, Lingqian, Matsumoto, Naomichi

“…Chromothripsis is a type of chaotic complex genomic rearrangement caused by a single event of chromosomal shattering and repair processes. Chromothripsis is…”
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Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum by Runtuwene, Lucky R., Tuda, Josef S. B., Mongan, Arthur E., Makalowski, Wojciech, Frith, Martin C., Imwong, Mallika, Srisutham, Suttipat, Nguyen Thi, Lan Anh, Tuan, Nghia Nguyen, Eshita, Yuki, Maeda, Ryuichiro, Yamagishi, Junya, Suzuki, Yutaka

“…Here, we report the application of a portable sequencer, MinION, for genotyping the malaria parasite Plasmodium falciparum . In the present study, an amplicon…”
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