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Simon Furney

Research Fellow

Conway Institute of Biomolecular & Biomedical Research

Tel: 353 1 716 6932
Email: simon.furney@ucd.ie

Biography

I recently returned to Ireland with a European Commission Marie Curie Fellowship after undertaking cutting-edge genomics research in world-leading institutes. Having initially focused on integrative genomics studies in cancer (Nat. Methods, 2010) and Alzheimer's disease (Mol. Psychiatry, 2011), I made a strategic move into the field of next generation sequencing (NGS) in 2010. I have devoted the last 6 years of my career to applying NGS in cancer resulting in high-impact first author publications (e.g. Genome Research, 2012; Cancer Discovery, 2013; Nature, 2014).

Currently, I am an Early Career Independent Investigator in the UCD School of Medicine Centre for Bioinformatics. I have established a research programme focused on Personalised Medicine and Cancer Bioinformatics underpinned by the application of bioinformatics to genomics and next generation sequencing (NGS) data. To complement my expertise in bioinformatics and genomics, I have built a network of national and international clinical and wet laboratory collaborators including the Irish Cancer Society BREAST-PREDICT consortium and the Genomics England (100,000 Genomes Project) Clinical Interpretation Partnership (GeCIP) for melanoma.

Recently, I was awarded the Irish Association for Cancer Research's Young Scientist (Senior Award) 2016.

Professional

Honours and Awards

Year: 2016.
Title: Irish Association for Cancer Research Senior Young Scientist Award
Year: 2013.
Title: Marie Curie Intra-European Fellowship
Year: 2013.
Title: Pathway to Independence Programme
Year: 2007.
Title: FEBS Young Scientists' Forum
Year: 2005.
Title: EMBO Short-term Fellowship
Year: 2003.
Title: Marie Curie Ph.D. Training Site Fellowship
Year: 2002.
Title: DMMC Postgraduate Scholarship

Associations

Association: European Association for Cancer Research, Function/Role: Member
Association: Global Alliance for Genomics & Health , Function/Role: Member
           

Education

Year 2007 Institution: University College Dublin
Qualification: PhD Subject: Medicine

Languages

Spanish:
French:
German:
       

Publications

     

Peer Reviewed Journals

Girotti MR, Gremel G, Lee R, Galvani E, Rothwell D, Viros A, Mandal AK, Lim KH, Saturno G, Furney SJ, Baenke F, Pedersen M, Rogan J, Swan J, Smith M, Fusi A, Oudit D, Dhomen N, Brady G, Lorigan P, Dive C, Marais R (2016) 'Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma'. Cancer Discovery, 6 (3):286-299. [Details]
Piraino SW, Furney SJ (2015) 'Beyond the exome: the role of non-coding somatic mutations in cancer'. Annals of Oncology, . [DOI] [Details]
Korfi K, Mandal A, Furney SJ, Wiseman D, Somervaille TC, Marais R (2015) 'A personalised medicine approach for ponatinib-resistant chronic myeloid leukaemia'. Annals of Oncology, . [Details]
Nho K, Kim S, Risacher SL, Shen L, Corneveaux JJ, Swaminathan S, Lin H, Ramanan VK, Liu Y, Foroud TM, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR Jr, Weiner MW, Baldwin CT, Lunetta KL, Farrer LA; MIRAGE (Multi-Institutional Research on Alzheimer Genetic Epidemiology) Study, Furney SJ, Lovestone S, Simmons A, Mecocci P, Vellas B, Tsolaki M, Kloszewska I, Soininen H; AddNeuroMed Consortium, McDonald BC, Farlow MR, Ghetti B; Indiana Memory and Aging Study, Huentelman MJ, Saykin AJ; Alzheimer's Disease Neuroimaging Initiative. (2015) 'Protective variant for hippocampal atrophy identified by whole exome sequencing'. Annals of Neurology, . [Details]
Viros A, Sanchez-Laorden B, Pedersen M, Furney SJ, Rae J, Hogan K, Ejiama S, Girotti MR, Cook M, Dhomen N, Marais R (2014) 'Ultraviolet radiation accelerates BRAF-driven melanomagenesis by targeting TP53'. Nature, . [Details]
Turajlic, S., Furney, S. J., Stamp, G., Rana, S., Ricken, G., Oduko, Y., Saturno, G., Springer, C., Hayes, A., Gore, M., Larkin, J., Marais, R. (2014) 'Whole-genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition'. Annals of Oncology, 25 (5):959-67. Available Online [Details]
Proitsi, P., Lee, S. H., Lunnon, K., Keohane, A., Powell, J., Troakes, C., Al-Sarraj, S., Furney, S., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Lovestone, S., Hodges, A., AddNeuroMed, Consortium (2014) 'Alzheimer's disease susceptibility variants in the MS4A6A gene are associated with altered levels of MS4A6A expression in blood'. Neurobiology of Aging, 35 (2):279-90. Available Online [Details]
Killick, R., Ribe, E. M., Al-Shawi, R., Malik, B., Hooper, C., Fernandes, C., Dobson, R., Nolan, P. M., Lourdusamy, A., Furney, S., Lin, K., Breen, G., Wroe, R., To, A. W., Leroy, K., Causevic, M., Usardi, A., Robinson, M., Noble, W., Williamson, R., Lunnon, K., Kellie, S., Reynolds, C. H., Bazenet, C., Hodges, A., Brion, J. P., Stephenson, J., Simons, J. P., Lovestone, S. (2014) 'Clusterin regulates beta-amyloid toxicity via Dickkopf-1-driven induction of the wnt-PCP-JNK pathway'. Molecular Psychiatry, 19 (1):88-98. Available Online [Details]
Furney SJ, Turajlic S, Stamp G, Meirion Thomas J, Hayes A, Strauss D, Gavrielides M, Xing W, Gore M, Larkin J, Marais R (2014) 'The mutational burden of acral melanoma revealed by whole genome sequencing and comparative analysis'. Pigment Cell & Melanoma Research, . [Details]
Furney, S. J., Pedersen, M., Gentien, D., Dumont, A. G., Rapinat, A., Desjardins, L., Turajlic, S., Piperno-Neumann, S., de la Grange, P., Roman-Roman, S., Stern, M. H., Marais, R. (2013) 'SF3B1 mutations are associated with alternative splicing in uveal melanoma'. Cancer Discovery, 3 (10):1122-9. Available Online [Details]
Nho, K., Corneveaux, J. J., Kim, S., Lin, H., Risacher, S. L., Shen, L., Swaminathan, S., Ramanan, V. K., Liu, Y., Foroud, T., Inlow, M. H., Siniard, A. L., Reiman, R. A., Aisen, P. S., Petersen, R. C., Green, R. C., Jack, C. R., Weiner, M. W., Baldwin, C. T., Lunetta, K., Farrer, L. A., Multi-Institutional Research on Alzheimer Genetic Epidemiology, Study, Furney, S. J., Lovestone, S., Simmons, A., Mecocci, P., Vellas, B., Tsolaki, M., Kloszewska, I., Soininen, H., AddNeuroMed, Consortium, McDonald, B. C., Farlow, M. R., Ghetti, B., Indiana, Memory, Aging, Study, Huentelman, M. J., Saykin, A. J., Alzheimer's Disease Neuroimaging, Initiative (2013) 'Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in mild cognitive impairment'. Molecular Psychiatry, 18 (7):781-7. Available Online [Details]
Nho, K., Corneveaux, J. J., Kim, S., Lin, H., Risacher, S. L., Shen, L., Swaminathan, S., Ramanan, V. K., Liu, Y., Foroud, T., Inlow, M. H., Siniard, A. L., Reiman, R. A., Aisen, P. S., Petersen, R. C., Green, R. C., Jack, C. R., Weiner, M. W., Baldwin, C. T., Lunetta, K., Farrer, L. A., Multi-Institutional Research on Alzheimer Genetic Epidemiology, Study, Furney, S. J., Lovestone, S., Simmons, A., Mecocci, P., Vellas, B., Tsolaki, M., Kloszewska, I., Soininen, H., AddNeuroMed, Consortium, McDonald, B. C., Farlow, M. R., Ghetti, B., Indiana, Memory, Aging, Study, Huentelman, M. J., Saykin, A. J., Alzheimer's Disease Neuroimaging, Initiative (2013) 'Identification of functional variants from whole-exome sequencing, combined with neuroimaging genetics'. Molecular Psychiatry, 18 (7):739. Available Online [Details]
Lunnon, K., Sattlecker, M., Furney, S. J., Coppola, G., Simmons, A., Proitsi, P., Lupton, M. K., Lourdusamy, A., Johnston, C., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Geschwind, D., Lovestone, S., Dobson, R., Hodges, A., dNeuroMed, Consortium (2013) 'A blood gene expression marker of early Alzheimer's disease'. Journal of Alzheimer's Disease, 33 (3):737-53. Available Online [Details]
Furney, S. J., Turajlic, S., Stamp, G., Nohadani, M., Carlisle, A., Thomas, J. M., Hayes, A., Strauss, D., Gore, M., van den Oord, J., Larkin, J., Marais, R. (2013) 'Genome sequencing of mucosal melanomas reveals that they are driven by distinct mechanisms from cutaneous melanoma'. Journal of Pathology, 230 (3):261-9. Available Online [Details]
Furney, S. J., Turajlic, S., Fenwick, K., Lambros, M. B., MacKay, A., Ricken, G., Mitsopoulos, C., Kozarewa, I., Hakas, J., Zvelebil, M., Lord, C. J., Ashworth, A., Reis-Filho, J. S., Herlyn, M., Murata, H., Marais, R. (2012) 'Genomic characterisation of acral melanoma cell lines'. Pigment Cell Melanoma Research, 25 (4):488-92. Available Online [Details]
Turajlic, S., Furney, S. J., Lambros, M. B., Mitsopoulos, C., Kozarewa, I., Geyer, F. C., Mackay, A., Hakas, J., Zvelebil, M., Lord, C. J., Ashworth, A., Thomas, M., Stamp, G., Larkin, J., Reis-Filho, J. S., Marais, R. (2012) 'Whole genome sequencing of matched primary and metastatic acral melanomas'. Genome Research, 22 (2):196-207. Available Online [Details]
Furney, S. J., Gundem, G., Lopez-Bigas, N. (2012) 'Oncogenomics methods and resources'. Cold Spring Harbor Protocols, 2012 (5). Available Online [Details]
Natrajan, R., Mackay, A., Lambros, M. B., Weigelt, B., Wilkerson, P. M., Manie, E., Grigoriadis, A., A'Hern, R., van der Groep, P., Kozarewa, I., Popova, T., Mariani, O., Turajlic, S., Furney, S. J., Marais, R., Rodruigues, D. N., Flora, A. C., Wai, P., Pawar, V., McDade, S., Carroll, J., Stoppa-Lyonnet, D., Green, A. R., Ellis, I. O., Swanton, C., van Diest, P., Delattre, O., Lord, C. J., Foulkes, W. D., Vincent-Salomon, A., Ashworth, A., Henri Stern, M., Reis-Filho, J. S. (2012) 'A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers'. Journal of Pathology, 227 (1):29-41. Available Online [Details]
Lunnon, K., Ibrahim, Z., Proitsi, P., Lourdusamy, A., Newhouse, S., Sattlecker, M., Furney, S., Saleem, M., Soininen, H., Kloszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Coppola, G., Geschwind, D., Simmons, A., Lovestone, S., Dobson, R., Hodges, A., AddNeuroMed, Consortium (2012) 'Mitochondrial dysfunction and immune activation are detectable in early Alzheimer's disease blood'. Journal of Alzheimer's Disease, 30 (3):685-710. Available Online [Details]
Furney, S. J., Kronenberg, D., Simmons, A., Guntert, A., Dobson, R. J., Proitsi, P., Wahlund, L. O., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Spenger, C., Lovestone, S. (2011) 'Combinatorial markers of mild cognitive impairment conversion to Alzheimer's disease--cytokines and MRI measures together predict disease progression'. J Alzheimers Dis, 26 Suppl 3 :395-405. Available Online [Details]
Furney, S. J., Simmons, A., Breen, G., Pedroso, I., Lunnon, K., Proitsi, P., Hodges, A., Powell, J., Wahlund, L. O., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Spenger, C., Lathrop, M., Shen, L., Kim, S., Saykin, A. J., Weiner, M. W., Lovestone, S., Alzheimer's Disease Neuroimaging, Initiative, AddNeuroMed, Consortium (2011) 'Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease'. Mol Psychiatry, 16 (11):1130-8. Available Online [Details]
Gundem, G., Perez-Llamas, C., Jene-Sanz, A., Kedzierska, A., Islam, A., Deu-Pons, J., Furney, S. J., Lopez-Bigas, N. (2010) 'IntOGen: integration and data mining of multidimensional oncogenomic data'. Nat Methods, 7 (2):92-3. Available Online [Details]
Thambisetty, M., Simmons, A., Velayudhan, L., Hye, A., Campbell, J., Zhang, Y., Wahlund, L. O., Westman, E., Kinsey, A., Guntert, A., Proitsi, P., Powell, J., Causevic, M., Killick, R., Lunnon, K., Lynham, S., Broadstock, M., Choudhry, F., Howlett, D. R., Williams, R. J., Sharp, S. I., Mitchelmore, C., Tunnard, C., Leung, R., Foy, C., O'Brien, D., Breen, G., Furney, S. J., Ward, M., Kloszewska, I., Mecocci, P., Soininen, H., Tsolaki, M., Vellas, B., Hodges, A., Murphy, D. G., Parkins, S., Richardson, J. C., Resnick, S. M., Ferrucci, L., Wong, D. F., Zhou, Y., Muehlboeck, S., Evans, A., Francis, P. T., Spenger, C., Lovestone, S. (2010) 'Association of plasma clusterin concentration with severity, pathology, and progression in Alzheimer disease'. Arch Gen Psychiatry, 67 (7):739-48. Available Online [Details]
Furney, S. J., Calvo, B., Larranaga, P., Lozano, J. A., Lopez-Bigas, N. (2008) 'Prioritization of candidate cancer genes--an aid to oncogenomic studies'. Nucleic Acids Res, 36 (18). Available Online [Details]
Furney, S. J., Madden, S. F., Kisiel, T. A., Higgins, D. G., Lopez-Bigas, N. (2008) 'Distinct patterns in the regulation and evolution of human cancer genes'. In Silico Biol, 8 (1):33-46. Available Online [Details]
Calvo, B., Lopez-Bigas, N., Furney, S. J., Larranaga, P., Lozano, J. A. (2007) 'A partially supervised classification approach to dominant and recessive human disease gene prediction'. Comput Methods Programs Biomed, 85 (3):229-37. Available Online [Details]
Furney, S. J.,Higgins, D. G.,Ouzounis, C. A.,Lopez-Bigas, N.; (2006) 'Structural and functional properties of genes involved in human cancer'. BMC Genomics, 7 :3. [Details]
Furney, S. J., Alba, M. M., Lopez-Bigas, N. (2006) 'Differences in the evolutionary history of disease genes affected by dominant or recessive mutations'. BMC Genomics, 7 :165. Available Online [Details]
Furney, S., Madden, S., Higgins, D., Lopez-Bigas, N., ; (2007) 'Properties and prediction of proto-oncogenes and tumour suppressor genes'. FEBS Journal, 274 :171-171. [Details]
                                                                                             

Research

Research Interests

Cancer Bioinformatics and Genomics, in particular the use of Next Generation Sequencing technologies in Cancer, such as Whole Genome Sequencing, Whole Exome Sequencing and RNA-seq.

Evolutionary Cancer Genomics.

Personalised Cancer Medicine.

UCD Medicine Research Centre: Bioinformatics

UCD Medicine Research Theme: Translational Oncology 

Research Projects

Sponsor : University College Dublin Foundation Ltd.
Title : Determination of differences in tumours in colorectal cancer patients with liver metastases
Start Date / End Date : 01-MAY-15 / 17-MAY-18
 

Current Postgraduate Students

Scott Piraino, Master of Science (MSc)   -   Thesis Supervisor

Collaborators

Internal Collaborators

Prof. Kieran Sheahan

Prof. Walter Kolch 

External Collaborators

Irish Cancer Society ¿7.5 million BREAST-PREDICT Collaboration

Genomics England (100,000 Genomes Project) Clinical Interpretation Partnership (GeCIP) for melanoma

 

Prof. Bryan Hennessy, Royal College of Surgeons in Ireland