SIMON FURNEY: Curriculum Vitae
contact details

Research Lecturer
Physiology & Medical Physics, RCSI

123 St Stephens Green, Dublin 2
simonfurney@rcsi.ie
Telephone: TBC
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education

2007: Ph.D., University College Dublin. Medicine

2002: M.Sc., University of Manchester. Bioinformatics

1999: B.A. (Hons.), Trinity College Dublin. Natural Sciences

summary of research career to date

Recruited through RCSI’s ambitious StAR programme (http://www.rcsi.ie/star), I am expanding my established research programme in Genomic Medicine and Cancer Bioinformatics at RCSI. Educated at Trinity College Dublin (B.A.), University of Manchester (M.Sc.) and University College Dublin (Ph.D.), I moved abroad to conduct post-doctoral genomics research in world-leading institutes. Having initially focused on integrative genomics studies in cancer (Nature Methods, 2010) and Alzheimer's disease (Molecular Psychiatry, 2011), I made a strategic move into the field of next generation sequencing (NGS) in 2010. I have devoted the last 7 years of my career to using NGS for the interpretation of cancer genomes, resulting in high-impact first author publications (e.g. Genome Research, 2012; Cancer Discovery, 2013; Nature, 2014) and scientific awards.

research interests

Cancer Bioinformatics and Genomics. The overarching theme of my research programme is the inference of mechanisms of tumour development and evolution from oncogenomic data. I have several collaborations with clinicians in which we are using next generation sequencing data from melanoma, neuroblastoma, breast and colorectal cancer patients to understand tumour development and tumour evolution in response to therapy. In addition, my research includes pan-cancer analyses of thousands of cancer genomes to uncover common and subtype-specific mechanisms of oncogenesis. I am a member of the Genomics England (100,000 Genomes Project) Clinical Interpretation Partnership (GeCIP) for melanoma, and the Irish Cancer Society BREAST-PREDICT Consortium.

research areas

Cancer

Memberships

Global Alliance for Genomics and Health (2015)

European Association for Cancer Research (2011)

Honours/Awards/Achievements

2016: Senior Young Scientist Award, Irish Association for Cancer Research

2013: Marie Curie Fellowship, European Commission

2013: Pathway to Independence Residential Programme, Institute of Cancer Research - Wellcome Trust Sanger Institute - BBSRC

2007: Young Scientists’ Forum, Federation of European Biochemical Societies

2005: EMBO Short-term Fellowship, European Molecular Biology Organisation

2003: Marie Curie Ph.D. Training Site Fellowship, European Bioinformatics Institute

Peer Reviewed Publications

Piraino SW and Furney SJ*
Identification of coding and non-coding mutational hotspots in cancer genomes
BMC Genomics 18(1):17     PMID: 28056774     (Jan 2017)

Toomey S, Madden SF, Furney SJ, Fan Y, McCormack M, Stapleton C, Cremona M, Cavalleri GL, Milewska M, Elster N, Carr A, Fay J, Kay EW, Kennedy S, Crown J, Gallagher WM, Hennessy BT, Eustace AJ
The impact of ERBB-family germline single nucleotide polymorphisms on survival response to adjuvant trastuzumab treatment in HER2-positive breast cancer
Oncotarget. 7(46):75518-75525     PMID: 27776352     (Nov 2016)

Girotti MR, Gremel G, Rothwell D, Viros A, Mandal A, Kok K, Furney SJ, Pedersen M, Rogan J, Swan J, Fusi A, Brady G, Lorigan P, Dive C, Marais R
Application of sequencing, liquid biopsies and patient derived xenografts for personalized medicine in melanoma
Cancer Discovery 6(3):286-99     PMID: 26715644     (Mar 2016)

Piraino SW and Furney SJ*
Beyond the exome – the role of non-coding somatic mutations in cancer
Annals of Oncology 27(2):240-8     PMID: 26598542     (Feb 2016)

Korfi K, Mandal A, Furney SJ, Wiseman D, Somervaille T and Marais R
A personalised medicine approach for ponatinib-resistant chronic myeloid leukaemia
Annals of Oncology 26(6):1180-7.     PMID: 25712455     (Jun 2015)

Nho K, Kim S, Risacher SL, Shen L, Corneveaux JJ, Swaminathan S, Lin H, Ramanan VK, Liu Y, Foroud T, Inlow MH,. Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta K, Lindsay A. Farrer LA, Furney SJ, Lovestone S, Simmons A, Huentelman MJ, Saykin AJ et al.
Protective Variant for Hippocampal Atrophy Identified by Whole Exome Sequencing
Annals of Neurology 77(3):547-52     PMID: 25559091     (Mar 2015)

Gavrielides M, Furney SJ*, Yates T, Miller CJ and Marais R
Onco-STS: a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments
Source Code Biol Med. 9(1).     PMID: 25580158     (Dec 2014)

Furney SJ*, Turajlic S, Stamp G, Hayes A, Gore M, Larkin J and Marais R
The mutational burden of acral melanoma revealed by whole genome sequencing and comparative analysis
Pigment Cell & Melanoma Research 27(5):835-8.     PMID: 24913711     (Sep 2014)

Viros A, Sanchez-Laorden B, Pedersen M, Furney SJ*, Rae J, Ejiama S, Dhomen N, Hogan K, Girotti MR, and Marais R
Ultraviolet radiation accelerates BRAF-driven melanomagenesis by targeting TP53
Nature 511(7510):478-82     PMID: 24919155     (Jul 2014)

Turajlic S, Furney SJ*, Stamp G, Rana S, Ricken G, Saturno G, Oduko Y, Hayes A, Gore M, Larkin J and Marais R
Whole genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition
Annals of Oncology 25(5):959-67     PMID: 24504448     (May 2014)

Proitsi, P Hyuck Lee SH, Lunnon K, Keohane A, Troakes C, Al-Sarraj S, Furney SJ, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Lovestone S and Hodges A
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     PMID: 24064185     (Feb 2014)

Killick R, Ribe EM, Al-Shawi R, Malik B, Hooper C, Fernandes C, Dobson R, Noaln PA, Lourdusamy A, Furney SJ, Lin K, Breen G, Wroe R, To AW, Leroy K, Causevic M, Usardi A, Robinson M, Noble W, Williamson R, Lunnon K, Kellie S, Reynolds CH, Bazenet C, Hodges A, Brion JP, Stephenson J, Simons JP, Lovestone S
ß-amyloid Increases Intracellular Clusterin, Activating Dkk1-Wnt-JNK Induction of Genes Mediating Neurotoxicity
Molecular Psychiatry 19(1):88-9     PMID: 23164821     (Jan 2014)

Furney SJ*, Pedersen M, Gentien D, Dumont AG, Rapinat A, Desjardins L, Turajlic S, Piperno-Neumann S, de la Grange P, Roman-Roman S, Stern MH and Marais R
SF3B1 mutations are associated with alternative splicing in uveal melanoma
Cancer Discovery 3(10):1122-9     PMID: 23861464     (Oct 2013)

Furney SJ*, Turajlic S, Stamp G, Nohadani M, Carlisle A, Thomas JM, Hayes A, Strauss A, Gore M, van den Oord J, Larkin J and Marais R
Genome sequencing of mucosal melanomas reveals that they are driven by distinct mechanisms from cutaneous melanoma
Journal of Pathology 230(3):261-9     PMID: 23620124     (Jul 2013)

Nho K, Corneveaux JJ, Kim S, Lin H, Risacher SL, Shen L, Swaminathan S, Ramanan VK, Liu Y, Foroud T, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta K, Farrer LA, Furney SJ, Lovestone S, Simmons A, Huentelman MJ, Saykin AJ et al.
Identification of functional variants from whole-exome sequencing, combined with neuroimaging genetics
Molecular Psychiatry (7):739.     PMID: 23787478     (Jul 2013)

Nho K, Corneveaux JJ, Kim S, Lin H, Risacher SL, Shen L, Swaminathan S, Ramanan VK, Liu Y, Foroud T, Inlow MH, Siniard AL, Reiman RA, Aisen PS, Petersen RC, Green RC, Jack CR, Weiner MW, Baldwin CT, Lunetta K, Farrer LA, Furney SJ, Lovestone S, Simmons A, Huentelman MJ, Saykin AJ et al.
Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in Mild Cognitive Impairment
Molecular Psychiatry (7):781-7     PMID: 23608917     (Jul 2013)

Lunnon K, Sattlecker M, Furney SJ*, Coppola G, Simmons A, Proitsi P, Lupton MK, Lourdusamy A, Johnston C, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Geschwind D, Lovestone S, Dobson R, Hodges A
A blood gene expression marker of early Alzheimer’s disease
Journal of Alzheimer’s Disease 33(3):737-53     PMID: 23042217     (May 2013)

Furney SJ*, Turajlic S, Fenwick K, Lambros MB, Mackay A, Ricken G, Mitsopoulos C, Kozarewa I, Hakas J, Zvelebil M, Lord CJ, Ashworth A, Reis-Filho JS, Herlyn M, Murata H, Marais R
Genomic characterisation of acral melanoma cell lines
Pigment Cell & Melanoma Research 25(4):488-492     PMID: 22578220     (Jul 2012)

Furney SJ*, Gundem G, Lopez-Bigas N
Oncogenomics methods and resources
Cold Spring Harbor protocols 2012(5)     PMID: 22550293     (May 2012)

Natrajan R, Mackay A, Lambros MB, Weigelt B, Wilkerson PM, Manie E, Grigoriadis A, A'Hern R, van der Groep P, Kozarewa I, Popova T, Mariani O, Turajlic S, Furney SJ, Marais R, Swanton C, Ashworth A, Henri Stern M, Reis-Filho JS
A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers
Journal of Pathology 227(1):29-41     PMID: 22362584     (May 2012)

Lunnon K, Ibrahim Z, Proitsi P, Lourdusamy A, Newhouse S, Sattlecker M, Furney SJ, Saleem M, Soininen H, Kloszewska I, Mecocci P, Tsolaki M, Vellas B, Coppola G, Geschwind D, Simmons A, Lovestone S, Dobson R, Hodges A
Mitochondrial dysfunction and immune activation are detectable in early Alzheimer's disease blood
Journal of Alzheimer's disease 30(3):685-710     PMID: 22466004     (Apr 2012)

Turajlic S, Furney SJ*, Lambros MB, Mitsopoulos C, Kozarewa I, Geyer FC, Mackay A, Hakas J, Zvelebil M, Lord CJ, Ashworth A, Thomas M, Stamp G, Larkin J, Reis-Filho JS, Marais R
Whole genome sequencing of matched primary and metastatic acral melanomas
Genome Research 22(2):196-207     PMID: 22183965     (Feb 2012)

Furney SJ*, Simmons A, Breen G, Pedroso I, Lunnon K, Proitsi P, Hodges A, Powell J, Wahlund LO, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Spenger C, Lathrop M, Shen L, Kim S, Saykin AJ, Weiner MW, Lovestone S
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease
Molecular Psychiatry 16(11):1130-1138     PMID: 21116278     (Nov 2011)

Furney SJ*, Kronenberg D, Simmons A, Guntert A, Dobson RJ, Proitsi P, Wahlund LO, Kloszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Spenger C, Lovestone S
Combinatorial markers of mild cognitive impairment conversion to Alzheimer's diseasecytokines and MRI measures together predict disease progression
Journal of Alzheimer's disease 26 Suppl 3:395-405     PMID: 21971479     (Sep 2011)

Thambisetty M, Simmons A, Velayudhan L, Hye A, Campbell J, Zhang Y, Wahlund LO, Westman E, Kinsey A, Guntert A, Proitsi P, Powell J, Causevic M, Killick R, Lunnon K, Lynham S, Broadstock M, Choudhry F, Howlett DR, Williams RJ, Sharp SI, Mitchelmore C, Tunnard C, Leung R, Foy C, O'Brien D, Breen G, Furney SJ, Ward M, Kloszewska I, Vellas B, Lovestone S
Association of plasma clusterin concentration with severity, pathology, and progression in Alzheimer disease
Archives of General Psychiatry 67(7):739-748     PMID: 20603455     (Jul 2010)

Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N
IntOGen: integration and data mining of multidimensional oncogenomic data
Nature Methods 7(2):92-93     PMID: 20111033     (Feb 2010)

Furney SJ*, Calvo B, Larranaga P, Lozano JA, Lopez-Bigas N
Prioritization of candidate cancer genesan aid to oncogenomic studies
Nucleic Acids Research 36(18):e115     PMID: 18710882     (Oct 2008)

Furney SJ*, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N
Distinct patterns in the regulation and evolution of human cancer genes
In Silico Biology 8(1):33-46     PMID: 18430988     (May 2008)

Calvo B, Lopez-Bigas N, Furney SJ, Larranaga P, Lozano JA
A partially supervised classification approach to dominant and recessive human disease gene prediction
Computer methods and programs in biomedicine 85(3):229-237     PMID: 17258838     (Mar 2007)

Furney SJ*, Alba MM, Lopez-Bigas N
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations
BMC Genomics 7:165     PMID: 16817963     (Jul 2006)

Furney SJ*, Higgins DG, Ouzounis CA, Lopez-Bigas N
Structural and functional properties of genes involved in human cancer
BMC Genomics 7:3     PMID: 16405732     (Jan 2006)