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
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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
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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
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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
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2018-2021- MRC Doctoral Training Partnership (DTP) Studentship, £83,280
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2018-2020- Academy of Medical Sciences Springboard Award, Characterisation of functional non-coding mutations in follicular lymphoma, £100,000
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2017-2022- Cancer Research UK, Programme Award, Improving outcome for patients with Poor Risk Acute Myeloid Leukaemia, £1.9M in total, Co-investigator
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2017-2020- MRC Doctoral Training Partnership (DTP) Studentship, £83,280
Recent Publications
Transmission of diffuse large B-cell lymphoma by an allogeneic stem-cell transplant. Araf S, Wang J, Ashton-Key M et al. Haematologica (2019) 104(2) e174-e177
https://www.ncbi.nlm.nih.gov/pubmed/29976740
Correction: Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma. Araf S, Wang J, Korfi K et al. Leukemia (2019) (2)
https://www.ncbi.nlm.nih.gov/pubmed/30903015
Epigenetic Regulation of iASPP-p63 Feedback Loop in Cutaneous Squamous Cell Carcinoma. Robinson DJ, Patel A, Purdie KJ et al. J Invest Dermatol (2019) (2)
https://www.ncbi.nlm.nih.gov/pubmed/30710576
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. Patel MB, Wang J High Throughput (2018) 8(2)
https://www.ncbi.nlm.nih.gov/pubmed/30577431
GATA2 monoallelic expression underlies reduced penetrance in inherited GATA2-mutated MDS/AML. Al Seraihi AF, Rio-Machin A, Tawana K et al. Leukemia (2018) 32(2) 2502-2507
https://www.ncbi.nlm.nih.gov/pubmed/29749400
The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Inman GJ, Wang J, Nagano A et al. Nat Commun (2018) 9(2) 3667
https://www.ncbi.nlm.nih.gov/pubmed/30202019
SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine. Dayem Ullah AZ, Oscanoa J, Wang J et al. Nucleic Acids Res (2018) 46(2) W109-W113
https://www.ncbi.nlm.nih.gov/pubmed/29757393
MicroRNA and transcriptome analysis in periocular Sebaceous Gland Carcinoma. Bladen JC, Wang J, Sangaralingam A et al. Sci Rep (2018) 8(2) 7531
https://www.ncbi.nlm.nih.gov/pubmed/29760516
IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome. Wang J, Dayem Ullah AZ, Chelala C Nucleic Acids Res (2018) 46(2) e47
https://www.ncbi.nlm.nih.gov/pubmed/29390075
CSF1R+ Macrophages Sustain Pancreatic Tumor Growth through T Cell Suppression and Maintenance of Key Gene Programs that Define the Squamous Subtype. Candido JB, Morton JP, Bailey P et al. Cell Rep (2018) 23(2) 1448-1460
https://www.ncbi.nlm.nih.gov/pubmed/29719257
Team
Postdoctoral Researchers
Dr Eleni Maniati, Dr Findlay Copley, Dr Faraz Khan
Bioinformatician
Mr Firat Uyulur
PhD Students
Ms Minal Patel, Ms Sheila Barasa
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.