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Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy.
Ishiura H, Doi K, Mitsui J, Yoshimura J, Matsukawa MK, Fujiyama A, Toyoshima Y, Kakita A, Takahashi H, Suzuki Y, Sugano S, Qu W, Ichikawa K, Yurino H, Higasa K, Shibata S, Mitsue A, Tanaka M, Ichikawa Y, Takahashi Y, Date H, Matsukawa T, Kanda J, Nakamoto FK, Higashihara M, Abe K, Koike R, Sasagawa M, Kuroha Y, Hasegawa N, Kanesawa N, Kondo T, Hitomi T, Tada M, Takano H, Saito Y, Sanpei K, Onodera O, Nishizawa M, Nakamura M, Yasuda T, Sakiyama Y, Otsuka M, Ueki A, Kaida KI, Shimizu J, Hanajima R, Hayashi T, Terao Y, Inomata-Terada S, Hamada M, Shirota Y, Kubota A, Ugawa Y, Koh K, Takiyama Y, Ohsawa-Yoshida N, Ishiura S, Yamasaki R, Tamaoka A, Akiyama H, Otsuki T, Sano A, Ikeda A, Goto J, Morishita S, Tsuji S. Ishiura H, et al. Among authors: ichikawa k, ichikawa y. Nat Genet. 2018 Apr;50(4):581-590. doi: 10.1038/s41588-018-0067-2. Epub 2018 Mar 5. Nat Genet. 2018. PMID: 29507423
A linear time algorithm for detecting long genomic regions enriched with a specific combination of epigenetic states.
Ichikawa K, Morishita S. Ichikawa K, et al. BMC Genomics. 2015;16 Suppl 2(Suppl 2):S8. doi: 10.1186/1471-2164-16-S2-S8. Epub 2015 Jan 21. BMC Genomics. 2015. PMID: 25708947 Free PMC article.
The program that implements the method is called "CSMinfinder" and is made available at: http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/Segmentation/...
The program that implements the method is called "CSMinfinder" and is made available at: http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa …
A Simple but Powerful Heuristic Method for Accelerating k-Means Clustering of Large-Scale Data in Life Science.
Ichikawa K, Morishita S. Ichikawa K, et al. IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):681-92. doi: 10.1109/TCBB.2014.2306200. IEEE/ACM Trans Comput Biol Bioinform. 2014. PMID: 26356339
These two distance measurements are equivalent in the sense that they yield the same k-means clustering result for identical sets of k initial centroids. Thus, an efficient algorithm used for one is applicable to the other. ...The BoostKCP software is available at h …
These two distance measurements are equivalent in the sense that they yield the same k-means clustering result for identical sets of …
AgIn: measuring the landscape of CpG methylation of individual repetitive elements.
Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S. Suzuki Y, et al. Among authors: ichikawa k. Bioinformatics. 2016 Oct 1;32(19):2911-9. doi: 10.1093/bioinformatics/btw360. Epub 2016 Jun 17. Bioinformatics. 2016. PMID: 27318202 Free PMC article.
Centromere evolution and CpG methylation during vertebrate speciation.
Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S. Ichikawa K, et al. Nat Commun. 2017 Nov 28;8(1):1833. doi: 10.1038/s41467-017-01982-7. Nat Commun. 2017. PMID: 29184138 Free PMC article.
Recompleting the Caenorhabditis elegans genome.
Yoshimura J, Ichikawa K, Shoura MJ, Artiles KL, Gabdank I, Wahba L, Smith CL, Edgley ML, Rougvie AE, Fire AZ, Morishita S, Schwarz EM. Yoshimura J, et al. Among authors: ichikawa k. Genome Res. 2019 Jun;29(6):1009-1022. doi: 10.1101/gr.244830.118. Epub 2019 May 23. Genome Res. 2019. PMID: 31123080 Free PMC article.
Finding long tandem repeats in long noisy reads.
Morishita S, Ichikawa K, Myers EW. Morishita S, et al. Among authors: ichikawa k. Bioinformatics. 2021 May 5;37(5):612-621. doi: 10.1093/bioinformatics/btaa865. Bioinformatics. 2021. PMID: 33031558 Free PMC article.
1,503 results