Find Research Outputs

Search in all content

Filters for Research Output

Search concepts
Selected filters

Publication Year

  • 2020
  • 2019
  • 2018
  • 2016

Author

  • Alistair Forrest
2018

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 others, Yamanaka, 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
9 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

2 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
7 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)
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

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
6 Citations (Scopus)
289 Downloads (Pure)
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

2018
Open Access
2 Citations (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)
2018

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

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)
2016

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

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)
2018
Open Access
5 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

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)

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)

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)
2020
Open Access
2019
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)

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)