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Items: 1 to 50 of 68

1.

Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease.

Sone J, Mitsuhashi S, Fujita A, Mizuguchi T, Hamanaka K, Mori K, Koike H, Hashiguchi A, Takashima H, Sugiyama H, Kohno Y, Takiyama Y, Maeda K, Doi H, Koyano S, Takeuchi H, Kawamoto M, Kohara N, Ando T, Ieda T, Kita Y, Kokubun N, Tsuboi Y, Katoh K, Kino Y, Katsuno M, Iwasaki Y, Yoshida M, Tanaka F, Suzuki IK, Frith MC, Matsumoto N, Sobue G.

Nat Genet. 2019 Aug;51(8):1215-1221. doi: 10.1038/s41588-019-0459-y. Epub 2019 Jul 22.

PMID:
31332381
2.

How sequence alignment scores correspond to probability models.

Frith MC.

Bioinformatics. 2019 Jul 22. pii: btz576. doi: 10.1093/bioinformatics/btz576. [Epub ahead of print]

PMID:
31329241
3.

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.

Mitsuhashi S, Frith MC, Mizuguchi T, Miyatake S, Toyota T, Adachi H, Oma Y, Kino Y, Mitsuhashi H, Matsumoto N.

Genome Biol. 2019 Mar 19;20(1):58. doi: 10.1186/s13059-019-1667-6.

4.

NanoPipe-a web server for nanopore MinION sequencing data analysis.

Shabardina V, Kischka T, Manske F, Grundmann N, Frith MC, Suzuki Y, Makałowski W.

Gigascience. 2019 Feb 1;8(2). pii: giy169. doi: 10.1093/gigascience/giy169.

5.

Evaluation and application of RNA-Seq by MinION.

Seki M, Katsumata E, Suzuki A, Sereewattanawoot S, Sakamoto Y, Mizushima-Sugano J, Sugano S, Kohno T, Frith MC, Tsuchihara K, Suzuki Y.

DNA Res. 2019 Feb 1;26(1):55-65. doi: 10.1093/dnares/dsy038.

6.

Biallelic COLGALT1 variants are associated with cerebral small vessel disease.

Miyatake S, Schneeberger S, Koyama N, Yokochi K, Ohmura K, Shiina M, Mori H, Koshimizu E, Imagawa E, Uchiyama Y, Mitsuhashi S, Frith MC, Fujita A, Satoh M, Taguri M, Tomono Y, Takahashi K, Doi H, Takeuchi H, Nakashima M, Mizuguchi T, Takata A, Miyake N, Saitsu H, Tanaka F, Ogata K, Hennet T, Matsumoto N.

Ann Neurol. 2018 Dec;84(6):843-853. doi: 10.1002/ana.25367. Epub 2018 Nov 30.

PMID:
30412317
7.

A Simplified Description of Child Tables for Sequence Similarity Search.

Frith MC, Shrestha AMS.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2067-2073. doi: 10.1109/TCBB.2018.2796064. Epub 2018 Feb 9.

PMID:
29994365
8.

Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum.

Runtuwene LR, Tuda JSB, Mongan AE, Makalowski W, Frith MC, Imwong M, Srisutham S, Nguyen Thi LA, Tuan NN, Eshita Y, Maeda R, Yamagishi J, Suzuki Y.

Sci Rep. 2018 May 29;8(1):8286. doi: 10.1038/s41598-018-26334-3.

9.

EAGLE: Explicit Alternative Genome Likelihood Evaluator.

Kuo T, Frith MC, Sese J, Horton P.

BMC Med Genomics. 2018 Apr 20;11(Suppl 2):28. doi: 10.1186/s12920-018-0342-1.

10.

A survey of localized sequence rearrangements in human DNA.

Frith MC, Khan S.

Nucleic Acids Res. 2018 Feb 28;46(4):1661-1673. doi: 10.1093/nar/gkx1266.

11.

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.

Shrestha AMS, Frith MC, Asai K, Richard H.

Nucleic Acids Res. 2018 Feb 16;46(3):e18. doi: 10.1093/nar/gkx1175.

12.

Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer.

Suzuki A, Suzuki M, Mizushima-Sugano J, Frith MC, Makalowski W, Kohno T, Sugano S, Tsuchihara K, Suzuki Y.

DNA Res. 2017 Dec 1;24(6):585-596. doi: 10.1093/dnares/dsx027.

13.

Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy.

Mitsuhashi S, Nakagawa S, Takahashi Ueda M, Imanishi T, Frith MC, Mitsuhashi H.

Sci Rep. 2017 Nov 1;7(1):14789. doi: 10.1038/s41598-017-13712-6.

14.

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Lim K, Yamada KD, Frith MC, Tomii K.

J Struct Funct Genomics. 2016 Dec;17(4):147-154. doi: 10.1007/s10969-016-9210-4. Epub 2017 Jan 12.

15.

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

Hamada M, Ono Y, Asai K, Frith MC.

Bioinformatics. 2017 Mar 15;33(6):926-928. doi: 10.1093/bioinformatics/btw742.

16.

ALP & FALP: C++ libraries for pairwise local alignment E-values.

Sheetlin S, Park Y, Frith MC, Spouge JL.

Bioinformatics. 2016 Jan 15;32(2):304-5. doi: 10.1093/bioinformatics/btv575. Epub 2015 Oct 1.

17.

Split-alignment of genomes finds orthologies more accurately.

Frith MC, Kawaguchi R.

Genome Biol. 2015 May 21;16:106. doi: 10.1186/s13059-015-0670-9.

18.

Frameshift alignment: statistics and post-genomic applications.

Sheetlin SL, Park Y, Frith MC, Spouge JL.

Bioinformatics. 2014 Dec 15;30(24):3575-82. doi: 10.1093/bioinformatics/btu576. Epub 2014 Aug 28.

19.

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

Ohmiya H, Vitezic M, Frith MC, Itoh M, Carninci P, Forrest AR, Hayashizaki Y, Lassmann T; FANTOM Consortium.

BMC Genomics. 2014 Apr 25;15:269. doi: 10.1186/1471-2164-15-269.

20.

Explaining the correlations among properties of mammalian promoters.

Frith MC; FANTOM consortium.

Nucleic Acids Res. 2014 Apr;42(8):4823-32. doi: 10.1093/nar/gku115. Epub 2014 Mar 27.

21.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

22.

Improved search heuristics find 20,000 new alignments between human and mouse genomes.

Frith MC, Noé L.

Nucleic Acids Res. 2014 Apr;42(7):e59. doi: 10.1093/nar/gku104. Epub 2014 Feb 3.

23.

A bioinformatician's guide to the forefront of suffix array construction algorithms.

Shrestha AM, Frith MC, Horton P.

Brief Bioinform. 2014 Mar;15(2):138-54. doi: 10.1093/bib/bbt081. Epub 2014 Jan 10.

24.

An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome.

Shrestha AM, Frith MC.

Bioinformatics. 2013 Apr 15;29(8):965-72. doi: 10.1093/bioinformatics/btt073. Epub 2013 Feb 14.

25.

Finding protein-coding genes through human polymorphisms.

Wijaya E, Frith MC, Horton P, Asai K.

PLoS One. 2013;8(1):e54210. doi: 10.1371/journal.pone.0054210. Epub 2013 Jan 22.

26.

Adding unaligned sequences into an existing alignment using MAFFT and LAST.

Katoh K, Frith MC.

Bioinformatics. 2012 Dec 1;28(23):3144-6. doi: 10.1093/bioinformatics/bts578. Epub 2012 Sep 27.

27.

Mammalian NUMT insertion is non-random.

Tsuji J, Frith MC, Tomii K, Horton P.

Nucleic Acids Res. 2012 Oct;40(18):9073-88. doi: 10.1093/nar/gks424. Epub 2012 Jul 3.

28.

A mostly traditional approach improves alignment of bisulfite-converted DNA.

Frith MC, Mori R, Asai K.

Nucleic Acids Res. 2012 Jul;40(13):e100. doi: 10.1093/nar/gks275. Epub 2012 Mar 28.

29.

Gentle masking of low-complexity sequences improves homology search.

Frith MC.

PLoS One. 2011;6(12):e28819. doi: 10.1371/journal.pone.0028819. Epub 2011 Dec 19.

30.

RecountDB: a database of mapped and count corrected transcribed sequences.

Wijaya E, Frith MC, Asai K, Horton P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1089-92. doi: 10.1093/nar/gkr1172. Epub 2011 Dec 1.

31.

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.

Hamada M, Wijaya E, Frith MC, Asai K.

Bioinformatics. 2011 Nov 15;27(22):3085-92. doi: 10.1093/bioinformatics/btr537. Epub 2011 Oct 5.

PMID:
21976422
32.

Inferring transcription factor complexes from ChIP-seq data.

Whitington T, Frith MC, Johnson J, Bailey TL.

Nucleic Acids Res. 2011 Aug;39(15):e98. doi: 10.1093/nar/gkr341. Epub 2011 May 20.

33.

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.

Hamada M, Yamada K, Sato K, Frith MC, Asai K.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W100-6. doi: 10.1093/nar/gkr290. Epub 2011 May 11.

34.

Adaptive seeds tame genomic sequence comparison.

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC.

Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Epub 2011 Jan 5.

35.

A new repeat-masking method enables specific detection of homologous sequences.

Frith MC.

Nucleic Acids Res. 2011 Mar;39(4):e23. doi: 10.1093/nar/gkq1212. Epub 2010 Nov 24.

36.

Recount: expectation maximization based error correction tool for next generation sequencing data.

Wijaya E, Frith MC, Suzuki Y, Horton P.

Genome Inform. 2009 Oct;23(1):189-201.

37.

Parameters for accurate genome alignment.

Frith MC, Hamada M, Horton P.

BMC Bioinformatics. 2010 Feb 9;11:80. doi: 10.1186/1471-2105-11-80.

38.

Incorporating sequence quality data into alignment improves DNA read mapping.

Frith MC, Wan R, Horton P.

Nucleic Acids Res. 2010 Apr;38(7):e100. doi: 10.1093/nar/gkq010. Epub 2010 Jan 27.

39.

Pseudocounts for transcription factor binding sites.

Nishida K, Frith MC, Nakai K.

Nucleic Acids Res. 2009 Feb;37(3):939-44. doi: 10.1093/nar/gkn1019. Epub 2008 Dec 23.

40.

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

Frith MC, Park Y, Sheetlin SL, Spouge JL.

Nucleic Acids Res. 2008 Oct;36(18):5863-71. doi: 10.1093/nar/gkn579. Epub 2008 Sep 16.

41.

Discovering sequence motifs with arbitrary insertions and deletions.

Frith MC, Saunders NF, Kobe B, Bailey TL.

PLoS Comput Biol. 2008 May 9;4(4):e1000071. doi: 10.1371/journal.pcbi.1000071.

42.

A code for transcription initiation in mammalian genomes.

Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A.

Genome Res. 2008 Jan;18(1):1-12. Epub 2007 Nov 21.

43.

Splicing bypasses 3' end formation signals to allow complex gene architectures.

Frith MC, Carninci P, Kai C, Kawai J, Bailey TL, Hayashizaki Y, Mattick JS.

Gene. 2007 Nov 15;403(1-2):188-93. Epub 2007 Aug 30.

PMID:
17897791
44.

Large-scale clustering of CAGE tag expression data.

Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y.

BMC Bioinformatics. 2007 May 21;8:161.

45.

Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function.

Baxter LL, Hsu BJ, Umayam L, Wolfsberg TG, Larson DM, Frith MC, Kawai J, Hayashizaki Y, Carninci P, Pavan WJ.

Pigment Cell Res. 2007 Jun;20(3):201-9.

PMID:
17516927
46.

Dynamic usage of transcription start sites within core promoters.

Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y.

Genome Biol. 2006;7(12):R118.

47.

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS.

RNA Biol. 2006 Jan-Mar;3(1):40-8. Epub 2006 Apr 3.

PMID:
17114936
48.

Evolutionary turnover of mammalian transcription start sites.

Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A.

Genome Res. 2006 Jun;16(6):713-22. Epub 2006 May 10. Erratum in: Genome Res. 2006 Jul;16(7):947. Hayshizaki, Yoshihide [corrected to Hayashizaki, Yoshihide].

49.

The abundance of short proteins in the mammalian proteome.

Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM.

PLoS Genet. 2006 Apr;2(4):e52. Epub 2006 Apr 28.

50.

Clusters of internally primed transcripts reveal novel long noncoding RNAs.

Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, Bult C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Mattick JS, Suzuki H.

PLoS Genet. 2006 Apr;2(4):e37. Epub 2006 Apr 28.

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