• The University of Western Australia (M575), 35 Stirling Highway,

    6009 Perth

    Australia

  • 13640 Citations
  • 46 h-Index
1994 …2023
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Research Output 1994 2019

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Article
2019
1 Citation (Scopus)

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

FANTOM Consortium, 15 Aug 2019, In : Molecular Neurobiology. 56, 8, p. 5392-5415 24 p.

Research output: Contribution to journalArticle

Open Access
Nervous System Heredodegenerative Disorders
Neurodegenerative Diseases
Long Noncoding RNA
Genes
Transcription Initiation Site

Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics

Roy, R., Winteringham, L. N., Lassmann, T. & Forrest, A. R. R., Dec 2019, In : Molecular Cancer Therapeutics. 18, 12, p. 2480-2489 10 p.

Research output: Contribution to journalArticle

Pharmaceutical Preparations
Neoplasms
Therapeutics
Genomics
Precision Medicine

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

Ha, T. J., Zhang, P. G. Y., Robert, R., Yeung, J., Swanson, D. J., Mathelier, A., Wasserman, W. W., Im, S., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., Carninci, P., Hayashizaki, Y., Forrest, A. R. R. & Goldowitz, D., 18 Sep 2019, In : BMC Genomics. 20, 1, 718.

Research output: Contribution to journalArticle

Open Access
Transcriptome
Genes
Gene Regulatory Networks
Regulator Genes
Computational Biology

Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions

Olivé, M., Engvall, M., Ravenscroft, G., Cabrera-Serrano, M., Jiao, H., Bortolotti, C. A., Pignataro, M., Lambrughi, M., Jiang, H., Forrest, A. R. R., Benseny-Cases, N., Hofbauer, S., Obinger, C., Battistuzzi, G., Bellei, M., Borsari, M., Di Rocco, G., Viola, H. M., Hool, L. C., Cladera, J. & 24 othersLagerstedt-Robinson, K., Xiang, F., Wredenberg, A., Miralles, F., Baiges, J. J., Malfatti, E., Romero, N. B., Streichenberger, N., Vial, C., Claeys, K. G., Straathof, C. S. M., Goris, A., Freyer, C., Lammens, M., Bassez, G., Kere, J., Clemente, P., Sejersen, T., Udd, B., Vidal, N., Ferrer, I., Edström, L., Wedell, A. & Laing, N. G., 1 Dec 2019, In : Nature Communications. 10, 1, 1396.

Research output: Contribution to journalArticle

Open Access
myoglobin
Myoglobin
Muscular Diseases
inclusions
muscles
3 Citations (Scopus)

scMatch: a single-cell gene expression profile annotation tool using reference datasets

Hou, R., Denisenko, E. & Forrest, A. R. R., 1 Nov 2019, In : Bioinformatics (Oxford, England). 35, 22, p. 4688-4695 8 p.

Research output: Contribution to journalArticle

Open Access
Gene Expression Profile
Transcriptome
Gene expression
Annotation
RNA

Systematic bias assessment in solid tissue 10x scRNA-seq workflows

Denisenko, E., Guo, B., Jones, M., Hou, R., De Kock, L., Lassmann, T., Poppe, D., Clement, O., Simmons, R. K., Lister, R. & Forrest, A., 6 Nov 2019, (Submitted) In : bioRxiv. p. 1-47 47 p., 832444.

Research output: Contribution to journalArticle

Small Cytoplasmic RNA
Workflow
RNA Sequence Analysis
Chromium
Genomics
2018
3 Citations (Scopus)
177 Downloads (Pure)

Bi-allelic mutations in MYL1 cause a severe congenital myopathy

Ravenscroft, G., Zaharieva, I. T., Bortolotti, C. A., Lambrughi, M., Pignataro, M., Borsari, M., Sewry, C. A., Phadke, R., Haliloglu, G., Ong, R., Goullée, H., Whyte, T., Consortium, U. K., Manzur, A., Talim, B., Kaya, U., Osborn, D. P. S., Forrest, A. R. R., Laing, N. G. & Muntoni, F., 15 Dec 2018, In : Human Molecular Genetics. 27, 24, p. 4263-4272 10 p.

Research output: Contribution to journalArticle

Open Access
File
Myotonia Congenita
Skeletal Muscle
Myosin Light Chains
Mutation
Exome
1 Citation (Scopus)
Open Access
Immediate-Early Genes
Genes
Chemical activation
Gene Expression
Untranslated RNA
2 Citations (Scopus)

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Zhang, P. G. Y., Yeung, J., Gupta, I., Ramirez, M., Ha, T., Swanson, D. J., Nagao-Sato, S., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., de Hoon, M., The FANTOM Consortium, Carninci, P., Forrest, A. R. R., Hayashizaki, Y. & Goldowitz, D., Jun 2018, In : Cerebellum. 17, 3, p. 308–325 18 p.

Research output: Contribution to journalArticle

Laser Capture Microdissection
Transcription Factors
Gene Expression Profiling
Transcriptome
Genes
5 Citations (Scopus)

Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity

Sakaue, S., Hirata, J., Maeda, Y., Kawakami, E., Nii, T., Kishikawa, T., Ishigaki, K., Terao, C., Suzuki, K., Akiyama, M., Suita, N., Masuda, T., Ogawa, K., Yamamoto, K., Saeki, Y., Matsushita, M., Yoshimura, M., Matsuoka, H., Ikari, K., Taniguchi, A. & 15 othersYamanaka, H., Kawaji, H., Lassmann, T., Itoh, M., Yoshitomi, H., Ito, H., Ohmura, K., R Forrest, A. R., Hayashizaki, Y., Carninci, P., Kumanogoh, A., Kamatani, Y., de Hoon, M., Yamamoto, K. & Okada, Y., 14 Dec 2018, In : Nucleic Acids Research. 46, 22, p. 11898-11909 12 p.

Research output: Contribution to journalArticle

Open Access
Organ Specificity
Gene Regulatory Networks
MicroRNAs
Biomarkers
Genome-Wide Association Study
4 Citations (Scopus)
Open Access
Genetic Loci
activity pattern
Genetic Predisposition to Disease
human diseases
Susceptibility
13 Citations (Scopus)

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

Roy, S., Schmeier, S., Kaczkowski, B., Arner, E., Alam, T., Ozturk, M., Tamgue, O., Parihar, S. P., Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Guler, R., Bajic, V. B., Brombacher, F. & Suzuki, H., 1 Dec 2018, In : Scientific Reports. 8, 1, 6758.

Research output: Contribution to journalArticle

Open Access
Mycobacterium Infections
Mycobacterium tuberculosis
Macrophages
Host-Pathogen Interactions
Interleukin-13
2017
23 Citations (Scopus)

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

Baillie, J. K., Arner, E., Daub, C. O., De Hoon, M. J. L., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Consortium, F., Faulkner, G. J., Wells, C. A., Rehli, M., Pavli, P., Summers, K. M. & Hume, D. A., 6 Mar 2017, In : PLoS Genetics. 13, 3, 36 p., 1006641.

Research output: Contribution to journalArticle

Open Access
262 Citations (Scopus)

An atlas of human long non-coding RNAs with accurate 5′ ends

Hon, C. C., Ramilowski, J. A., Harshbarger, J., Bertin, N., Rackham, O. J. L., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T. M., Severin, J., Lizio, M., Kawaji, H., Kasukawa, T., Itoh, M., Burroughs, A. M., Noma, S., Djebali, S., Alam, T., Medvedeva, Y. A., Testa, A. C. & 19 othersLipovich, L., Yip, C. W., Abugessaisa, I., Mendez, M., Hasegawa, A., Tang, D., Lassmann, T., Heutink, P., Babina, M., Wells, C. A., Kojima, S., Nakamura, Y., Suzuki, H., Daub, C. O., De Hoon, M. J. L., Arner, E., Hayashizaki, Y., Carninci, P. & Forrest, A. R. R., 9 Mar 2017, In : Nature. 543, 7644, p. 199-204 6 p.

Research output: Contribution to journalArticle

Open Access
Long Noncoding RNA
Atlases
RNA
Nucleotides
Polymorphism
84 Citations (Scopus)

An integrated expression atlas of miRNAs and their promoters in human and mouse

de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Astrom, G., Babina, M., Bertin, N., Burroughs, A. M., Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., Harshbarger, J. & 50 othersHasegawa, A., Hashimoto, K., Herlyn, M., Heutink, P., Hitchens, K. J., Hon, C. C., Huang, E., Ishizu, Y., Kai, C., Kasukawa, T., Klinken, P., Lassmann, T., Lecellier, C-H., Lee, W., Lizio, M., Makeev, V., Mathelier, A., Medvedeva, Y. A., Mejhert, N., Mungall, C. J., Noma, S., Ohshima, M., Okada-Hatakeyama, M., Persson, H., Rizzu, P., Roudnicky, F., Saetrom, P., Sato, H., Severin, J., Shin, J. W., Swoboda, R. K., Tarui, H., Toyoda, H., Vitting-Seerup, K., Winteringham, L., Yamaguchi, Y., Yasuzawa, K., Yoneda, M., Yumoto, N., Zabierowski, S., Zhang, P. G., Wells, C. A., Summers, K. M., Kawaji, H., Sandelin, A., Rehli, M., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & de Hoon, M. J. L., Sep 2017, In : Nature Biotechnology. 35, 9, p. 872–878

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny

Sugiyama, D., Joshi, A., Kulkeaw, K., Tan, K. S., Yokoo-Inoue, T., Mizuochi-Yanagi, C., Yasuda, K., Doi, A., Iino, T., Itoh, M., Nagao-Sato, S., Tani, K., Akashi, K., Hayashizaki, Y., Suzuki, H., Kawaji, H., Carninci, P. & Forrest, A. R. R., 1 Mar 2017, In : Stem Cells and Development. 26, 5, p. 314-327 14 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Data Descriptor: Monitoring transcription initiation activities in rat and dog

Lizio, M., Mukarram, A. K., Ohno, M., Watanabe, S., Itoh, M., Hasegawa, A., Lassmann, T., Severin, J., Harshbarger, J., Abugessaisa, I., Kasukawa, T., Hon, C. C., Carninci, P., Hayashizaki, Y., Forrest, A. R. R. & Kawaji, H., 28 Nov 2017, In : Scientific Data. 4, 170173.

Research output: Contribution to journalArticle

Open Access
Transcription
Descriptors
Rats
Genes
Gene expression
21 Citations (Scopus)

FANTOM5 CAGE profiles of human and mouse samples

Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R. I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S. & 158 othersSaijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Kenneth Baillie, J., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, B. A. S., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J. I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Peter Klinken, S., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., MacKay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H., Mummery, C. L., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nozaki, T., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Passier, R., Patrikakis, M., Pombo, A., Pradhan-Bhatt, S., Qin, X. Y., Rehli, M., Rizzu, P., Roy, S., Sajantila, A., Sakaguchi, S., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schmidl, C., Schneider, C., Schulze-Tanzil, G. G., Schwegmann, A., Sheng, G., Shin, J. W., Sugiyama, D., Sugiyama, T., Summers, K. M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tomoiu, A., Toyoda, H., Wetering, M., Berg, L. M. V. D., Verardo, R., Vijayan, DI., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yamaguchi, Y., Yamamoto, M., Yanagi-Mizuochi, C., Yoneda, M., Yonekura, Y., Zhang, P. G., Zucchelli, S., Abugessaisa, I., Arner, E., Harshbarger, J., Kondo, A., Lassmann, T., Lizio, M., Sahin, S., Sengstag, T., Severin, J., Shimoji, H., Suzuki, M., Suzuki, H., Kawai, J., Kondo, N., Itoh, M., Daub, C. O., Kasukawa, T., Kawaji, H., Carninci, P., Forrest, A. R. R. & Hayashizaki, Y., 29 Aug 2017, In : Scientific Data. 4, 170112.

Research output: Contribution to journalArticle

Open Access
Gene Expression Profile
Gene expression
Mouse
Transcription
Cell
8 Citations (Scopus)

Integrative CAGE and DNA methylation profiling identify epigenetically regulated genes in NSCLC

Horie, M., Kaczkowski, B., Ohshima, M., Matsuzaki, H., Noguchi, S., Mikami, Y., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Takai, D., Yamaguchi, Y., Micke, P., Saito, A. & Nagase, T., 1 Oct 2017, In : Molecular Cancer Research. 15, 10, p. 1354-1365 12 p.

Research output: Contribution to journalArticle

DNA Fingerprinting
DNA Methylation
Non-Small Cell Lung Carcinoma
Lung Neoplasms
Gene Expression
3 Citations (Scopus)

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Bertin, N., Mendez, M., Hasegawa, A., Lizio, M., Abugessaisa, I., Severin, J., Sakai-Ohno, M., Lassmann, T., Kasukawa, T., Kawaji, H., Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Plessy, C., 3 Oct 2017, In : Scientific Data. 4, 8 p., 170147.

Research output: Contribution to journalArticle

Open Access
9 Citations (Scopus)

Systematic analysis of transcription start sites in avian development

Lizio, M., Deviatiiarov, R., Nagai, H., Galan, L., Arner, E., Itoh, M., Lassmann, T., Kasukawa, T., Hasegawa, A., Ros, M. A., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Kawaji, H., Gusev, O. & Sheng, G., Sep 2017, In : PLoS Biology. 15, 9, 23 p., 2002887.

Research output: Contribution to journalArticle

Open Access
9 Citations (Scopus)

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution

Ehrlund, A., Mejhert, N., Bjork, C., Andersson, R., Kulyte, A., Astrom, G., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Sandelin, A., Ingelsson, E., FANTOM Consortium, Ryden, M., Laurencikiene, J., Arner, P. & Arner, E., Jan 2017, In : Diabetes. 66, 1, p. 218-230 13 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Francescatto, M., Lizio, M., Philippens, I., Bontrop, R., Sakai, M., Watanabe, S., Itoh, M., Hasegawa, A., Lassmann, T., Severin, J., Harshbarger, J., Abugessaisa, I., Kasukawa, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Kawaji, H., Rizzu, P. & Heutink, P., 31 Oct 2017, In : Scientific Data. 4, 170163.

Research output: Contribution to journalArticle

Open Access
Neurology
Transcription
Profiling
RNA
Genes
4 Citations (Scopus)

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

Qin, X. Y., Hara, M., Arner, E., Kawaguchi, Y., Inoue, I., Tatsukawa, H., Furutani, Y., Nagatsuma, K., Matsuura, T., Wei, F., Kikuchi, J., Sone, H., Daub, C., Kawaji, H., Lassmann, T., Itoh, M., Suzuki, H., Carninci, P., Hayashizaki, Y., Kokudo, N. & 3 othersForrest, A. R. R., Kojima, S. & The FANTOM Consortium, 1 Oct 2017, In : EBioMedicine. 24, p. 257-266 10 p.

Research output: Contribution to journalArticle

Open Access
Orosomucoid
Gene Expression Profiling
Hepatocytes
Liver
Hepatectomy
34 Citations (Scopus)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D. J., Mathelier, A., Medvedeva, Y. A., Lennartsson, A., Drablos, F., Ramilowski, J. A., Rackham, O. J. L., Gough, J., Andersson, R., Sandelin, A., Ienasescu, H., Ono, H., Bono, H. & 5 othersHayashizaki, Y., Carninci, P., Forrest, A. R. R., Kasukawa, T. & Kawaji, H., 4 Jan 2017, In : Nucleic Acids Research. 45, D1, p. D737-D743 7 p.

Research output: Contribution to journalArticle

Open Access
2016
99 Citations (Scopus)

A predictive computational framework for direct reprogramming between human cell types

Rackham, O. J. L., Firas, J., Fang, H., Oates, M. E., Holmes, M. L., Knaupp, A. S., Suzuki, H., Nefzger, C. M., Daub, C. O., Shin, J. W., Petretto, E., Forrest, A., Hayashizaki, Y., Polo, J. M. & Gough, J., Mar 2016, In : Nature Genetics. 48, 3, p. 331-335 4 p.

Research output: Contribution to journalArticle

Transcription Factors
Regenerative Medicine
Information Services
Atlases
Gene Expression
5 Citations (Scopus)

CAGEd-oPOSSUM: Motif enrichment analysis from CAGE-derived TSSs

Arenillas, D. J., Forrest, A., Kawaji, H., Lassmann, T., Wasserman, W. W. & Mathelier, A., 2016, In : Bioinformatics. 32, 18, p. 2858-2860

Research output: Contribution to journalArticle

Open Access
Transcription Initiation Site
Transcription
Gene expression
Gene Expression
Transcription factors
4 Citations (Scopus)

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C

Klein, S., Dieterich, L. C., Mathelier, A., Chong, C., Sliwa-Primorac, A., Hong, Y. K., Shin, J. W., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., Carninci, P., Hayashizaki, Y., Forrest, A., Wasserman, W. W. & Detmar, M., 2016, In : Journal of Cell Science. 129, 13, p. 2573-2585

Research output: Contribution to journalArticle

Vascular Endothelial Growth Factor Receptor-3
Vascular Endothelial Growth Factor C
Transcription Factors
Lymphangiogenesis
Endothelial Cells
24 Citations (Scopus)

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

Abugessaisa, I., Shimoji, H., Sahin, S., Kondo, A., Harshbarger, J., Lizio, M., Hayashizaki, Y., Carninci, P., Forrest, A., Kasukawa, T., Kawaji, H. & Consortium, F., 9 Jul 2016, In : Database. 2016, 10 p., 105.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)
311 Downloads (Pure)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

lenasescu, H., Li, K., Andersson, R., Vitezic, M., Rennie, S., Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Bornholdt, J., Kawaji, H., Lassmann, T., The FANTOM Consortium, Forrest, A. & Carninci, P., 2016, In : Database-The Journal of Biological Databases and Curation. p. 1-10 10 p., baw144.

Research output: Contribution to journalArticle

Open Access
File
14 Citations (Scopus)

Reinforcing the association between distal 1q CNVs and structural brain disorder: A case of a complex 1q43-q44 CNV and a review of the literature

Hemming, I. A., Forrest, A., Shipman, P., Woodward, K. J., Walsh, P., Ravine, D. G. & Heng, J., 2016, In : American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 171, 3, p. 458-467

Research output: Contribution to journalArticle

Microcephaly
Brain Diseases
Viverridae
Seizures
Group II Malformations of Cortical Development
6 Citations (Scopus)

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

Horie, M., Yamaguchi, Y., Saito, A., Nagase, T., Lizio, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Suzutani, T., Kappert, K., Micke, P. & Ohshima, M., 2016, In : Scientific Reports. 6, p. 1-15 15 p.

Research output: Contribution to journalArticle

Open Access
Periodontitis
Gene Expression Profiling
Fibroblasts
Extracellular Matrix
Transcription Factors
32 Citations (Scopus)

Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers

Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itoh, M., Lassmann, T., Hayashizaki, Y., Carninci, P. & Forrest, A., 2016, In : Cancer Research. 76, 2, p. 216-226

Research output: Contribution to journalArticle

Gene Expression Profiling
Tumor Biomarkers
Genes
Neoplasms
Short Interspersed Nucleotide Elements
8 Citations (Scopus)

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Chen, C. Y., Shi, W., Balaton, B. P., Matthews, A. M., Li, Y., Arenillas, D. J., Mathelier, A., Itoh, M., Kawaji, H., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Brown, C. J. & Wasserman, W. W., 18 Nov 2016, In : Scientific Reports. 6, 37324.

Research output: Contribution to journalArticle

Open Access
Sex Characteristics
YY1 Transcription Factor
Long Noncoding RNA
X Chromosome Inactivation
Transcription Initiation Site
2015
78 Citations (Scopus)

A draft network of ligand-receptor-mediated multicellular signalling in human

Ramilowski, J. A., Goldberg, T., Harshbarger, J., Kloppman, E., Lizio, M., Satagopam, V. P., Itoh, M., Kawaji, H., Carninci, P., Rost, B. & Forrest, A., 2015, In : Nature Communications. 6, p. 1-12

Research output: Contribution to journalArticle

Open Access
draft
Ligands
ligands
cells
Cell Communication

Application of gene expression trajectories initiated from ErbB receptor activation highlights the dynamics of divergent promoter usage

Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A., Carninci, P., Hayashizaki, Y., Daub, C. O., Okada-Hatakeyama, M. & Mar, J. C., 2015, In : PLoS One. 10, 12, p. 1-22

Research output: Contribution to journalArticle

Open Access
Gene expression
trajectories
Genes
Chemical activation
promoter regions
20 Citations (Scopus)

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

Hashimoto, K., Suzuki, A. M., Dos Santos, A., Desterke, C., Collino, A., Ghisletti, S., Braun, E., Bonetti, A., Fort, A., Qin, X-Y., Radaelli, E., Kaczkowski, B., Forrest, A., Kojima, S., Samuel, D., Natoli, G., Buendia, M. A., Faivre, J. & Carninci, P., 2015, In : Genome Research. 25, p. 1812-1824

Research output: Contribution to journalArticle

Open Access
45 Citations (Scopus)

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

Haberle, V., Forrest, A., Hayashizaki, Y., Carninci, P. & Lenhard, B., 2015, In : Nucleic Acids Research. 43, 8, p. 1-11

Research output: Contribution to journalArticle

Open Access
30 Citations (Scopus)

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

Yu, N. Y-L., Hallström, B. M., Fagerberg, L., Ponten, F., Kawaji, H., Carninci, P., Forrest, A., Hayashizaki, Y., Uhlén, M., Daub, C. O., Alam, I., Albanese, D., Altschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, E., Arner, P., Babina, M., Baillie, K. & 244 othersBajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Bertin, N., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Davis, C., De Hoon, M., De Lima Morais, D., Detmar, M., Diehl, A., Dimont, E., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Freeman, T., Frith, M., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hide, W., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hori, F., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Itoh, M., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kwashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulalovskiy, I., Kwon, A. T. J., Laros, J., Lassmann, T., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Lizio, M., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Meehan, T. F., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Mungall, C. J., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rehli, M., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sandelin, A., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schultes, E. A., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Severin, J., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, M., Suzuki, N., Swoboda, R., T Hoen, P., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Taylor, M., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X. & Zucchelli, S., 2015, In : Nucleic Acids Research. 43, p. 6787-6798

Research output: Contribution to journalArticle

Open Access
62 Citations (Scopus)

Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and inneurochemical models of Parkinson's disease

Carrieri, C., Forrest, A., Santoro, C., Persichetti, F., Carninci, P., Zucchelli, S. & Gustincich, S., 2015, In : Frontiers in Cellular Neuroscience. 9, p. 1-11

Research output: Contribution to journalArticle

Open Access
221 Citations (Scopus)

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C. J., Arner, E., Baillie, J. K., Bertin, N., Bono, H., De Hoon, M., Diehl, A. D., Dimont, E., Freeman, T. C., Fujieda, K. & 249 othersHide, W., Kaliyaperumal, R., Katayama, T., Lassmann, T., Meehan, T. F., Nishikata, K., Ono, H., Rehli, M., Sandelin, A., Schultes, E. A., T Hoen, P. A. C., Tatum, Z., Thompson, M., Toyoda, T., Wright, D. W., Daub, C. O., Itoh, M., Carninci, P., Hayashizaki, Y., Forrest, A., Kawaji, H., Alam, I., Albanese, D., Altschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, P., Babina, M., Bajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Davis, C., De Lima Morais, D., Detmar, M., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Frith, M., Fujita, R., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Katayama, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okzaki, Y., Orlando, V., Ovchinnokov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Sheng, G., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, M., Suzuki, N., Swoboda, R., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Taylor, M., Toyoda, H., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X. & Zucchelli, S., 2015, In : Genome Biology. 16, p. 1-14

Research output: Contribution to journalArticle

Open Access
Atlases
atlas
Transcription Factors
promoter regions
Cell Line
131 Citations (Scopus)

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

Fraser, J., Ferrai, C., Chiariello, A. M., Schueler, M., Rito, T., Laudanno, G., Barbieri, M., Moore, B. L., Kraemer, D. C. A., Aitken, S., Xie, S. Q., Morris, K. J., Itoh, M., Kawaji, H., Jaeger, I., Hayashizaki, Y., Carninci, P., Forrest, A., Alam, I., Albanese, D. & 256 othersAltschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, E., Arner, P., Babina, M., Baillie, K., Bajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Bertin, N., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Daub, C., Davis, C., De Hoon, M., De Lima Morais, D., Detmar, M., Diehl, A., Dimont, E., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Freeman, T., Frith, M., Fujita, R., Fukudo, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hide, W., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hori, F., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lassmann, T., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Lizio, M., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Meehan, T. F., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Mothashi, H., Mummery, C., Mungall, C. J., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Niskiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rehli, M., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sandelin, A., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schultes, E. A., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Severin, J., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, M., Swoboda, R., T Hoen, P., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatasukawa, H., Tatum, Z., Taylor, M., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X., Zucchelli, S., Semple, C. A., Dostie, J., Pombo, A. & Nicodemi, M., 2015, In : Molecular Systems Biology. 11, p. 1-14

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

Mapping mammalian cell-type-specific transcriptional regulatory networks using KD-CAGE and ChIP-seq data in the TC-YIK cell line

Lizio, M., Ishizu, Y., Itoh, M., Lassmann, T., Hasegawa, A., Kubosaki, A., Severin, J., Kawaji, H., Nakamura, Y., Suzuki, H., Hayashizaki, Y., Carninci, P. & Forrest, A., 2015, In : Frontiers in Genetics. 6, p. 1-17

Research output: Contribution to journalArticle

Open Access
Gene Regulatory Networks
Transcription Factors
Gene Expression
Cell Line
Gene Knock-In Techniques
17 Citations (Scopus)

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ERBB receptors in breast cancer cells

Mina, M., Magi, S., Jurman, G., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A., Carninci, P., Hayashizaki, Y., Daub, C. O., Okada-Hatakeyama, M. & Furlanello, C., 2015, In : Scientific Reports. 5, p. 1-13

Research output: Contribution to journalArticle

Open Access
Neuregulin-1
Cluster Analysis
Transcription Factor AP-1
Breast Neoplasms
Gene Expression
27 Citations (Scopus)

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Roy, S., Schmeier, S., Arner, E., Alam, T., Parihar, S. P., Ozturk, M., Tamgue, O., Kawaji, H., De Hoon, M. J. L., Itoh, M., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A., Bajic, V. B., Guler, R., Brombacher, F., Suzuki, H., Alam, I., Albanese, D. & 244 othersAltschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, P., Babina, M., Baillie, K., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Bertin, N., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Daub, C., Davis, C., De Lima Morais, D., Detmar, M., Diehl, A., Dimon, E., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Freeman, T., Frith, M., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, D., Goldowitz, D., Gough, J., Guhl, S., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hide, W., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hori, F., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, K., Kasianov, A., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Lizio, M., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Meehan, T. F., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Mungall, C. J., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rehli, M., Rizzu, P., Roncador, M., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sandelin, A., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmidl, C., Schneider, C., Schultes, E. A., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Severin, J., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, M., Suzuki, N., Swoboda, R., T Hoen, P., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Taylor, M., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X. & Zucchelli, S., 2015, In : Nucleic Acids Research. 43, p. 6969-6982

Research output: Contribution to journalArticle

Open Access
8 Citations (Scopus)

Retinoic acid potentiates inflammatory cytokines in human mast cells: Identification of mast cells as prominent constituents of the skin retinoid network

Babina, M., Guhl, S., Motakis, E., Artuc, M., Hazzan, T., Worm, M., Forrest, A. & Zuberbier, T., 2015, In : Molecular and Cellular Endocrinology. 406, p. 49-59

Research output: Contribution to journalArticle

13 Citations (Scopus)

Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Joshi, A., Pooley, C., Freeman, T. C., Lennartsson, A., Babina, M., Schmidl, C., Geijtenbeek, T., Michoel, T., Severin, J., Itoh, M., Lassmann, T., Kawaji, H., Hayashizaki, Y., Carninci, P., Forrest, A., Rehli, M. & Hume, D. A., 2015, In : Journal of Leukocyte Biology. 97, 5, p. 985-995

Research output: Contribution to journalArticle

Open Access
Myelopoiesis
Myeloid Cells
Transcription Factors
Myeloid Progenitor Cells
Untranslated RNA
10 Citations (Scopus)

The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

Hurst, L. D., Ghanbarian, A. T., Forrest, A., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E. & 239 othersSchmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Baker, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Ho Sui, S. J., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B. R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A. S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y. I., Khachigian, L. M., Kitamura, T., Klinken, P., Knox, A. J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A. T., Laros, J. F. J., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-Sim, A., Manabe, R., Mar, J. C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., De Lima Morais, D. A., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C. L., Murata, M., Nagao-Sato, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J. G. D., Rackham, O. J. L., Ramilowski, J. A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M. B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E. A., Schulze-Tanzil, G. G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shim, J. W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R. K., T Hoen, P. A. C., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L. M., Verardo, R., Vijayan, D., Vorontsov, I. E., Wasserman, W. W., Watanabe, S., Wells, C. A., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S. E., Zhang, P. G., Zhao, X., Zucchelli, S., Summers, K. M., Suzuki, H., Daub, C. O., Kawai, J., Heutink, P., Hide, W., Freeman, T. C., Lenhard, B., Bajic, V. B., Taylor, M. S., Makeev, V. J., Sandelin, A., Hume, D. A., Carninci, P. & Hayashizaki, Y., 2015, In : PLoS Biology. 13, p. 1-48

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20 Citations (Scopus)

The frequent evolutionary birth and death of functional promoters in mouse and human

Young, R. S., Hayashizaki, Y., Andersson, R., Sandelin, A., Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Bickmore, W. A., Forrest, A., Taylor, M. S., Alam, I., Albanese, D., Altschuler, G., Arakawa, T., Archer, J., Arner, E., Arner, P., Babina, M., Baillie, K. & 242 othersBajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Bertin, N., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Daub, C., Davis, C., De Hoon, M., De Lima Morais, D., Detmar, M., Diehl, A., Dimont, E., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Francescatto, M., Freeman, T., Frith, M., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Heutink, P., Hide, W., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hori, F., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawai, J., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Lizio, M., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Meehan, T. F., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Mungall, C. J., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rehli, M., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schultes, E. A., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Severin, J., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, N., Swoboda, R., T Hoen, P., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Taylor, M., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorontzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X. & Zucchelli, S., 2015, In : Genome Research. 25, p. 1546-1557

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23 Citations (Scopus)

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, C., Alam, I., Albanese, D., Altschuler, G., Andersson, R., Arakawa, T., Archer, J., Arner, E., Arner, P., Babina, M., Baillie, K., Bajic, V., Baker, S., Balic, A., Balwierz, P., Beckhouse, A., Bertin, N., Blake, J. A., Blumenthal, A., Bodega, B. & 242 othersBonetti, A., Briggs, J., Brombacher, F., Burroughs, M., Califano, A., Cannistraci, C., Carbajo, D., Carninci, P., Chen, Y., Chierici, M., Ciani, Y., Clevers, H., Dalla, E., Daub, C., Davis, C., De Hoon, M., De Lima Morais, D., Detmar, M., Diehl, A., Dimont, E., Dohi, T., Drabros, F., Edge, A., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G., Favorov, A., Fisher, M., Forrest, A., Francescatto, M., Freeman, T., Frith, M., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J-I., Geijtenbeek, T. B. H., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T., Haberle, V., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Hayashizaki, Y., Herlyn, M., Heutink, P., Hide, W., Hitchens, K., Ho Sui, S., Hofmann, O., Hoof, I., Hori, F., Hume, D., Huminiecki, L., Ilda, K., Ikawa, T., Ishizu, Y., Itoh, M., Jankovic, B., Jia, H., Jorgensen, M., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y., Kawashima, T., Kempfle, J., Kenna, T., Kere, J., Khachigian, L., Kitamura, T., Klinken, P., Knox, A., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kulakovskiy, I., Kwon, A. T. J., Laros, J., Lassmann, T., Lenhard, B., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Lizio, M., Mackay-Sim, A., Makeev, V., Manabe, R., Mar, J., Marchand, B., Mathelier, A., Medvedeva, Y., Meehan, T. F., Mejhert, N., Meynert, A., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C., Mungall, C. J., Murata, M., Nagao, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Pain, A., Passier, R., Persson, H., Piazza, S., Plessy, C., Pradhan-Bhatt, S., Prendergast, J., Rackham, O., Ramilowski, J., Rashid, M., Ravasi, T., Rehli, M., Rizzu, P., Roncador, M., Roy, S., Rye, M., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sandelin, A., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schaefer, U., Schmeier, S., Schmidl, C., Schneider, C., Schultes, E. A., Schulze-Tanzil, G., Schwegmann, A., Semple, C., Sengstag, T., Severin, J., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J., Simon, C., Sugiyama, D., Sugiyama, T., Summers, K., Suzuki, H., Suzuki, M., Suzuki, N., Swoboda, R., T Hoen, P., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Taylor, M., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L., Van Nimwegen, E., Verardo, R., Vijayan, D., Vitezic, M., Vorotzov, I., Wasserman, W., Watanabe, S., Wells, C., Winteringham, L., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Young, R., Zabierowski, S. E., Zhang, P., Zhao, X., Zucchelli, S. & Wagner, G. P., 2015, In : Nature Communications. 6, p. 1-6

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