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1. Full Text An atlas of human long non-coding RNAs with accurate 5′ ends
by Hon, Chung-Chau and Ramilowski, Jordan A and Harshbarger, Jayson and Bertin, Nicolas and Rackham, Owen J.L and Gough, Julian and Denisenko, Elena and Schmeier, Sebastian and Poulsen, Thomas M and Severin, Jessica and Lizio, Marina and Kawaji, Hideya and Kasukawa, Takeya and Itoh, Masayoshi and Burroughs, A. Maxwell and Noma, Shohei and Djebali, Sarah and Alam, Tanvir and Medvedeva, Yulia A and Testa, Alison C and Lipovich, Leonard and Yip, Chi-Wai and Abugessaisa, Imad and Mendez, Mickal and Hasegawa, Akira and Tang, Dave and Lassmann, Timo and Heutink, Peter and Babina, Magda and Wells, Christine A and Kojima, Soichi and Nakamura, Yukio and Suzuki, Harukazu and Daub, Carsten O and De Hoon, Michiel J.L and Arner, Erik and Hayashizaki, Yoshihide and Carninci, Piero and Forrest, Alistair R.R
Nature, ISSN 0028-0836, 03/2017, Volume 543, Issue 7644, pp. 199 - 204
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we... 
EVOLUTION | DATABASE | LANDSCAPE | ANNOTATION | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES | TRANSCRIPTION | GENE-EXPRESSION | ARCHITECTURE | GENOME-WIDE ASSOCIATION | LNCRNA | Conserved Sequence - genetics | Genome-Wide Association Study | Datasets as Topic | RNA, Long Noncoding - chemistry | Epigenesis, Genetic | Genomics | Humans | Molecular Sequence Annotation | RNA, Messenger - genetics | Cells, Cultured | Gene Expression Regulation | Databases, Genetic | Gene Expression Profiling | RNA, Long Noncoding - genetics | Transcriptome - genetics | RNA Stability | Promoter Regions, Genetic - genetics | Genome, Human - genetics | Organ Specificity - genetics | Enhancer Elements, Genetic - genetics | Polymorphism, Single Nucleotide | Internet | Quantitative Trait Loci - genetics | RNA sequencing | Usage | Research | Genetic transcription | Human genome | Biosynthesis | RNA polymerase | Index Medicus | Life Sciences
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2. Full Text An atlas of active enhancers across human cell types and tissues
by Andersson, Robin and Gebhard, Claudia and Miguel-Escalada, Irene and Hoof, Ilka and Bornholdt, Jette and Boyd, Mette and Chen, Yun and Zhao, Xiaobei and Schmidl, Christian and Suzuki, Takahiro and Ntini, Evgenia and Arner, Erik and Valen, Eivind and Li, Kang and Schwarzfischer, Lucia and Glatz, Dagmar and Raithel, Johanna and Lilje, Berit and Rapin, Nicolas and Bagger, Frederik Otzen and Jørgensen, Mette and Andersen, Peter Refsing and Bertin, Nicolas and Rackham, Owen and Burroughs, A. Maxwell and Baillie, J. Kenneth and Ishizu, Yuri and Shimizu, Yuri and Furuhata, Erina and Maeda, Shiori and Negishi, Yutaka and Mungall, Christopher J and Meehan, Terrence F and Lassmann, Timo and Itoh, Masayoshi and Kawaji, Hideya and Kondo, Naoto and Kawai, Jun and Lennartsson, Aneas and Daub, Carsten O and Heutink, Peter and Hume, David A and Jensen, Torben Heick and Suzuki, Harukazu and Hayashizaki, Yoshihide and Müller, Ferenc and Forrest, Alistair R. R and Carninci, Piero and Rehli, Michael and Sandelin, Albin and de Hoon, Michiel J. L and Haberle, Vanja and Kulakovskiy, Ivan V and Lizio, Marina and Mungall, Christoher J and Schmeier, Sebastian and Dimont, Emmanuel and Schmid, Christian and Schaefer, Ulf and Medvedeva, Yulia A and Plessy, Charles and Vitezic, Morana and Severin, James and Semple, Colin A and Young, Robert S and Francescatto, Margherita and Alam, Intikhab and Albanese, Davide and Altschuler, Gabriel M and Arakawa, Takahiro and Archer, John A. C and Arner, Peter and Babina, Magda and Rennie, Sarah and Balwierz, Piotr J and Beckhouse, Anthony G and Pradhan-Bhatt, Swati and Blake, Judith A and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessano and Briggs, James and Brombacher, Frank and Califano, Anea and Cannistracti, Carlo V and Carbajo, Daniel and Chierici, Marco and Ciani, Yari and Clevers, Hans C and Dalla, Emiliano and Davis, Carrie A and Detmar, Michael and Diehl, Alexander D and Dohi, Taeko and bløs, Finn and Edge, Albert S. B and Edinger, Matthias and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and ... and FANTOM Consortium and The FANTOM Consortium
Nature, ISSN 0028-0836, 2014, Volume 507, Issue 7493, pp. 455 - 461
Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory... 
TRANSCRIPTION FACTORS | ZEBRAFISH EMBRYOS | ELEMENTS | HUMAN GENOME | DNA METHYLATION | RNA-SEQ | MULTIDISCIPLINARY SCIENCES | CAP-ANALYSIS | GENE-EXPRESSION | PROMOTER DIRECTIONALITY | REGULATORY SEQUENCES | Cell Line | Genetic Predisposition to Disease - genetics | Atlases as Topic | Gene Expression Regulation - genetics | Humans | Molecular Sequence Annotation | RNA, Messenger - genetics | Cells, Cultured | Organ Specificity | Promoter Regions, Genetic - genetics | RNA, Messenger - biosynthesis | Transcription Initiation Site | Polymorphism, Single Nucleotide - genetics | Enhancer Elements, Genetic - genetics | HeLa Cells | Transcription Initiation, Genetic | Cluster Analysis | Physiological aspects | Genetic aspects | Promoters (Genetics) | Research | Gene expression | Cells | Proteins | Tissue | Binding sites | Index Medicus
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3. Full Text Novel Small Noncoding RNAs in Mouse Spermatozoa, Zygotes and Early Embryos
by Kawano, Mitsuoki and Kawaji, Hideya and Grandjean, Valérie and Kiani, Jafar and Rassoulzadegan, Minoo
PLoS ONE, ISSN 1932-6203, 09/2012, Volume 7, Issue 9, pp. e44542 - e44542
The recent discovery of a significant amount of RNA in spermatozoa contradicted the previously held belief that paternal contribution was limited to one copy... 
SPERM | SERVER | MULTIDISCIPLINARY SCIENCES | OOCYTES | SIRNAS | MICRORNAS | INHERITANCE | PIWI-INTERACTING RNAS | RNA, Small Interfering - genetics | RNA Processing, Post-Transcriptional | Epigenesis, Genetic | Male | MicroRNAs - metabolism | Gene Expression Profiling | Spermatozoa - metabolism | Animals | Chromosomes - genetics | Gene Expression Regulation, Developmental | Reverse Transcriptase Polymerase Chain Reaction - methods | Oxygen - chemistry | RNA, Small Untranslated - genetics | Spermatozoa - physiology | Cell Differentiation | Mice | Spermatozoa - cytology | Zygote - physiology | DNA, Complementary - metabolism | RNA - metabolism | Animal experimentation | Epigenetic inheritance | Embryonic development | Spermatozoa | Messenger RNA | MicroRNA | Analysis | Genomics | Genomes | Post-transcription | Sperm | Heredity | Gene expression | Ribonucleic acid--RNA | Embryos | Oocytes | Gene sequencing | Embryonic growth stage | Zygotes | Oxidation resistance | Embryogenesis | Acids | MicroRNAs | Technology assessment | Epigenetics | Oxidation | Life sciences | Chromosome 17 | Index Medicus | Life Sciences | Development Biology | RNA | Ribonucleic acid
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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
SYSTEM | PROJECT | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENOME BROWSER | 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 Genome annotation
by Abugessaisa, Imad and Kasukawa, Takeya and Kawaji, Hideya
Methods in Molecular Biology, ISSN 1064-3745, 2017, Volume 1525, pp. 107 - 121
The dynamic structure and functions of genomes are being revealed simultaneously with the progress of technologies and researches in genomics. Evidence... 
Gene functions | Genome annotation | Epigenetic marks | Genome browser | RNA-Seq | Databases, Genetic | Software | Genomics - methods | Epigenesis, Genetic - genetics | Index Medicus
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6. 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
Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene... 
CAGE | RRBS | DNA methylation | Transcription factor binding sites | Transcriptional regulation | Bioinformatics | Computational biology | CpG " traffic lights" | PROMOTER DNA METHYLATION | PROTEIN | CPG ISLAND | APRT GENE PROMOTER | HUMAN GENOME | CANCER EPIGENETICS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | GENETICS & HEREDITY | EPIGENETIC REGULATION | WEIGHT MATRICES | EXPRESSION | CpG "traffic lights" | 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 | Physiological aspects | Transcription factors | Genetic aspects | Cytosine | Research | Methylation | Chromatin | Analysis | DNA binding proteins | Cell division | Biology | Preventive medicine | Gene expression | Experiments | Studies | Education | Epigenetics | Life sciences | Binding sites | Deoxyribonucleic acid--DNA | Index Medicus
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7. 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
Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions... 
CELL COMMUNICATION | EVOLUTION | DATABASE | MULTIDISCIPLINARY SCIENCES | PROTEIN FAMILIES | GENE-EXPRESSION | CHEMOKINE RECEPTOR | GROWTH-FACTOR | DIFFERENTIATION | IDENTIFICATION | T-CELLS | Animals | Humans | Cell Communication | Receptors, Cell Surface - metabolism | Ligands | Software | Evolution, Molecular | Index Medicus
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8. 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
Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains ( TAD s), which are arranged into compartments spanning multiple... 
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 | Index Medicus
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9. 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, pp. e46255 - n/a
We have fully integrated public chromatin chromatin immunoprecipitation sequencing (Ch IP ‐seq) and DN ase‐seq data ( n > 70,000) derived from six... 
transcription factor | enhancer | data mining | seq | ase‐seq | ChIP-seq | DNase-seq | READ ALIGNMENT | BROWSER | CHROMATIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | IDENTIFICATION | GENOME | FIBROBLASTS | CELL BIOLOGY | ENCYCLOPEDIA | DNA ELEMENTS | 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 | ChIP‐seq | DNase‐seq
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10. Full Text The Systems Biology Graphical Notation
by Wu, Guanming and Mi, Huaiyu and Kim, Sohyoung and Luna, Augustin and Sorokin, Anatoly and Jouraku, Akiya and Li, Lu and Wimalaratne, Sarala M and Wegner, Katja and Watterson, Steven and Bergman, Frank T and Villéger, Alice and Kawaji, Hideya and Sahle, Sven and Ghosh, Samik and Schreiber, Falk and Demir, Emek and Kohn, Kurt and Funahashi, Akira and Kolpakov, Fedor and Sander, Chris and Kitano, Hiroaki and Schmidt, Esther and Sauro, Herbert and Goryanin, Igor and Kell, Douglas B and Ghazal, Peter and Aladjem, Mirit I and Novère, Nicolas Le and Moodie, Stuart and Calzone, Laurence and Matsuoka, Yukiko and Courtot, Melanie and Freeman, Tom C and Snoep, Jacky L and Boyd, Sarah E and Hucka, Michael and Gauges, Ralph and Dogrusoz, Ugur
Nature Biotechnology, ISSN 1087-0156, 08/2009, Volume 27, Issue 8, pp. 735 - 741
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity,... 
COLLABORATIVE CONSTRUCTION | REPRESENTATION | CELLULAR PATHWAYS | NETWORKS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DIAGRAM | Computer Graphics - history | Software | Internet | History, 20th Century | Systems Biology - history | Usage | Chemistry | Visual programming (Computer science) | Systems biology | Visual programming languages (Computer science) | Information management | Notation | Biochemistry | Biomedical research | Symbols | Standards | Index Medicus
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11. 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
Background: Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena.... 
DOUBLE-STRANDED-RNA | CAENORHABDITIS-ELEGANS | DROSOPHILA-MELANOGASTER | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATURE TRANSFER-RNA | REVERSE TRANSCRIPTION | GENETICS & HEREDITY | GENE-EXPRESSION | TRANSPOSABLE ELEMENTS | C-ELEGANS | SACCHAROMYCES-CEREVISIAE | NON-MESSENGER RNAS | 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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