PUBLICATIONS
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Anna Sozanska, Charles Fletcher, Dora Bihary and Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi:
Laura D. Martens, Oisin Faust, Liviu Pirvan, Dora Bihary, and Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi:
Machine Classification of Methylomes in Cancer.
Isabelle Newsham, Marcin Sendera, SriGanesh Jammula, Rebecca Fitzgerald, Charles Massie, Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi:
Liviu Pirvan, Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi:
Locus-specific induction of gene expression from heterochromatin loci during cellular senescence.
Kosuke Tomimatsu, Dóra Bihary, Ioana Olan, Aled Parry, Stefan Schoenfelder, Adelyne Chan, Guy Slater, Yoko Ito, Peter Rugg-Gunn, Kristina Kirschner, Camino Bermejo-Rodriguez, Masako Narita, Tomomi Seko, Hiroyuki Kugoh, Ken Shiraishi, Koji Sayama, Hiroshi Kimura, Peter Fraser, Shamith Samarajiwa*, Masashi Narita* In Review (preprint)
Sequential Inverse Dysregulation of the RNA Helicases DDX3X and DDX3Y Facilitates MYC-Driven Lymphomagenesis.
Chun Gong*, Joanna A Krupka*, Jie Gao, Nicholas F Grigoropoulos, Michael Screen, Zelvera Usheva, Francesco Cucco, Sharon Barrans, Daniel Painter, Nurmahirah Binte Mohammad Zaini, Björn Haupl, Susanne Bornelöv, Igor Ruiz De Los Mozos, Wei Meng, Peixun Zhou, Alex E Blain, Sorcha Forde, Jamie Matthews, Michelle Tan Guet Khim, G. A. Amos Burke, Siu Kwan Sze, Philip Beer, Cathy Burton, Peter Campbell, Vikki Rand, Suzanne Turner, Jernej Ule, Eve Roman, Reuben Tooze, Thomas Oellerich, Martin Turner, Ming-Qing Du, Shamith Samarajiwa¶ & Daniel J Hodson¶ under review.
Neuron-specific increase in lamin B1 disrupts nuclear function in Huntington’s disease
Rafael Alcalá-Vida, Marta Garcia-Forn, Jordi Creus-Muncunill, Yoko Ito, Enrique Blanco, Carla Castany-Pladevall, Killian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez-Navarro. EMBO Mol. Med., 2020 Dec, doi: https://doi.org/10.15252/emmm.202012105
Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence
Ioana Olan, Aled J. Parry, Stefan Schoenfelder, Masako Narita, Yoko Ito, Adelyne S.L. Chan, Guy St.C. Slater, Dóra Bihary, Masashige Bando, Katsuhiko Shirahige, Hiroshi Kimura, Shamith A. Samarajiwa, Peter Fraser, Masashi Narita. Nat. Commun 2020 Nov 27; 11:6049
A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma
Saiful E. Syafruddin, Paulo Rodrigues, Erika Vojtasova, Saroor A. Patel, M. Nazhif Zaini, Johanna Burge, Anne Y. Warren, Grant D. Stewart, Tim Eisen, Dóra Bihary, Shamith A. Samarajiwa & Sakari Vanharanta Nat. Commun 2019 Mar 11; 10:1152
Exploring the role of stromal osmoregulation in cancer and disease using executable modelling
NF-κB–Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis.
Paulo Rodrigues, Saroor A. Patel, Louise Harewood, Ioana Olan, Erika Vojtasova, Saiful E. Syafruddin, M. Nazhif Zaini, Emma K. Richardson, Johanna Burge, Anne Y. Warren, Grant D. Stewart, Kourosh Saeb-Parsy, Shamith A. Samarajiwa and Sakari Vanharanta
Cancer Discovery 2018
Challenges and cases of genomic data integration across technologies and biological scales.
Shamith A. Samarajiwa*, Ioana Olan and Dóra Bihary. In: Giabbanelli P., Mago V., Papageorgiou E. (eds) Advanced Data Analytics in Health. Smart Innovation, Systems and Technologies, vol 93. Springer, Cham 2018
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence.
Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity.
Turrell FK, Kerr EM, Gao M, Thorpe H, Doherty GJ, Cridge J, Shorthouse D, Speed A, Samarajiwa S, Hall BA, Griffiths M, Martins CP. Genes Dev. 2017 Aug 8.
Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer.
Zhi Hu, Jian-Hua Mao, Christina Curtis, Ge Huang, Shenda Gu, Laura Heiser, Marc E Lenburg, James E Korkola, Nora Bayani, Shamith Samarajiwa, Jose A Seoane, Mark A Dane, Amanda Esch, Heidi S Feiler, Nicholas J Wang, Mary Ann Hardwicke, Sylvie Laquerre, Jeff Jackson, Kenneth Wood, Barbara Weber, Paul T Spellman, Samuel Aparicio, Richard Wooster, Carlos Caldas, Joe W Gray Breast Cancer Res. 2016 18 (1), 70
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.
Kirschner K*, Samarajiwa SA*, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M. PLoS Genet. 2015 Mar 19;11(3):e1005053. *equal contribution
Samarajiwa SA, Mangan NE, Hardy MP, Najdovska M, Dubach D, Braniff SJ, Owczarek CM, Hertzog PJ. J Immunol. 2014 May 1;192(9):4425-35.
Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape.
Bidwell BN, Slaney CY, Withana NP, Forster S, Cao Y, Loi S, Andrews D, Mikeska T, Mangan NE, Samarajiwa SA, de Weerd NA, Gould J, Argani P, Möller A, Smyth MJ, Anderson RL, Hertzog PJ, Parker BS. Nat Med. 2012 Aug;18(8):1224-31.
Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M. Mol Cell. 2012 Jul 27;47(2):203-14.
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Curtis C*, Shah SP*, Chin SF*, Turashvili G*, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S. Nature. 2012 Apr 18;486(7403):346-52.
Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers.
Ana-Teresa Maia, Antonis C Antoniou, Martin O'Reilly, Shamith Samarajiwa, Mark Dunning, Christiana Kartsonaki, Suet-Feung Chin, Christina N Curtis, Lesley McGuffog, Susan M Domchek, Douglas F Easton, Susan Peock, Debra Frost, D Gareth Evans, Ros Eeles, Louise Izatt, Julian Adlard, Diana Eccles, Olga M Sinilnikova, Sylvie Mazoyer, Dominique Stoppa-Lyonnet, Marion Gauthier-Villars, Laurence Faivre, Laurence Venat-Bouvet, Capucine Delnatte, Heli Nevanlinna, Fergus J Couch, Andrew K Godwin, Maria Adelaide Caligo, Rosa B Barkardottir, Xiaoqing Chen, Jonathan Beesley, Sue Healey, Carlos Caldas, Georgia Chenevix-Trench, Bruce AJ Ponder Breast Cancer Res. 14 (2), R63
Spatial coupling of mTOR and autophagy augments secretory phenotypes.
Narita M*, Young AR*, Arakawa S, Samarajiwa SA, Nakashima T, Yoshida S, Hong S, Berry LS, Reichelt S, Ferreira M, Tavaré S, Inoki K, Shimizu S, Narita M. Science. 2011 May 20;332(6032):966-70.
Daniel G Holland, Angela Burleigh, Anna Git, Mae A Goldgraben, Pedro A Perez‐Mancera, Suet‐Feung Chin, Antonio Hurtado, Alejandra Bruna, H Raza Ali, Wendy Greenwood, Mark J Dunning, Shamith Samarajiwa, Suraj Menon, Oscar M Rueda, Andy G Lynch, Steven McKinney, Ian O Ellis, Connie J Eaves, Jason S Carroll, Christina Curtis, Samuel Aparicio, Carlos Caldas EMBO Mol Med 2011 3 (3), 167-180
Systems biology of interferon responses.
P Hertzog, S Forster, S Samarajiwa. J Interferon Cytokine Res. 2011 Jan;31(1):5-11.
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
NL Barbosa-Morais, MJ Dunning, SA Samarajiwa, JFJ Darot, ME Ritchie, Andy G Lynch, Simon Tavaré Nucleic Acids Res. 38 (3), e17-e17
AN Harman, J Lai, S Turville, S Samarajiwa, Lachlan Gray, Valerie Marsden, Sarah K Mercier, Kate Jones, Najla Nasr, Arjun Rustagi, Helen Cumming, Heather Donaghy, Johnson Mak, Michael Gale, Melissa Churchill, Paul Hertzog, Anthony L Cunningham. Blood. 2011 Jul 14;118(2):298-308
INTERFEROME: the database of interferon-regulated genes
Samarajiwa SA*, Forster S, Auchettl K, Hertzog PJ. Nucleic Acids Res. 2009 Jan;37:D852-7.
Type I interferon receptors: biochemistry and biological functions
NA de Weerd, SA Samarajiwa, PJ Hertzog. Journal of Biological Chemistry 2007 282 (28), 20053-20057
Type I interferons: genetics and structure
SA Samarajiwa*, W Wilson, PJ Hertzog 2006 The Interferons: Characterization and Application Wiley‐VCH Verlag GmbH & Co. KGaA
