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1. Full Text ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
by Oki, Shinya and Ohta, Tazro and Shioi, Go and Hatanaka, Hideki and Ogasawara, Osamu and Okuda, Yoshihiro and Kawaji, Hideya and Nakaki, Ryo and Sese, Jun and Meno, Chikara
EMBO reports, ISSN 1469-221X, 12/2018, Volume 19, Issue 12, p. n/a
transcription factor | enhancer | data mining | ChIP‐seq | DNase‐seq | ChIP-seq | DNase-seq | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Transcription Factors - metabolism | Animals | Chromatin Immunoprecipitation | Humans | Data Mining | Enhancer Elements, Genetic - genetics | Genetic Loci | Internet | Sequence Analysis, DNA | Deoxyribonuclease | Regulators | Chromatin | Immunoprecipitation | Yeast | Target recognition | Transcription | Genes | Data processing | Genomes | Data mining | Loci | Proteins | Web services | Histones | Fruit flies | Gene loci | Binding sites | Index Medicus | Methods & Resources | Chromatin, Epigenetics, Genomics & Functional Genomics | Resource
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2. Full Text A draft network of ligand-receptor-mediated multicellular signalling in human
by Ramilowski, Jordan A and Goldberg, Tatyana and Harshbarger, Jayson and Kloppman, Edda and Lizio, Marina and Satagopam, Venkata P and Itoh, Masayoshi and Kawaji, Hideya and Carninci, Piero and Rost, Burkhard and Forrest, Alistair R.R
Nature communications, ISSN 2041-1723, 07/2015, Volume 6, Issue 1, pp. 7866 - 7866
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Animals | Humans | Cell Communication | Receptors, Cell Surface - metabolism | Ligands | Software | Evolution, Molecular | Index Medicus
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3. Full Text Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
by Fraser, James and Ferrai, Carmelo and Chiariello, Andrea M and Schueler, Markus and Rito, Tiago and Laudanno, Giovanni and Barbieri, Mariano and Moore, Benjamin L and Kraemer, Dorothee CA and Aitken, Stuart and Xie, Sheila Q and Morris, Kelly J and Itoh, Masayoshi and Kawaji, Hideya and Jaeger, Ines and Hayashizaki, Yoshihide and Carninci, Piero and Forrest, Alistair RR and Semple, Colin A and Dostie, Josée and Pombo, Ana and Nicodemi, Mario and FANTOM Consortium and The FANTOM Consortium
Molecular systems biology, ISSN 1744-4292, 12/2015, Volume 11, Issue 12, pp. 852 - n/a
polymer modelling | chromosome architecture | chromatin contacts | epigenetics | gene expression | Animals | Epigenesis, Genetic | Cells, Cultured | Gene Expression Regulation | Chromatin Assembly and Disassembly | Mouse Embryonic Stem Cells - cytology | Neurons - cytology | Transcription, Genetic | Cell Differentiation | Chromosomes - chemistry | Mice | Chromatin - chemistry | Chromatin | Genomes | Cellular biology | Gene expression | Chromosomes | Substructures | Trees | Transcription | Neurons | Differentiation (biology) | Innovations | Cell division | Mammals | Structural hierarchy | Datasets | Domains | Stem cells | Packaging | Folding | Deoxyribonucleic acid--DNA | Index Medicus
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4. Full Text Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
by Severin, Jessica and Lizio, Marina and Harshbarger, Jayson and Kawaji, Hideya and Daub, Carsten O and Hayashizaki, Yoshihide and Bertin, Nicolas and Forrest, Alistair R. R and Beckhouse, Anthony and Wells, Christine and Vijayan, Dipti and Mason, Elizabeth and Wolvetang, Ernst and Hitchens, Kelly and Le Cao, Kim-Anh and Nielsen, Lars and Hayashizaki, Yoshihide and Fearnley, Liam and Kenna, Tony and FANTOM Consortium and The FANTOM Consortium
Nature biotechnology, ISSN 1087-0156, 03/2014, Volume 32, Issue 3, pp. 217 - 219
Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Sequence Analysis, RNA - methods | User-Computer Interface | Humans | Gene Expression Profiling - methods | Software | Internet | Genomics - methods | RNA sequencing | Nucleotide sequencing | Innovations | DNA sequencing | Index Medicus
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5. Full Text Effects of cytosine methylation on transcription factor binding sites
by Medvedeva, Yulia A and Khamis, Abdullah M and Kulakovskiy, Ivan V and Ba-Alawi, Wail and Bhuyan, Md Shariful I and Kawaji, Hideya and Lassmann, Timo and Harbers, Matthias and Forrest, Alistair R.R and Bajic, Vladimir B and FANTOM Consortium and FANTOM consortium and The FANTOM consortium
BMC genomics, ISSN 1471-2164, 03/2014, Volume 15, Issue 1, pp. 119 - 119
CAGE | RRBS | DNA methylation | Transcription factor binding sites | Transcriptional regulation | Bioinformatics | Computational biology | CpG " traffic lights" | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Transcription Factors - metabolism | Promoter Regions, Genetic | DNA Methylation | Algorithms | Transcription Factors - chemistry | Cytosine - metabolism | Humans | Transcription Initiation Site | Computational Biology | CpG Islands | Cytosine - chemistry | Binding Sites | Chromatin | Analysis | DNA binding proteins | Transcription factors | Cell division | Biology | Preventive medicine | Gene expression | Experiments | Studies | Education | Epigenetics | Life sciences | Binding sites | Deoxyribonucleic acid--DNA | Index Medicus
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6. Full Text Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells
by Yoshida, Tokuyuki and Naito, Yuki and Yasuhara, Hidenori and Sasaki, Kiyomi and Kawaji, Hideya and Kawai, Jun and Naito, Mikihiko and Okuda, Haruhiro and Obika, Satoshi and Inoue, Takao
Genes to cells : devoted to molecular & cellular mechanisms, ISSN 1356-9597, 12/2019, Volume 24, Issue 12, pp. 827 - 835
pre‐mRNA | microarray analysis | Gapmer | off‐target effects | antisense | Genetics & Heredity | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Sequence Analysis, RNA - methods | Algorithms | Oligonucleotides, Antisense - genetics | Base Pairing | Humans | Oligonucleotides, Antisense - chemistry | Oligonucleotides, Antisense - metabolism | Cell Line, Tumor | Base Pair Mismatch | RNA - chemistry | RNA - genetics | RNA - metabolism | Complementarity | Nucleotide sequence | Toxicity | Antisense oligonucleotides | Ribonuclease H | Genomes | Ribonucleic acid--RNA | Index Medicus | Original
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7. Full Text Hidden layers of human small RNAs
by Kawaji, Hideya and Nakamura, Mari and Takahashi, Yukari and Sandelin, Albin and Katayama, Shintaro and Fukuda, Shiro and Daub, Carsten O and Kai, Chikatoshi and Kawai, Jun and Yasuda, Jun and Carninci, Piero and Hayashizaki, Yoshihide
BMC genomics, ISSN 1471-2164, 04/2008, Volume 9, Issue 1, pp. 157 - 157
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Multigene Family - genetics | Gene Library | Humans | Molecular Sequence Data | RNA - genetics | Blotting, Northern | Sequence Alignment | Sequence Analysis, RNA | Base Pairing | Base Sequence | RNA - classification | Evolution, Molecular | RNA - metabolism | Origin | Life | Research | RNA | Identification and classification | Index Medicus
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8. Full Text refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites
by Abugessaisa, Imad and Noguchi, Shuhei and Hasegawa, Akira and Kondo, Atsushi and Kawaji, Hideya and Carninci, Piero and Kasukawa, Takeya
Journal of molecular biology, ISSN 0022-2836, 06/2019, Volume 431, Issue 13, pp. 2407 - 2422
annotation | data integration | transcription start sites | transcriptional regulation | reference data | Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Genetic research | Genetic transcription | DNA binding proteins | Analysis | Genes | Genomics | Index Medicus
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9. Full Text Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes
by Yagi, Yohsuke and Ohkubo, Takuya and Kawaji, Hideya and Machida, Akira and Miyata, Haruka and Goda, Saori and Roy, Sugata and Hayashizaki, Yoshihide and Suzuki, Harukazu and Yokota, Takanori
Neuroscience letters, ISSN 0304-3940, 01/2017, Volume 636, pp. 48 - 57
microRNA | Digital PCR | Next-generation sequencing | Cerebrospinal fluid | Small RNA | Exosome | Neurosciences | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | Brain - metabolism | Exosomes - metabolism | Sequence Analysis, RNA | MicroRNAs - cerebrospinal fluid | Humans | Gene Expression Profiling | High-Throughput Nucleotide Sequencing | MicroRNAs - blood | MicroRNA | Medicine, Preventive | Genomics | College graduates | Preventive health services | RNA | Nervous system diseases | Index Medicus
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10. Full Text Hotspots of De Novo Point Mutations in Induced Pluripotent Stem Cells
by Yoshihara, Masahito and Araki, Ryoko and Kasama, Yasuji and Sunayama, Misato and Abe, Masumi and Nishida, Kohji and Kawaji, Hideya and Hayashizaki, Yoshihide and Murakawa, Yasuhiro
Cell reports (Cambridge), ISSN 2211-1247, 10/2017, Volume 21, Issue 2, pp. 308 - 315
iPSCs | genomics | iPSC-based cell therapy | lamina-associated domains | point mutation | epigenetics | heterochromatin | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Cell Line | Point Mutation | Animals | Heterochromatin - genetics | Humans | Mutation Rate | Mice | Polymorphism, Single Nucleotide | Induced Pluripotent Stem Cells - cytology | Cellular Reprogramming | Induced Pluripotent Stem Cells - metabolism | Index Medicus
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