Martin C Frith

Martin C Frith

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Martin C Frith

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A Simplified Description of Child Tables for Sequence Similarity Search.

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

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http://dx.doi.org/10.1109/TCBB.2018.2796064DOI Listing
July 2019

How sequence alignment scores correspond to probability models.

Authors:
Martin C Frith

Bioinformatics 2019 Jul 22. Epub 2019 Jul 22.

Artificial Intelligence Research Center, AIST, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btz576DOI Listing
July 2019

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

Genome Biol 2019 03 19;20(1):58. Epub 2019 Mar 19.

Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.

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http://dx.doi.org/10.1186/s13059-019-1667-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425644PMC
March 2019

Evaluation and application of RNA-Seq by MinION.

DNA Res 2019 Feb;26(1):55-65

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1093/dnares/dsy038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379022PMC
February 2019

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

Gigascience 2019 02;8(2)

Institue of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, Muenster, 48149, Germany.

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http://dx.doi.org/10.1093/gigascience/giy169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377397PMC
February 2019

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

Sci Rep 2018 05 29;8(1):8286. Epub 2018 May 29.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.

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http://www.nature.com/articles/s41598-018-26334-3
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http://dx.doi.org/10.1038/s41598-018-26334-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974085PMC
May 2018

EAGLE: Explicit Alternative Genome Likelihood Evaluator.

BMC Med Genomics 2018 04 20;11(Suppl 2):28. Epub 2018 Apr 20.

Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

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http://dx.doi.org/10.1186/s12920-018-0342-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918433PMC
April 2018

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

Nucleic Acids Res 2018 02;46(3):e18

Sorbonne Universités, UPMC Univ Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 4 place Jussieu, 75005 Paris, France.

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http://dx.doi.org/10.1093/nar/gkx1175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815140PMC
February 2018

A survey of localized sequence rearrangements in human DNA.

Nucleic Acids Res 2018 02;46(4):1661-1673

Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/nar/gkx1266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829575PMC
February 2018

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

DNA Res 2017 Dec;24(6):585-596

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1093/dnares/dsx027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726485PMC
December 2017

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

Sci Rep 2017 11 1;7(1):14789. Epub 2017 Nov 1.

Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan.

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http://dx.doi.org/10.1038/s41598-017-13712-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665936PMC
November 2017

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

Bioinformatics 2017 03;33(6):926-928

Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351549PMC
March 2017

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

J Struct Funct Genomics 2016 Dec 12;17(4):147-154. Epub 2017 Jan 12.

Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

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http://link.springer.com/10.1007/s10969-016-9210-4
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http://dx.doi.org/10.1007/s10969-016-9210-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274646PMC
December 2016

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

Bioinformatics 2016 Jan 1;32(2):304-5. Epub 2015 Oct 1.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.

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http://dx.doi.org/10.1093/bioinformatics/btv575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739181PMC
January 2016

Split-alignment of genomes finds orthologies more accurately.

Genome Biol 2015 May 21;16:106. Epub 2015 May 21.

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

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http://link.springer.com/content/pdf/10.1186%2Fs13059-015-06
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http://genomebiology.com/2015/16/1/106
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http://dx.doi.org/10.1186/s13059-015-0670-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464727PMC
May 2015

Frameshift alignment: statistics and post-genomic applications.

Bioinformatics 2014 Dec 28;30(24):3575-82. Epub 2014 Aug 28.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA and Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253828PMC
December 2014

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

Nucleic Acids Res 2014 Apr 3;42(7):e59. Epub 2014 Feb 3.

Computational Biology Research Center, AIST, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan and LIFL (UMR 8022)/INRIA Lille Nord-Europe, bat M3 Ext., Université Lille1 59655 Villeneuve d'Ascq Cedex, France.

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http://dx.doi.org/10.1093/nar/gku104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985675PMC
April 2014

Explaining the correlations among properties of mammalian promoters.

Authors:
Martin C Frith

Nucleic Acids Res 2014 Apr 27;42(8):4823-32. Epub 2014 Mar 27.

Computational Biology Research Center, AIST, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gku115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005656PMC
April 2014

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

BMC Genomics 2014 Apr 25;15:269. Epub 2014 Apr 25.

RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045 Yokohama, Japan.

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http://dx.doi.org/10.1186/1471-2164-15-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029093PMC
April 2014

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

Brief Bioinform 2014 Mar 10;15(2):138-54. Epub 2014 Jan 10.

Computational Biology Research Center, AIST, Tokyo, Japan.

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http://dx.doi.org/10.1093/bib/bbt081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956071PMC
March 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Finding protein-coding genes through human polymorphisms.

PLoS One 2013 22;8(1):e54210. Epub 2013 Jan 22.

Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054210PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551959PMC
July 2013

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

Bioinformatics 2013 Apr 14;29(8):965-72. Epub 2013 Feb 14.

Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btt073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624798PMC
April 2013

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

Bioinformatics 2012 Dec 27;28(23):3144-6. Epub 2012 Sep 27.

Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita 565-0871, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bts578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516148PMC
December 2012

Mammalian NUMT insertion is non-random.

Nucleic Acids Res 2012 Oct 3;40(18):9073-88. Epub 2012 Jul 3.

Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.

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http://dx.doi.org/10.1093/nar/gks424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467031PMC
October 2012

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

Nucleic Acids Res 2012 Jul 28;40(13):e100. Epub 2012 Mar 28.

Computational Biology Research Center, National Institute for Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gks275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401460PMC
July 2012

Gentle masking of low-complexity sequences improves homology search.

Authors:
Martin C Frith

PLoS One 2011 19;6(12):e28819. Epub 2011 Dec 19.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028819PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242753PMC
April 2012

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

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

Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan.

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http://dx.doi.org/10.1093/nar/gkr1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245132PMC
January 2012

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

Bioinformatics 2011 Nov 5;27(22):3085-92. Epub 2011 Oct 5.

Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btr537DOI Listing
November 2011

Inferring transcription factor complexes from ChIP-seq data.

Nucleic Acids Res 2011 Aug 20;39(15):e98. Epub 2011 May 20.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkr341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159476PMC
August 2011

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

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

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.

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http://dx.doi.org/10.1093/nar/gkr290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125741PMC
July 2011

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

Authors:
Martin C Frith

Nucleic Acids Res 2011 Mar 24;39(4):e23. Epub 2010 Nov 24.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gkq1212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045581PMC
March 2011

Adaptive seeds tame genomic sequence comparison.

Genome Res 2011 Mar 5;21(3):487-93. Epub 2011 Jan 5.

Department of Computational Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany.

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http://dx.doi.org/10.1101/gr.113985.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044862PMC
March 2011

Incorporating sequence quality data into alignment improves DNA read mapping.

Nucleic Acids Res 2010 Apr 27;38(7):e100. Epub 2010 Jan 27.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gkq010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853142PMC
April 2010

Parameters for accurate genome alignment.

BMC Bioinformatics 2010 Feb 9;11:80. Epub 2010 Feb 9.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829014PMC
February 2010

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

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

AIST, Computational Biology Research Center, 2-42 Aomi, Koutou-Ku, Tokyo 135-0064, Japan.

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October 2009

Pseudocounts for transcription factor binding sites.

Nucleic Acids Res 2009 Feb 23;37(3):939-44. Epub 2008 Dec 23.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.

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http://dx.doi.org/10.1093/nar/gkn1019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647310PMC
February 2009

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

Nucleic Acids Res 2008 Oct 16;36(18):5863-71. Epub 2008 Sep 16.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gkn579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566872PMC
October 2008

Discovering sequence motifs with arbitrary insertions and deletions.

PLoS Comput Biol 2008 May 9;4(4):e1000071. Epub 2008 May 9.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pcbi.1000071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323616PMC
May 2008

A code for transcription initiation in mammalian genomes.

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

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.6831208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134772PMC
January 2008

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

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

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Centre (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1016/j.gene.2007.08.012DOI Listing
November 2007

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

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

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.4161/rna.3.1.2789DOI Listing
September 2007

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

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

Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA.

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http://dx.doi.org/10.1111/j.1600-0749.2007.00372.xDOI Listing
June 2007

Dynamic usage of transcription start sites within core promoters.

Genome Biol 2006 ;7(12):R118

NTT Software Corporation, 209 Yamashita-cho Nakak-ku, Yokohama, Kanagawa, 231-8551, Japan.

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http://dx.doi.org/10.1186/gb-2006-7-12-r118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794431PMC
May 2007

Large-scale clustering of CAGE tag expression data.

BMC Bioinformatics 2007 May 21;8:161. Epub 2007 May 21.

Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1186/1471-2105-8-161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1890301PMC
May 2007

Evolutionary turnover of mammalian transcription start sites.

Genome Res 2006 Jun 10;16(6):713-22. Epub 2006 May 10.

Genome Exploration Research Group, RIKEN Genomic Sciences Centre (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.5031006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473182PMC
June 2006

Pseudo-messenger RNA: phantoms of the transcriptome.

PLoS Genet 2006 Apr 28;2(4):e23. Epub 2006 Apr 28.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.doi.org/10.1371/journal.pgen.0020023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449882PMC
April 2006

Clusters of internally primed transcripts reveal novel long noncoding RNAs.

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

Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449886PMC
April 2006

The abundance of short proteins in the mammalian proteome.

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

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.plos.org/10.1371/journal.pgen.0020052
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449894PMC
April 2006

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function.

Trends Genet 2006 Jan 10;22(1):1-5. Epub 2005 Nov 10.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia.

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http://dx.doi.org/10.1016/j.tig.2005.10.003DOI Listing
January 2006

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.

Genome Res 2006 Jan 12;16(1):11-9. Epub 2005 Dec 12.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia.

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http://dx.doi.org/10.1101/gr.4200206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356124PMC
January 2006

The amazing complexity of the human transcriptome.

Eur J Hum Genet 2005 Aug;13(8):894-7

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http://dx.doi.org/10.1038/sj.ejhg.5201459DOI Listing
August 2005

Genomic targets of nuclear estrogen receptors.

Mol Endocrinol 2004 Aug 18;18(8):1859-75. Epub 2004 Mar 18.

Department of Biology, Boston University, 5 Cummington Street, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1210/me.2003-0044DOI Listing
August 2004

CARRIE web service: automated transcriptional regulatory network inference and interactive analysis.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W213-6

Bioinformatics Program and Biomedical Engineering Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441540PMC
July 2004

MotifViz: an analysis and visualization tool for motif discovery.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W420-3

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441564PMC
July 2004

Site2genome: locating short DNA sequences in whole genomes.

Bioinformatics 2004 Jun 12;20(9):1468-9. Epub 2004 Feb 12.

Bioinformatics Program, Boston University, MA 02215, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth094DOI Listing
June 2004

Detection of functional DNA motifs via statistical over-representation.

Nucleic Acids Res 2004 26;32(4):1372-81. Epub 2004 Feb 26.

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC390287PMC
June 2004

Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses.

Brain Res 2004 Mar;1000(1-2):156-73

Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA.

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http://dx.doi.org/10.1016/j.brainres.2003.11.072DOI Listing
March 2004

Finding functional sequence elements by multiple local alignment.

Nucleic Acids Res 2004 2;32(1):189-200. Epub 2004 Jan 2.

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkh169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373279PMC
January 2004

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

Nucleic Acids Res 2003 Jul;31(13):3666-8

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168947PMC
http://dx.doi.org/10.1093/nar/gkg540DOI Listing
July 2003

A ubiquitous and conserved signal for RNA localization in chordates.

Curr Biol 2002 Oct;12(20):1756-61

Department of Biology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1016/s0960-9822(02)01220-4DOI Listing
October 2002

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.

Nucleic Acids Res 2002 Jul;30(14):3214-24

Bioinformatics Program, Boston University, 44 Cummington Street, Boston MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkf438DOI Listing
July 2002