Research Focus
My main research interests lie in applying bioinformatics and computational approaches to analyse large-scale cancer datasets to uncover novel diagnostic and prognostic features. I also lead the Cancer Research UK Barts Centre Bioinformatics Core Facility.
Key Publications
The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Nature Commun (2018) 9(2) 3667. PMID: 30202019
IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritising genetic variations in the noncoding genome. Nucleic Acids Research (2018) 46(8):e47. PMID: 29390075
Reduced expression of histone methyltransferases KMT2C and KMT2D correlates with improved outcome in pancreatic ductal adenocarcinoma. Cancer Research (2016) 76(16):4861-71. PMID: 27280393
Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nature Genetics (2014) 46(2):176-81. PMID: 24362818
Major Funding
-
2019-2022- Barts Charity Large Project Award, Investigation of the immune environment of keratinocyte skin cancer progression with implications for risk prediction and targeted prevention, Co-Investigator, £498,534.52 in total, £166,000 awarded to JW
-
2018-2023- Cancer Research UK Accelerator Award, Early detection and intervention: Understanding the mechanisms of transformation and hidden resistance of incurable haematological malignancies, Co-investigator, £1.6M in total, £149,000 to JW
- 2018-2020- Academy of Medical Sciences Springboard Award, Characterisation of functional non-coding mutations in follicular lymphoma, £100,000
Research
My main research interests lie in applying bioinformatics and computational approaches to analyse large-scale cancer datasets to uncover novel diagnostic and prognostic features.
I also lead the BCC Bioinformatics Core Service.
Cancer is a complex genetic disease caused by DNA abnormalities. The significant reduction in sequencing costs has allowed individual researchers to carry out “routine” DNA/RNA sequencing tasks to decipher these genetic aberrations. Given the increasing amount of omics datasets and cancer big-data, the challenges are in how to analyse large-scale datasets and interpret the results accurately and efficiently, and to identify “driver” events and predictive biomarkers in tumour development and progression.
Our research interests include the following:
- Discovery of novel driver events and diagnostic / prognostic signatures in cancer development and progression based on large-scale cancer multi-omics datasets and data integration.
- Identification of clonal evolutionary patterns using sequential and spatial tumour samples.
- Roles of noncoding sequence variants and dysregulated noncoding RNAs in cancer. We have recently developed a novel computational algorithm termed "IW-Scoring" to facilitate the discovery of functional noncoding mutations and variants. We aim to identify noncoding driver events using a combination of ChIP-seq, RNA-seq, WGS and targeted sequencing.
- Investigation of immune and stroma landscape and its application in patient subgrouping and prognostic signatures in cancer.
Major Funding
-
2019 - 2022- Barts Charity Large Project Award, Investigation of the immune environment of keratinocyte skin cancer progression with implications for risk prediction and targeted prevention, Co-Investigator, £498,534.52 in total, £166,000 awarded to JW
-
2018-2023- Cancer Research UK Accelerator Award, Early detection and intervention: Understanding the mechanisms of transformation and hidden resistance of incurable haematological malignancies, Co-investigator, £1.6M in total, £149,000 to JW
-
2018-2021- MRC Doctoral Training Partnership (DTP) Studentship, £83,280
-
2018-2020- Academy of Medical Sciences Springboard Award, Characterisation of functional non-coding mutations in follicular lymphoma, £100,000
-
2017-2022- Cancer Research UK, Programme Award, Improving outcome for patients with Poor Risk Acute Myeloid Leukaemia, £1.9M in total, Co-investigator
-
2017-2020- MRC Doctoral Training Partnership (DTP) Studentship, £83,280
Recent Publications
The complex genetic landscape of familial MDS and AML reveals pathogenic germline variants Rio-Machin A, Vulliamy T, Hug N et al. Nature Communications (2020) 11(7)
Integration of Deep Multi-Omics Profiling Veals New Insights into the Biology of Poor-Risk Acute Myeloid Leukemia Rio-Machin A, Casado-Izquierdo P, Miettinen J et al. Blood (2020) 136(10) 39-40
mTOR-dependent translation amplifies microglia priming in aging mice. Keane L, Antignano I, Riechers S-P et al. J Clin Invest (2020) (2)
https://www.ncbi.nlm.nih.gov/pubmed/33108356
Specific mechanisms of chromosomal instability indicate therapeutic sensitivities in high-grade serous ovarian carcinoma. Mcclelland S, Tamura N, Shaikh N et al. Cancer Research (2020) (1)
Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer Gadaleta E, Fourgoux P, Pirró S et al. npj Breast Cancer (2020) 6(1)
The MAFA gene mutation responsible for familial insulinomatosis and diabetes impairs insulin secretion and results in downregulation of critical cell cycle regulators Iacovazzo D, Thong LC, Quezado R et al. Endocrine Abstracts (2020) (10)
A frameshift variant in the specificity protein 1 triggers superactivation of SP1-mediated transcription in familial bone marrow failure. Dokal I, Tummala H, Vulliamy T et al. Proceedings of the National Academy of Sciences of USA (2020) (1)
Abstract A31: Tumor stroma in the development of acquired cancer therapy resistance Gomez-Escudero J, Maniati E, Whiting F et al. (2020) (10) a31-a31
Genetic heterogeneity highlighted by differential FDG-PET response in diffuse large B-cell lymphoma Araf S, Korfi K, Bewicke-Copley F et al. Haematologica (2020) 105(7) E318-E321
Tumor stroma in the development of acquired cancer therapy resistance. Gomez-Escudero J, Maniati E, Whiting F et al. CANCER RESEARCH (2020) 80(11) 48-48
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000537844900070&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=612ae0d773dcbdba3046f6df545e9f6a
Team
Postdoctoral Researchers
Dr Eleni Maniati, Dr Findlay Copley, Dr Faraz Khan
Bioinformatician
Mr Firat Uyulur
PhD Students
Ms Minal Patel, Ms Sheila Barasa, Connor Knight
Biography
- 2016- : Lecturer in Bioinformatics / Computational Biology, BCI, QMUL.
- 2010-2016: Postdoctoral Fellow in Bioinformatics and Cancer Genomics, Barts Cancer Institute (BCI), QMUL.
- 2008-2010: Postdoctoral Fellow in Bioinformatics, Department of Plant Science, Rothamsted Research.
- 2004-2008: PhD in Evolutionary Biology, Institute of Evolutionary Biology, University of Edinburgh - Dorothy Hodgkin Postgraduate Award.
- 2003-2004: MSc in Quantitative Genetics and Genome Analysis, Institute of Cell, Animal and Population Biology, University of Edinburgh.
- 1999-2003: BEng in Biological Engineering, College of Life Sciences & Biotechnology, Shanghai Jiao Tong University.