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  • Alistair Forrest
2017

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)

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 others, Saijyo, 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
33 Citations (Scopus)
2016

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
10 Citations (Scopus)
2017

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 others, Hayashizaki, 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
46 Citations (Scopus)
2020

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., 2020, (Submitted) bioRxiv, p. 1-47 47 p.

Research output: Contribution to specialist publicationArticle

2017

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

10 Citations (Scopus)
2016

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

2017

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)
2016

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)

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

15 Citations (Scopus)
2017

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
11 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)
2019

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)
2016

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

5 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
28 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
8 Citations (Scopus)
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
2016

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

34 Citations (Scopus)
2017

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 others, Lipovich, 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
316 Citations (Scopus)
2016

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)
2020

Human genetics and genomics meetings going virtual: practical lessons learned from two international meetings in early 2020

Forrest, A. R. R., Repetto, G. M. & Reichardt, J. K. V., 8 Jul 2020, In : Human genomics. 14, 1, 1 p.

Research output: Contribution to journalArticle

Open Access
2016

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
5 Citations (Scopus)
369 Downloads (Pure)
2019

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 others, Lagerstedt-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)
2017

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)

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 others, Hasegawa, 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
117 Citations (Scopus)
2020
Open Access
2017

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

10 Citations (Scopus)
2019
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
29 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

105 Citations (Scopus)
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
2 Citations (Scopus)
2017

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
16 Citations (Scopus)
2019

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
7 Citations (Scopus)
2017

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
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 others, Forrest, 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
5 Citations (Scopus)