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ArticlesPeer ReviewedFull Text
Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes
Author / Creator:Narita, Masako ; Young, Andrew R. J. ; Arakawa, Satoko ; Samarajiwa, Shamith A. ; Nakashima, Takayuki ; Yoshida, Sei ; Hong, Sungki ; Berry, Lorraine S. ; Reichelt, Stefanie ; Ferreira, Manuela ; Tavaré, Simon ; Inoki, Ken ; Shimizu, Shigeomi ; Narita, Masashi
Publisher:Washington, DC: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2011-05, Vol.332 (6032), p.966-970
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ArticlesPeer ReviewedFull Text
Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape
Author / Creator:Bidwell, Bradley N ; Slaney, Clare Y ; Withana, Nimali P ; Forster, Sam ; Cao, Yuan ; Loi, Sherene ; Andrews, Daniel ; Mikeska, Thomas ; Mangan, Niamh E ; Samarajiwa, Shamith A ; de Weerd, Nicole A ; Gould, Jodee ; Argani, Pedram ; Möller, Andreas ; Smyth, Mark J ; Anderson, Robin L ; Hertzog, Paul J ; Parker, Belinda S
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2012-08, Vol.18 (8), p.1224-1231
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A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma
Author / Creator:Syafruddin, Saiful E. ; Rodrigues, Paulo ; Vojtasova, Erika ; Patel, Saroor A. ; Zaini, M. Nazhif ; Burge, Johanna ; Warren, Anne Y. ; Stewart, Grant D. ; Eisen, Tim ; Bihary, Dóra ; Samarajiwa, Shamith A. ; Vanharanta, Sakari
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-03, Vol.10 (1), p.1152-13, Article 1152
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ArticlesPeer ReviewedFull Text
Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence
Author / Creator:Olan, Ioana ; Parry, Aled J. ; Schoenfelder, Stefan ; Narita, Masako ; Ito, Yoko ; Chan, Adelyne S. L. ; Slater, Guy St.C. ; Bihary, Dóra ; Bando, Masashige ; Shirahige, Katsuhiko ; Kimura, Hiroshi ; Samarajiwa, Shamith A. ; Fraser, Peter ; Narita, Masashi
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-11, Vol.11 (1), p.6049-14, Article 6049
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ArticlesPeer ReviewedFull Text
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence
Author / Creator:Parry, Aled J. ; Hoare, Matthew ; Bihary, Dóra ; Hänsel-Hertsch, Robert ; Smith, Stephen ; Tomimatsu, Kosuke ; Mannion, Elizabeth ; Smith, Amy ; D’Santos, Paula ; Russell, I. Alasdair ; Balasubramanian, Shankar ; Kimura, Hiroshi ; Samarajiwa, Shamith A. ; Narita, Masashi
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-05, Vol.9 (1), p.1840-15, Article 1840
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ArticlesPeer ReviewedFull Text
The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer
Author / Creator:Patel, Saroor A. ; Hirosue, Shoko ; Rodrigues, Paulo ; Vojtasova, Erika ; Richardson, Emma K. ; Ge, Jianfeng ; Syafruddin, Saiful E. ; Speed, Alyson ; Papachristou, Evangelia K. ; Baker, David ; Clarke, David ; Purvis, Stephenie ; Wesolowski, Ludovic ; Dyas, Anna ; Castillon, Leticia ; Caraffini, Veronica ; Bihary, Dóra ; Yong, Cissy ; Harrison, David J. ; Stewart, Grant D. ; Machiela, Mitchell J. ; Purdue, Mark P. ; Chanock, Stephen J. ; Warren, Anne Y. ; Samarajiwa, Shamith A. ; Carroll, Jason S. ; Vanharanta, Sakari
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2022-06, Vol.606 (7916), p.999-1006
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Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53
Author / Creator:Kirschner, Kristina ; Samarajiwa, Shamith A ; Cairns, Jonathan M ; Menon, Suraj ; Pérez-Mancera, Pedro A ; Tomimatsu, Kosuke ; Bermejo-Rodriguez, Camino ; Ito, Yoko ; Chandra, Tamir ; Narita, Masako ; Lyons, Scott K ; Lynch, Andy G ; Kimura, Hiroshi ; Ohbayashi, Tetsuya ; Tavaré, Simon ; Narita, Masashi
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2015-03, Vol.11 (3), p.e1005053-e1005053
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ArticlesPeer ReviewedFull Text
Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns
Author / Creator:Newsham, Izzy ; Sendera, Marcin ; Jammula, Sri Ganesh ; Samarajiwa, Shamith A
Publisher:England: Oxford University Press
Journal title:Biology methods and protocols, 2024, Vol.9 (1), p.bpae028
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ArticlesPeer ReviewedFull Text
Exploring the role of stromal osmoregulation in cancer and disease using executable modelling
Author / Creator:Shorthouse, David ; Riedel, Angela ; Kerr, Emma ; Pedro, Luisa ; Bihary, Dóra ; Samarajiwa, Shamith ; Martins, Carla P. ; Shields, Jacqueline ; Hall, Benjamin A.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-08, Vol.9 (1), p.3011-15, Article 3011
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ArticlesPeer ReviewedFull Text
Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Author / Creator:Alcalá‐Vida, Rafael ; Garcia‐Forn, Marta ; Castany‐Pladevall, Carla ; Creus‐Muncunill, Jordi ; Ito, Yoko ; Blanco, Enrique ; Golbano, Arantxa ; Crespí‐Vázquez, Kilian ; Parry, Aled ; Slater, Guy ; Samarajiwa, Shamith ; Peiró, Sandra ; Di Croce, Luciano ; Narita, Masashi ; Pérez‐Navarro, Esther
Publisher:London: Nature Publishing Group UK
Journal title:EMBO molecular medicine, 2021-02, Vol.13 (2), p.e12105-n/a
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Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis
Author / Creator:Xavier, Joana M. ; Magno, Ramiro ; Russell, Roslin ; de Almeida, Bernardo P. ; Jacinta-Fernandes, Ana ; Besouro-Duarte, André ; Dunning, Mark ; Samarajiwa, Shamith ; O’Reilly, Martin ; Maia, António M. ; Rocha, Cátia L. ; Rosli, Nordiana ; Ponder, Bruce A. J. ; Maia, Ana-Teresa
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-09, Vol.14 (1), p.22526-19, Article 22526
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ArticlesPeer ReviewedFull Text
Locus-specific induction of gene expression from heterochromatin loci during cellular senescence
Author / Creator:Tomimatsu, Kosuke ; Bihary, Dóra ; Olan, Ioana ; Parry, Aled J ; Schoenfelder, Stefan ; Chan, Adelyne S L ; Slater, Guy St C ; Ito, Yoko ; Rugg-Gunn, Peter J ; Kirschner, Kristina ; Bermejo-Rodriguez, Camino ; Seko, Tomomi ; Kugoh, Hiroyuki ; Shiraishi, Ken ; Sayama, Koji ; Kimura, Hiroshi ; Fraser, Peter ; Narita, Masako ; Samarajiwa, Shamith A ; Narita, Masashi
Publisher:United States: Nature Publishing Group
Journal title:Nature aging, 2022-01, Vol.2 (1), p.31-45
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ArticlesPeer ReviewedFull Text
Fumarate induces vesicular release of mtDNA to drive innate immunity
Author / Creator:Zecchini, Vincent ; Paupe, Vincent ; Herranz-Montoya, Irene ; Janssen, Joëlle ; Wortel, Inge M. N. ; Morris, Jordan L. ; Ferguson, Ashley ; Chowdury, Suvagata Roy ; Segarra-Mondejar, Marc ; Costa, Ana S. H. ; Pereira, Gonçalo C. ; Tronci, Laura ; Young, Timothy ; Nikitopoulou, Efterpi ; Yang, Ming ; Bihary, Dóra ; Caicci, Federico ; Nagashima, Shun ; Speed, Alyson ; Bokea, Kalliopi ; Baig, Zara ; Samarajiwa, Shamith ; Tran, Maxine ; Mitchell, Thomas ; Johnson, Mark ; Prudent, Julien ; Frezza, Christian
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-03, Vol.615 (7952), p.499-506
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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
Author / Creator:Curtis, Christina ; Shah, Sohrab P. ; Chin, Suet-Feung ; Turashvili, Gulisa ; Rueda, Oscar M. ; Dunning, Mark J. ; Speed, Doug ; Lynch, Andy G. ; Samarajiwa, Shamith ; Yuan, Yinyin ; Gräf, Stefan ; Ha, Gavin ; Haffari, Gholamreza ; Bashashati, Ali ; Russell, Roslin ; McKinney, Steven ; Langerød, Anita ; Green, Andrew ; Provenzano, Elena ; Wishart, Gordon ; Pinder, Sarah ; Watson, Peter ; Markowetz, Florian ; Murphy, Leigh ; Ellis, Ian ; Purushotham, Arnie ; Børresen-Dale, Anne-Lise ; Brenton, James D. ; Tavaré, Simon ; Caldas, Carlos ; Aparicio, Samuel
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2012-06, Vol.486 (7403), p.346-352
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Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature
Author / Creator:Samarajiwa, Shamith A ; Pirvan, Liviu
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-04
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A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation
Author / Creator:Steindel, Maike ; Davis, Oliver ; Neumann, Katrin ; Pirvan, Liviu ; Agsu, Gokce ; Kranz, Andre ; Adhya, Dwaipayan ; Morf, Jorg ; Yang, Shuyue ; Zhang, Ziwei ; Fu, Jun ; Barile, Melania ; Wurmser, Annabelle ; Strawbridge, Stanley ; Mohorianu, Irina ; Madapura, Pradeepa ; Huntly, Brian ; Gottgens, Berthold ; Holcman, David ; Samarajiwa, Shamith ; Klenerman, David ; Anastassiadis, Konstantinos ; Stewart, Adrian Francis ; Basu, Srinjan
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2025-02
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ArticlesPeer ReviewedFull Text
Systems biology of interferon responses
Author / Creator:Hertzog, Paul ; Forster, Sam ; Samarajiwa, Shamith
Publisher:United States: Mary Ann Liebert, Inc
Journal title:Journal of interferon & cytokine research, 2011-01, Vol.31 (1), p.5-11
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ArticlesFull Text
SpiderSeqR: an R package for crawling the web of high-throughput multi-omic data repositories for data-sets and annotation
Author / Creator:Sozanska, Anna M ; Fletcher, Charles ; Bihary, Dóra ; Samarajiwa, Shamith A
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-04
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ArticlesFull Text
Machine Classification of Methylomes in Cancer
Author / Creator:Newsham, Isabelle ; Sendera, Marcin ; Jammula, Sriganesh ; Fitzgerald, Rebecca ; Massie, Charles ; Samarajiwa, Shamith A
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-04
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ArticlesFull Text
Identifying regulatory and spatial genomic architectural elements using cell type independent machine and deep learning models
Author / Creator:Martens, Laura D ; Faust, Oisín ; Pirvan, Liviu ; Bihary, Dóra ; Samarajiwa, Shamith A
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-05
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Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes

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Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape

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A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma

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Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

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NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence

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The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer

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Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53

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Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns

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Exploring the role of stromal osmoregulation in cancer and disease using executable modelling

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Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease

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Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis

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Locus-specific induction of gene expression from heterochromatin loci during cellular senescence

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Fumarate induces vesicular release of mtDNA to drive innate immunity

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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

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Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature

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A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation

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Systems biology of interferon responses

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SpiderSeqR: an R package for crawling the web of high-throughput multi-omic data repositories for data-sets and annotation

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Machine Classification of Methylomes in Cancer

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Identifying regulatory and spatial genomic architectural elements using cell type independent machine and deep learning models

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