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Shamith Samarajiwa

 Shamith profile picDr Shamith Samarajiwa 

 Biography | PubMed

Group Webpage

 

 

Integrative Systems Biomedicine of Carcinogenesis

- Computational & Systems Biology approaches for battling Cancer

 

 

My lab develops multi-disciplinary Data Science, Data engineering and Computational Biology solutions to understand multi-scale biological systems involved in immunity, inflammation and cancer. We are particularly interested in the complex systems underlying carcinogenesis, and interactions between the immune system and cancer.

 

Research themes:

 

More details on the Group Web Page https://www.samarajiwa-lab.org

 

 

CELLULAR REGULOMES & GENOMIC ARCHITECTURE

 

We study (epi)Genomic regulatory logic, chromatin dynamics, translatome regulation and cellular information flow in both normal cells and during carcinogenic perturbations through the joint integration of multi-omic data-sets from a variety of interacting biological layers generated by high-throughput technologies.

CR

 

 

 

 

DATA SCIENCE & AI

 

    • CNN  Artificial Intelligence methods for cancer 'Omics'
      •   Machine Learning & Deep Learning for regulatory genomics
      •   Knowledge Graphs, Neural Graphs, Generative models for genomics
      •   Methods for early detection and diagnosis of Cancer
    •   Biomedical Natural Language Processing
    •   Biomedical Data Integration
      •   Statistical & computational methods for integration​ of biomedical data
      •   Information Visualisation

     

    BIOMEDICAL COMPLEX SYSTEMS

     

    We develop Systems Biology approaches to understand the complex  interactions between Immunity, Inflammation and Cancer.

    TP53

     

    •   Systems Immunology 
    •   Network Biology
    •   Cancer Genomics & Systems Modelling

     

     

     

     

     

     

     

     

     

    Contact: 

    Click to contact Dr. Shamith Samarajiwa by email.                     

     

    Google Scholar Citations: 

    https://scholar.google.co.uk/citations?user=vUsVyRUAAAAJ

     

    Selected Publications:

     

    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.  bioRxiv, 2019 Oct 30, 2019

     

    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

    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.

    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

    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

    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.

    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.

    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.

     

    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

     

    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

     

    ​​INTERFEROME: the database of interferon-regulated genes

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