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Items: 1 to 50 of 95

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.

Quantification of Thermal Oxidation in Metallic Glass Powder using Ultra-small Angle X-ray Scattering.

Paul T, Zhang L, Biswas S, Loganathan A, Frith MG, Ilavsky J, Kuzmenko I, Puckette J, Kalkan AK, Agarwal A, Harimkar SP.

Sci Rep. 2019 May 2;9(1):6836. doi: 10.1038/s41598-019-43317-0.

4.

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.

5.

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.

6.

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.

7.

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
8.

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
9.

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.

10.

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.

11.

Pemphigus Foliaceus Demonstrating Pathergy After Mohs Micrographic Surgery.

Tolkachjov SN, Frith M, Cooper LD, Harmon CB.

Dermatol Surg. 2018 Oct;44(10):1352-1353. doi: 10.1097/DSS.0000000000001452. No abstract available.

PMID:
29293109
12.

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.

13.

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.

14.

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.

15.

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.

16.

Rapid Diffusion and Nanosegregation of Hydrogen in Magnesium Alloys from Exposure to Water.

Brady MP, Ievlev AV, Fayek M, Leonard DN, Frith MG, Meyer HM 3rd, Ramirez-Cuesta AJ, Daemen LL, Cheng Y, Guo W, Poplawsky JD, Ovchinnikova OS, Thomson J, Anovitz LM, Rother G, Shin D, Song GL, Davis B.

ACS Appl Mater Interfaces. 2017 Nov 1;9(43):38125-38134. doi: 10.1021/acsami.7b10750. Epub 2017 Oct 18.

PMID:
29016100
17.

Serotyping dengue virus with isothermal amplification and a portable sequencer.

Yamagishi J, Runtuwene LR, Hayashida K, Mongan AE, Thi LAN, Thuy LN, Nhat CN, Limkittikul K, Sirivichayakul C, Sathirapongsasuti N, Frith M, Makalowski W, Eshita Y, Sugano S, Suzuki Y.

Sci Rep. 2017 Jun 14;7(1):3510. doi: 10.1038/s41598-017-03734-5.

18.

Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads.

Poulsen TM, Frith M.

BMC Bioinformatics. 2017 Jun 12;18(1):299. doi: 10.1186/s12859-017-1710-0.

19.

A Survey of Clinicians Working in Brain Injury Rehabilitation: Are Social Cognition Impairments on the Radar?

Kelly M, McDonald S, Frith MHJ.

J Head Trauma Rehabil. 2017 Jul/Aug;32(4):E55-E65. doi: 10.1097/HTR.0000000000000269.

PMID:
28489703
20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

Assessment practices of speech-language pathologists for cognitive communication disorders following traumatic brain injury in adults: an international survey.

Frith M, Togher L, Ferguson A, Levick W, Docking K.

Brain Inj. 2014;28(13-14):1657-66. doi: 10.3109/02699052.2014.947619. Epub 2014 Aug 26.

PMID:
25158134
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

Improvement of enzyme transport in wood chips for thermomechanical pulp refining.

Pelletier A, Li K, Zhao Y, Court G, Luo J, Frith M.

Carbohydr Polym. 2013 Jun 5;95(1):25-31. doi: 10.1016/j.carbpol.2013.02.025. Epub 2013 Feb 26.

PMID:
23618235
32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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
40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

MEME SUITE: tools for motif discovery and searching.

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20.

48.

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.

49.

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.

50.

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.

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