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Papers authored by Hayashizaki Y

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Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment.

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Ito F, Usui K, Kawahara D, Suenaga A, Maki T, Kidoaki S, Suzuki H, Taiji M, Itoh M, Hayashizaki Y, and Matsuda T

Biomaterials 31(1):58-66, 2010 Jan - Who cited this? | PubMed ID: 19836832 | Fulltext

TagDust--a program to eliminate artifacts from next generation sequencing data.

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Lassmann T, Hayashizaki Y, and Daub CO

Bioinformatics (Oxford, England) 25(21):2839-40, 2009 Nov 1 - Who cited this? | PubMed ID: 19737799 | Fulltext

NMR solution structures of actin depolymerizing factor homology domains.

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Goroncy AK, Koshiba S, Tochio N, Tomizawa T, Sato M, Inoue M, Watanabe S, Hayashizaki Y, Tanaka A, Kigawa T, and Yokoyama S

Protein science : a publication of the Protein Society 18(11):2384-92, 2009 Nov - Who cited this? | PubMed ID: 19768801 | Fulltext

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.

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Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, and Faulkner GJ

Bioinformatics (Oxford, England) 25(19):2613-4, 2009 Oct 1 - Who cited this? | PubMed ID: 19605420 | Fulltext

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA.

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Maida Y, Yasukawa M, Furuuchi M, Lassmann T, Possemato R, Okamoto N, Kasim V, Hayashizaki Y, Hahn WC, and Masutomi K

Nature 461(7261):230-5, 2009 Sep 10 - Who cited this? | PubMed ID: 19701182 | Fulltext

Small RNAs derived from snoRNAs.

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Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, and Mattick JS

RNA (New York, N.Y.) 15(7):1233-40, 2009 Jul - Who cited this? | PubMed ID: 19474147 | Fulltext

Corrigendum: Tiny RNAs associated with transcription start sites in animals.

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Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C,

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Nature genetics 41(7):859, 2009 Jul - Who cited this? | PubMed ID: 19557082 | Fulltext

Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks.

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Usui K, Maki T, Ito F, Suenaga A, Kidoaki S, Itoh M, Taiji M, Matsuda T, Hayashizaki Y, and Suzuki H

Protein science : a publication of the Protein Society 18(7):1571, 2009 Jul - Who cited this? | PubMed ID: 19459183 | Fulltext

Rapid and cost-effective SNP detection method: application of SmartAmp2 to pharmacogenomics research.

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Mitani Y, Lezhava A, Sakurai A, Horikawa A, Nagakura M, Hayashizaki Y, and Ishikawa T

Pharmacogenomics 10(7):1187-97, 2009 Jul - Who cited this? | PubMed ID: 19604094 | Fulltext

Tail variation of the folding primer affects the SmartAmp2 process differently.

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Kimura Y, Oguchi-Katayama A, Kawai Y, Naito K, Mitani Y, Morlighem JE, Hayashizaki Y, and Lezhava A

Biochemical and biophysical research communications 383(4):455-9, 2009 Jun 12 - Who cited this? | PubMed ID: 19371726 | Fulltext

Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type?.

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Toyoda Y, Sakurai A, Mitani Y, Nakashima M, Yoshiura K, Nakagawa H, Sakai Y, Ota I, Lezhava A, Hayashizaki Y, Niikawa N, and Ishikawa T

The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 23(6):2001-13, 2009 Jun - Who cited this? | PubMed ID: 19383836 | Fulltext

Role of survival motor neuron complex components in small nuclear ribonucleoprotein assembly.

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Ogawa C, Usui K, Ito F, Itoh M, Hayashizaki Y, and Suzuki H

The Journal of biological chemistry 284(21):14609-17, 2009 May 22 - Who cited this? | PubMed ID: 19321448 | Fulltext

Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches.

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Brinkmeier ML, Davis SW, Carninci P, Macdonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, and Camper SA

Genomics 93(5):449-60, 2009 May - Who cited this? | PubMed ID: 19121383 | Fulltext

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

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FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M,

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Nature genetics 41(5):553-62, 2009 May - Who cited this? | PubMed ID: 19377474 | Fulltext

The regulated retrotransposon transcriptome of mammalian cells.

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Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR,

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Nature genetics 41(5):563-71, 2009 May - Who cited this? | PubMed ID: 19377475 | Fulltext

Tiny RNAs associated with transcription start sites in animals.

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Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C,

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Nature genetics 41(5):572-8, 2009 May - Who cited this? | PubMed ID: 19377478 | Fulltext

Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks.

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Usui K, Maki T, Ito F, Suenaga A, Kidoaki S, Itoh M, Taiji M, Matsuda T, Hayashizaki Y, and Suzuki H

Protein science : a publication of the Protein Society 18(5):960-9, 2009 May - Who cited this? | PubMed ID: 19384998 | Fulltext

Rapid Single-Nucleotide Polymorphism Detection of Cytochrome P450 (CYP2C9) and Vitamin K Epoxide Reductase (VKORC1) Genes for the Warfarin Dose Adjustment by the SMart-Amplification Process Version 2.

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Aomori T, Yamamoto K, Oguchi-Katayama A, Kawai Y, Ishidao T, Mitani Y, Kogo Y, Lezhava A, Fujita Y, Obayashi K, Nakamura K, Kohnke H, Wadelius M, Ekström L, Skogastierna C, Rane A,

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Clinical chemistry 55(4):804-12, 2009 Apr - Who cited this? | PubMed ID: 19181737 | Fulltext

Genetics, gene expression and bioinformatics of the pituitary gland.

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Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, and Camper SA

Hormone research 71 Suppl 2:101-15, 2009 Apr - Who cited this? | PubMed ID: 19407506 | Fulltext

Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi.

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Tomaru Y, Nakanishi M, Miura H, Kimura Y, Ohkawa H, Ohta Y, Hayashizaki Y, and Suzuki M

Nucleic acids research 37(4):1049-60, 2009 Mar - Who cited this? | PubMed ID: 19129217 | Fulltext

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

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Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T,

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Genome research 19(2):255-65, 2009 Feb - Who cited this? | PubMed ID: 19074369 | Fulltext

Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes.

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Miura H, Tomaru Y, Nakanishi M, Kondo S, Hayashizaki Y, and Suzuki M

Nucleic acids research 37(3):778-92, 2009 Feb - Who cited this? | PubMed ID: 19074951 | Fulltext

Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.

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Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J,

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PLoS ONE 4(1):e4219, 2009 - Who cited this? | PubMed ID: 19156205 | Fulltext

Preparation of full-length cDNA libraries: focus on metazoans.

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Harada M and Hayashizaki Y

Methods in molecular biology (Clifton, N.J.) 533:1-39, 2009 - Who cited this? | PubMed ID: 19277561 | Fulltext

Generation of full-length cDNA libraries: focus on plants.

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Seki M, Kamiya A, Carninci P, Hayashizaki Y, and Shinozaki K

Methods in molecular biology (Clifton, N.J.) 533:1-20, 2009 - Who cited this? | PubMed ID: 19277562 | Fulltext

Data-driven normalization strategies for high-throughput quantitative RT-PCR.

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Mar JC, Kimura Y, Schroder K, Irvine KM, Hayashizaki Y, Suzuki H, Hume D, and Quackenbush J

BMC bioinformatics 10:110, 2009 - Who cited this? | PubMed ID: 19374774 | Fulltext

SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes.

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Kawaji H, Hayashizaki Y, and Daub CO

BMC bioinformatics 10:133, 2009 - Who cited this? | PubMed ID: 19422683 | Fulltext

Chromatin conformation signatures of cellular differentiation.

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Fraser J, Rousseau M, Shenker S, Ferraiuolo MA, Hayashizaki Y, Blanchette M, and Dostie J

Genome biology 10(4):R37, 2009 - Who cited this? | PubMed ID: 19374771 | Fulltext

Transcriptional features of genomic regulatory blocks.

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Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, and Lenhard B

Genome biology 10(4):R38, 2009 - Who cited this? | PubMed ID: 19374772 | Fulltext

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.

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Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, and Forrest AR

Genome biology 10(4):R39, 2009 - Who cited this? | PubMed ID: 19374773 | Fulltext

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

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Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, and Daub CO

Genome biology 10(4):R40, 2009 - Who cited this? | PubMed ID: 19374775 | Fulltext

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation.

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Kubosaki A, Tomaru Y, Tagami M, Arner E, Miura H, Suzuki T, Suzuki M, Suzuki H, and Hayashizaki Y

Genome biology 10(4):R41, 2009 - Who cited this? | PubMed ID: 19374776 | Fulltext

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns.

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Kawaura K, Mochida K, Enju A, Totoki Y, Toyoda A, Sakaki Y, Kai C, Kawai J, Hayashizaki Y, Seki M, Shinozaki K, and Ogihara Y

BMC genomics 10:271, 2009 - Who cited this? | PubMed ID: 19534823 | Fulltext

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

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Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, and van Nimwegen E

Genome biology 10(7):R79, 2009 - Who cited this? | PubMed ID: 19624849 | Fulltext

Detection of SNP by the isothermal smart amplification method.

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Lezhava A and Hayashizaki Y

Methods in molecular biology (Clifton, N.J.) 578:437-51, 2009 - Who cited this? | PubMed ID: 19768611 | Fulltext

Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential.

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Hoat TX, Bertin N, Ninomiya N, Fukuda S, Usui K, Kawai J, Hayashizaki Y, and Suzuki H

BMC cell biology 10:69, 2009 - Who cited this? | PubMed ID: 19772597 | Fulltext

Genome-wide analysis of cancer/testis gene expression.

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Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ,

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Proceedings of the National Academy of Sciences of the United States of America 105(51):20422-7, 2008 Dec 23 - Who cited this? | PubMed ID: 19088187 | Fulltext

An epigenetic aberration increased in intergenic regions of cloned mice.

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Nishida H, Kondo S, Suzuki T, Tsujimura Y, Komatsu S, Wakayama T, and Hayashizaki Y

Mammalian genome : official journal of the International Mammalian Genome Society 19(10-12):667-74, 2008 Dec - Who cited this? | PubMed ID: 18958525 | Fulltext

Rapidly evolving human promoter regions.

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Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, and Semple CA

Nature genetics 40(11):1262-3; author reply 1263-4, 2008 Nov - Who cited this? | PubMed ID: 18957975 | Fulltext

Metagenomic diagnosis of bacterial infections.

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Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, Kataoka C, Honda T, Yasunaga T, Nakaya T, Kawai J, Hayashizaki Y, Horii T, and Iida T

Emerging infectious diseases 14(11):1784-6, 2008 Nov - Who cited this? | PubMed ID: 18976571 | Fulltext

Rapid Screening Assay for KRAS Mutations by the Modified Smart Amplification Process.

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Tatsumi K, Mitani Y, Watanabe J, Takakura H, Hoshi K, Kawai Y, Kikuchi T, Kogo Y, Oguchi-Katayama A, Tomaru Y, Kanamori H, Baba M, Ishidao T, Usui K, Itoh M, Cizdziel PE,

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The Journal of molecular diagnostics : JMD, 2008 Oct 2 - Who cited this? | PubMed ID: 18832461 | Fulltext

Galpha14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue.

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Shindo Y, Miura H, Carninci P, Kawai J, Hayashizaki Y, Ninomiya Y, Hino A, Kanda T, and Kusakabe Y

Biochemical and biophysical research communications, 2008 Sep 16 - Who cited this? | PubMed ID: 18801333 | Fulltext

Transcriptome-based systematic identification of extracellular matrix proteins.

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Manabe RI, Tsutsui K, Yamada T, Kimura M, Nakano I, Shimono C, Sanzen N, Furutani Y, Fukuda T, Oguri Y, Shimamoto K, Kiyozumi D, Sato Y, Sado Y, Senoo H, Yamashina S,

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Proceedings of the National Academy of Sciences of the United States of America, 2008 Aug 29 - Who cited this? | PubMed ID: 18757743 | Fulltext

Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation.

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Tochitani S and Hayashizaki Y

Biochemical and biophysical research communications 372(4):691, 2008 Aug 8 - Who cited this? | PubMed ID: 18538132 | Fulltext

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.

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Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Güntert P, Tanaka A, Hayashizaki Y, Muto Y, and Yokoyama S

Nucleic acids research 36(14):4754-67, 2008 Aug - Who cited this? | PubMed ID: 18641416 | Fulltext

Structure of the C-terminal PID domain of Fe65L1 complexed with the cytoplasmic tail of APP reveals a novel peptide binding Mode.

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Li H, Koshiba S, Hayashi F, Tochio N, Tomozawa T, Kasai T, Yabuki T, Motoda Y, Harada T, Watanabe S, Inoue M, Hayashizaki Y, Tanaka A, Kigawa T, and Yokoyama S

The Journal of biological chemistry, 2008 Jul 23 - Who cited this? | PubMed ID: 18650440 | Fulltext

FOXP1 is an androgen-responsive transcription factor that negatively regulates androgen receptor signaling in prostate cancer cells.

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Takayama K, Horie-Inoue K, Ikeda K, Urano T, Murakami K, Hayashizaki Y, Ouchi Y, and Inoue S

Biochemical and biophysical research communications, 2008 Jul 17 - Who cited this? | PubMed ID: 18640093 | Fulltext

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.

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Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P,

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BioTechniques 45(1):95-7, 2008 Jul - Who cited this? | PubMed ID: 18611171 | Fulltext

Sensitive detection of EGFR mutations using a competitive probe to suppress background in the SMart Amplification Process.

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Kawai Y, Kikuchi T, Mitani Y, Kogo Y, Itoh M, Usui K, Kanamori H, Kaiho A, Takakura H, Hoshi K, Cizdziel PE, and Hayashizaki Y

Biologicals : journal of the International Association of Biological Standardization 36(4):234-8, 2008 Jul - Who cited this? | PubMed ID: 18440823 | Fulltext

Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.

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Kuwasako K, Takahashi M, Tochio N, Abe C, Tsuda K, Inoue M, Terada T, Shirouzu M, Kobayashi N, Kigawa T, Taguchi S, Tanaka A, Hayashizaki Y, Güntert P, Muto Y, and Yokoyama S

Biochemistry 47(24):6437, 2008 Jun 17 - Who cited this? | PubMed ID: 18500819 | Fulltext

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