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Accurate detection and differentiation of benign and malignant renal tumour sub-types with Methyl-BoostER: an epigenetic marker driven learning framework

Sabrina Rossi†, Isabel Newsham†, Sara Pita, Gahee Park, Radoslaw Lach, Anne Babbage, Christopher Smith, Kevin Brennan, Hong Zeng, Tom Mitchell, Anne Warren, John Leppert, Olivier Gevaert, Grant D. Stewart, Charles Massie*, and Shamith A. Samarajiwa*. Sci Adv. 2022

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Renal lineage factor PAX8 integrates oncogenic signaling by somatic and inherited genetic alterations in kidney cancer.

Saroor A. Patel, Shoko Hirosue, Paulo Rodrigues, Erika Vojtasova, Emma K. Richardson, Saiful E. Syafruddin, Evangelia K. Papachristou, Ludovic Wesolowski, Veronica Caraffini, Dóra Bihary, Grant D. Stewart, Anne Y. Warren, Shamith A. Samarajiwa, Jason S. Carroll, and
Sakari Vanharanta*. Nature 2022

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Mapping of cis-regulatory variants by differential allelic expression analysis identifies candidate risk variants and target genes of 27 breast cancer risk loci.

Joana M Xavier, Ramiro Magno, Roslin Russell, Bernardo P de Almeida, Ana Jacinta-Fernandes, André Duarte, Mark Dunning, Shamith Samarajiwa, Martin O'Reilly, Cátia L Rocha, Nordiana Rosli, Bruce AJ Ponder, Ana-Teresa Maia* medRxiv 2022

https://doi.org/10.1101/2022.03.08.22271889

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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*  Nat. Aging 2021

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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* Mol. Cell. 2021

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SGK1 mutations in DLBCL generate hyperstable protein neoisoforms that promote AKT independence.

Jie Gao, Eirini Sidiropoulou, Ieuan Walker, Joanna Alicja Krupka, Karol Mizielinski, Zelvera Usheva, Shamith A Samarajiwa, Daniel J Hodson. Blood, 2021 May, doi: https://doi.org/10.1182/blood.2020010432

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SpiderSeqR: an R package for crawling the web of high-throughput multi-omic data repositories for useful sequencing data-sets.

Anna Sozanska, Charles Fletcher, Dora Bihary and Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi: https://doi.org/10.1101/2020.04.13.039420

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

Laura D. Martens, Oisin Faust, Liviu Pirvan, Dora Bihary, and Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi: https://doi.org/10.1101/2020.04.19.049585

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Machine Classification of Methylomes in Cancer.

Isabelle Newsham, Marcin Sendera, SriGanesh Jammula, Rebecca Fitzgerald, Charles Massie, Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi: https://doi.org/10.1101/2020.04.04.025155

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

Liviu Pirvan, Shamith A. Samarajiwa*. bioRxiv, 2020 Apr, doi: https://doi.org/10.1101/2020.04.02.022517

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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

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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

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

David Shorthouse, Angela Riedel, Emma Kerr, Luisa Pedro, Dóra Bihary, Shamith Samarajiwa, Carla P. Martins, Jacqueline Shields & Benjamin A. Hall Nat. Commun 2018 Aug 1; 9:3011

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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

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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. 

Aled J. Parry, Matthew Hoare, Dóra Bihary, Robert Hänsel-Hertsch, Stephen Smith, Kosuke Tomimatsu, Elizabeth Mannion, Amy Smith, Paula D’Santos, I. Alasdair Russell, Shankar Balasubramanian, Hiroshi Kimura, Shamith A. Samarajiwa*, Masashi Narita*. Nat. Commun 2018 May 9;9(1):1840

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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

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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

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Soluble IFN receptor potentiates in vivo type I IFN signaling and exacerbates TLR4-mediated septic shock. 

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.

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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.

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Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. 

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.

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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

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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.

 

ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium.

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.

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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

 

HIV infection of dendritic cells subverts the IFN induction pathway via IRF-1 and inhibits type 1 IFN production.

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

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INTERFEROME: the database of interferon-regulated genes 

Samarajiwa SA*, Forster S, Auchettl K, Hertzog PJ. Nucleic Acids Res. 2009 Jan;37:D852-7.

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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