• The University of Western Australia (M519), 35 Stirling Highway,

    6009 Perth

    Australia

  • 13860 Citations
  • 47 h-Index
1994 …2023

Research output per year

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Research Output

2020

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

Bayati, M., Rabiee, H. R., Mehrbod, M., Vafaee, F., Ebrahimi, D., Forrest, A. R. R. & Alinejad-Rokny, H., 1 Dec 2020, In : Scientific Reports. 10, 1, 1286.

Research output: Contribution to journalArticle

Open Access
2019

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
1 Citation (Scopus)

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

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
1 Citation (Scopus)

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
1 Citation (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
4 Citations (Scopus)

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

2018

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
5 Citations (Scopus)
216 Downloads (Pure)

Circulating MDSC modulate IPF progression by orchestrating immunosuppressive and pro-fibrotic networks

Fernandez, I. E., Greiffo, F. R., Roi, R., Behr, J., Forrest, A. & Eickelberg, O., 15 Sep 2018, In : European Respiratory Journal. 52, 1 p.

Research output: Contribution to journalAbstract/Meeting Abstract

Open Access
1 Citation (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

2 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
6 Citations (Scopus)
Open Access
5 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
14 Citations (Scopus)

Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease

Sadlon, T., Brown, C. Y., Bandara, V., Hope, C. M., Schjenken, J. E., Pederson, S. M., Breen, J., Forrest, A., Beyer, M., Robertson, S. & Barry, S. C., 27 Feb 2018, In : Clinical & Translational Immunology. 7, 2, 15 p., 1011.

Research output: Contribution to journalReview article

Open Access
6 Citations (Scopus)
2017

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
23 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
274 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
95 Citations (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

1 Citation (Scopus)

Comment: The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

Kawaji, H., Kasukawa, T., Forrest, A., Carninci, P. & Hayashizaki, Y., 29 Aug 2017, In : Scientific Data. 4, 3 p., 170113.

Research output: Contribution to journalEditorial

Open Access
13 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
2 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
26 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

8 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
3 Citations (Scopus)

New era in genetics of early-onset muscle disease: Breakthroughs and challenges

Ravenscroft, G., Davis, M. R., Lamont, P., Forrest, A. & Laing, N. G., Apr 2017, In : Seminars in Cell and Developmental Biology. 64, p. 160-170 11 p.

Research output: Contribution to journalReview article

12 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
10 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

9 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
2 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
4 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
37 Citations (Scopus)
2016

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

100 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
5 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

4 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
25 Citations (Scopus)

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
4 Citations (Scopus)
331 Downloads (Pure)

Recurrent transcriptome alterations across multiple cancer types

Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A., Andersson, R., Itot, M., Lassmann, T., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & FANTOM5 Consortium, Jul 2016, In : Cancer Research. 76, 3 p.

Research output: Contribution to journalAbstract/Meeting Abstract

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

14 Citations (Scopus)

Transcription Factor NKX6.3 Sheds Light on Gastric Cancer Progression

Testa, A. C. & Forrest, A. R. R., 2016, In : EBioMedicine. 9, p. 9-10 2 p.

Research output: Contribution to journalLetter

Open Access
2 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
6 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

32 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
9 Citations (Scopus)
2015

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
85 Citations (Scopus)

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

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
21 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
49 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

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32 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

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64 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

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229 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

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134 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

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5 Citations (Scopus)