Riu Yamashita

Riu Yamashita

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Riu Yamashita

Riu Yamashita

Publications by authors named "Riu Yamashita"

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Multifocal origin of occupational cholangiocarcinoma revealed by comparison of multilesion mutational profiles.

Carcinogenesis 2019 Jun 20. Epub 2019 Jun 20.

Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwanoha, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1093/carcin/bgz120DOI Listing
June 2019

Comparative sequence analysis of patient-matched primary colorectal cancer, metastatic, and recurrent metastatic tumors after adjuvant FOLFOX chemotherapy.

BMC Cancer 2019 Mar 21;19(1):255. Epub 2019 Mar 21.

Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.

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http://dx.doi.org/10.1186/s12885-019-5479-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429751PMC
March 2019

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

PLoS One 2016 22;11(4):e0154389. Epub 2016 Apr 22.

Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154389PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841512PMC
March 2017

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide.

Nature 2017 01 26;541(7636):228-232. Epub 2016 Dec 26.

Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA.

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http://www.nature.com/articles/nature21034
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http://dx.doi.org/10.1038/nature21034DOI Listing
January 2017

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals.

PLoS One 2015 29;10(6):e0131607. Epub 2015 Jun 29.

Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131607PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487993PMC
April 2016

Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells.

Int J Mol Sci 2012 3;13(7):8259-72. Epub 2012 Jul 3.

Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.).

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http://www.mdpi.com/1422-0067/13/7/8259
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http://dx.doi.org/10.3390/ijms13078259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430232PMC
August 2015

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.

Nucleic Acids Res 2015 Jan 5;43(Database issue):D87-91. Epub 2014 Nov 5.

Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan

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http://dx.doi.org/10.1093/nar/gku1080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383915PMC
January 2015

The Babesia bovis gene and promoter model: an update from full-length EST analysis.

BMC Genomics 2014 Aug 13;15:678. Epub 2014 Aug 13.

National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555, Japan.

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http://dx.doi.org/10.1186/1471-2164-15-678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148916PMC
August 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.

Nucleic Acids Res 2012 Jan 15;40(Database issue):D150-4. Epub 2011 Nov 15.

Frontier Research Initiative, Institute of Medical Science, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr1005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245115PMC
January 2012

Profiling ascidian promoters as the primordial type of vertebrate promoter.

BMC Genomics 2011 Nov 30;12 Suppl 3:S7. Epub 2011 Nov 30.

Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-S3-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333190PMC
November 2011

Predicting promoter activities of primary human DNA sequences.

Nucleic Acids Res 2011 Jun 12;39(11):e75. Epub 2011 Apr 12.

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

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http://dx.doi.org/10.1093/nar/gkr173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113590PMC
June 2011

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.

Genome Res 2011 May 3;21(5):775-89. Epub 2011 Mar 3.

Frontier Research Initiative, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1101/gr.110254.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083095PMC
May 2011

RANK signaling induces interferon-stimulated genes in the fetal thymic stroma.

Biochem Biophys Res Commun 2011 May 19;408(4):530-6. Epub 2011 Apr 19.

Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2011.04.049DOI Listing
May 2011

Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer.

DNA Res 2010 Jun 17;17(3):169-83. Epub 2010 Apr 17.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568, Japan.

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http://dx.doi.org/10.1093/dnares/dsq007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885271PMC
June 2010

Effects of Alu elements on global nucleosome positioning in the human genome.

BMC Genomics 2010 May 17;11:309. Epub 2010 May 17.

Department of Medical Genome Sciences, University of Tokyo, Minato-ku, Japan.

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http://dx.doi.org/10.1186/1471-2164-11-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878307PMC
May 2010

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Nucleic Acids Res 2010 Jan 12;38(Database issue):D98-104. Epub 2009 Nov 12.

Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkp1017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808897PMC
January 2010

Massive transcriptional start site analysis of human genes in hypoxia cells.

Nucleic Acids Res 2009 Apr 22;37(7):2249-63. Epub 2009 Feb 22.

Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1093/nar/gkp066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673422PMC
April 2009

Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis.

Gene 2009 Feb 21;430(1-2):44-9. Epub 2008 Oct 21.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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https://linkinghub.elsevier.com/retrieve/pii/S03781119080052
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http://dx.doi.org/10.1016/j.gene.2008.10.002DOI Listing
February 2009

Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics.

Nucleic Acids Res 2008 Jun 14;36(11):3707-15. Epub 2008 May 14.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkn248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441802PMC
June 2008

Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells.

J Hum Genet 2008 17;53(2):185-91. Epub 2008 Jan 17.

Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan.

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http://dx.doi.org/10.1007/s10038-007-0228-0DOI Listing
April 2008

Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.

BMC Genomics 2008 Apr 2;9:152. Epub 2008 Apr 2.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335122PMC
April 2008

DBTSS: database of transcription start sites, progress report 2008.

Nucleic Acids Res 2008 Jan 16;36(Database issue):D97-101. Epub 2007 Oct 16.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkm901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238895PMC
January 2008

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.

Nucleic Acids Res 2007 Jul 30;35(Web Server issue):W227-31. Epub 2007 May 30.

Mitsui Knowledge Industry Co. Ltd, University of Tokyo, Japan.

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http://dx.doi.org/10.1093/nar/gkm362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933176PMC
July 2007

Intrinsic promoter activities of primary DNA sequences in the human genome.

DNA Res 2007 Apr 23;14(2):71-7. Epub 2007 May 23.

Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/dnares/dsm006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779894PMC
April 2007

Diverse DNA methylation statuses at alternative promoters of human genes in various tissues.

DNA Res 2006 Aug 26;13(4):155-67. Epub 2006 Oct 26.

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

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https://academic.oup.com/dnaresearch/article-lookup/doi/10.1
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http://dx.doi.org/10.1093/dnares/dsl008DOI Listing
August 2006

DBTGR: a database of tunicate promoters and their regulatory elements.

Nucleic Acids Res 2006 Jan;34(Database issue):D552-5

Human Genome Center, The Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkj064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347427PMC
January 2006

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.

Nucleic Acids Res 2006 Jan;34(Database issue):D86-9

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkj129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347491PMC
January 2006

Large-scale collection and characterization of promoters of human and mouse genes.

In Silico Biol 2004 ;4(4):429-44

Human Genome Center, The Institute of Medical Science, The University of Tokyo: 4-6-1 Shirokanedai, Tokyo, 108-8639, Japan.

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June 2005

Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity.

Gene 2005 May 19;350(2):129-36. Epub 2005 Mar 19.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokane-dai Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1016/j.gene.2005.01.012DOI Listing
May 2005

Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions.

Genome Res 2004 Sep;14(9):1711-8

Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.

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http://dx.doi.org/10.1101/gr.2435604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC515316PMC
September 2004

[Transcriptome analyses and transcriptome databases].

Tanpakushitsu Kakusan Koso 2004 Aug;49(11 Suppl):1859-65

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August 2004

Small open reading frames in 5' untranslated regions of mRnas.

C R Biol 2003 Oct-Nov;326(10-11):987-91

Laboratory of Genome Database, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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May 2004

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004.

Nucleic Acids Res 2004 Jan;32(Database issue):D78-81

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkh076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308810PMC
January 2004

Complete sequencing and characterization of 21,243 full-length human cDNAs.

Authors:
Toshio Ota Yutaka Suzuki Tetsuo Nishikawa Tetsuji Otsuki Tomoyasu Sugiyama Ryotaro Irie Ai Wakamatsu Koji Hayashi Hiroyuki Sato Keiichi Nagai Kouichi Kimura Hiroshi Makita Mitsuo Sekine Masaya Obayashi Tatsunari Nishi Toshikazu Shibahara Toshihiro Tanaka Shizuko Ishii Jun-ichi Yamamoto Kaoru Saito Yuri Kawai Yuko Isono Yoshitaka Nakamura Kenji Nagahari Katsuhiko Murakami Tomohiro Yasuda Takao Iwayanagi Masako Wagatsuma Akiko Shiratori Hiroaki Sudo Takehiko Hosoiri Yoshiko Kaku Hiroyo Kodaira Hiroshi Kondo Masanori Sugawara Makiko Takahashi Katsuhiro Kanda Takahide Yokoi Takako Furuya Emiko Kikkawa Yuhi Omura Kumi Abe Kumiko Kamihara Naoko Katsuta Kazuomi Sato Machiko Tanikawa Makoto Yamazaki Ken Ninomiya Tadashi Ishibashi Hiromichi Yamashita Katsuji Murakawa Kiyoshi Fujimori Hiroyuki Tanai Manabu Kimata Motoji Watanabe Susumu Hiraoka Yoshiyuki Chiba Shinichi Ishida Yukio Ono Sumiyo Takiguchi Susumu Watanabe Makoto Yosida Tomoko Hotuta Junko Kusano Keiichi Kanehori Asako Takahashi-Fujii Hiroto Hara Tomo-o Tanase Yoshiko Nomura Sakae Togiya Fukuyo Komai Reiko Hara Kazuha Takeuchi Miho Arita Nobuyuki Imose Kaoru Musashino Hisatsugu Yuuki Atsushi Oshima Naokazu Sasaki Satoshi Aotsuka Yoko Yoshikawa Hiroshi Matsunawa Tatsuo Ichihara Namiko Shiohata Sanae Sano Shogo Moriya Hiroko Momiyama Noriko Satoh Sachiko Takami Yuko Terashima Osamu Suzuki Satoshi Nakagawa Akihiro Senoh Hiroshi Mizoguchi Yoshihiro Goto Fumio Shimizu Hirokazu Wakebe Haretsugu Hishigaki Takeshi Watanabe Akio Sugiyama Makoto Takemoto Bunsei Kawakami Masaaki Yamazaki Koji Watanabe Ayako Kumagai Shoko Itakura Yasuhito Fukuzumi Yoshifumi Fujimori Megumi Komiyama Hiroyuki Tashiro Akira Tanigami Tsutomu Fujiwara Toshihide Ono Katsue Yamada Yuka Fujii Kouichi Ozaki Maasa Hirao Yoshihiro Ohmori Ayako Kawabata Takeshi Hikiji Naoko Kobatake Hiromi Inagaki Yasuko Ikema Sachiko Okamoto Rie Okitani Takuma Kawakami Saori Noguchi Tomoko Itoh Keiko Shigeta Tadashi Senba Kyoka Matsumura Yoshie Nakajima Takae Mizuno Misato Morinaga Masahide Sasaki Takushi Togashi Masaaki Oyama Hiroko Hata Manabu Watanabe Takami Komatsu Junko Mizushima-Sugano Tadashi Satoh Yuko Shirai Yukiko Takahashi Kiyomi Nakagawa Koji Okumura Takahiro Nagase Nobuo Nomura Hisashi Kikuchi Yasuhiko Masuho Riu Yamashita Kenta Nakai Tetsushi Yada Yusuke Nakamura Osamu Ohara Takao Isogai Sumio Sugano

Nat Genet 2004 Jan 21;36(1):40-5. Epub 2003 Dec 21.

Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan.

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http://dx.doi.org/10.1038/ng1285DOI Listing
January 2004

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.

Nucleic Acids Res 2002 Jan;30(1):328-31

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99097PMC
http://dx.doi.org/10.1093/nar/30.1.328DOI Listing
January 2002