Bioinformatics
The Centre for Computational Biology champions a multidisciplinary approach to research and teaching in Data Sciences for Life Sciences. Our researchers link the fields of Mathematics, Statistics, and Computer Sciences to Biology and Medicine, while reaching a broad 黑料吃瓜网 of data scientists on campus. We lead the development of novel integrative and analytical approaches to data starting with Omics and Clinical.
Our Data Sciences experts have partnered with scientists and healthcare professionals of Chengdu’s West China Hospital – one of China’s biggest and best hospitals – to help link innovative ‘Omics’ data with clinical information for a range of conditions. This collaborative working is vital to help transform the lives of patients, as well as understanding the cause of diseases.
Theme Co-Leads
Professor Jean-Baptiste Cazier
Chair of Bioinformatics
Director of the Centre for Computational Biology
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Professor Georgios Gkoutos
Chair of Clinical Bioinformatics
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Research groups
| PI | Research Group |
|---|
| Dr Roland Arnold |
Bioinformatics analyses of transcription in cancer |
| Professor Jean-Baptiste Cazier |
Bioinformatics, Data Science for Life Sciences, Precision Medicine, Population Diversity |
| Dr Deena Gendoo |
Bioinformatics characterization of preclinical disease models and their applications in therapy |
| Professor Georgios Gkoutos |
Clinical Bioinformatics, health data science, precision medicine |
| Dr Marc Haber |
Genetic variation in humans to explain the differences between populations in disease incidence and progression |
| Dr Andreas Karwath |
Applying machine learning to health care |
| Dr Animesh Acharjee |
Integrative Analytics, diagnostics, and development of bioinformatics tools and workflows |
| Dr Csilla Várnai |
Structural bioinformatics |
Spotlight on research using drug structure analysis to identify new therapeutics for breast cancer
In a study led by Deena Gendoo’s lab, an integrative pharmacogenomics pipeline was developed to identify novel and effective therapeutics for breast cancer therapy. This pipeline, mevalonate drug-network fusion (MVA-DNF), integrated drug-induced gene perturbation signatures, drug sensitivity, and drug structure profiles to generate a pathway-centric network of drugs that can target the mevalonate (MVA) pathway.
The mevalonate pathway is a metabolic pathway that is a hallmark of many cancer types, including breast cancer, as it produces cholesterol and other isoprenoids that are essential for cell proliferation and survival. Dipyridamole (DP) is a drug which synergizes with statins to potentiate the pro-apopotic activity of statins as part of the mevalonate pathway, but this drug has limited clinical utility for cancer patients. Using MVA-DNF, new statin-drug combinations were identified that target the MVA pathway, and these hits have been validated by testing on cancer cell-lines and patient-derived organoids, showing their potential for breast cancer therapy.
Accordingly, this work identified several actionable compounds and novel and effective therapeutics to help combat difficult-to-treat triple-negative breast cancer.
van Leeuwen J.E., Ba-Alawi W., Branchard E, Cruickshank J, Schormann W, Longo J, Silvester J, Gross P, Andrews D, Cescon D, Haibe-Kains B, Linda P, Gendoo D. . Nat Commun 13, 6323 (2022).
Spotlight on COVID-19 and Leukaemia
New study describes which cancer patients are more vulnerable to COVID-19.
Lancet Oncology 21: 1309-1316 (2020). Lee LYW, JB Cazier, T Starkey, SEW Briggs, R Arnold, V Bisht, . . . UKCCMP Team. COVID-19 prevalence and mortality in patients with cancer and the effect of primary tumour subtype and patient demographics: a prospective cohort study.
A newly published study involving Lennard Lee and Jean-Baptiste Cazier has found that, compared to other cancers, patients with blood cancers are more vulnerable to the effects of the coronavirus pandemic. The researchers were able to determine that patients with haematological cancers, particularly older patients and those with leukaemia, had a more severe COVID-19 trajectory compared to patients with solid organ tumours.
Selected Highlights from this Research Theme
Eur Heart J (2023). Gill SK, A Karwath, HW Uh, VR Cardoso, Z Gu, A Barsky, . . . GV Gkoutos, D Kotecha, BigData@Heart Consortium and the cardAIc group. . doi: 10.1093/eurheartj/ehac758
JAMA Netw Open 5:e220130 (2022). Varnai C, C Palles, R Arnold, HM Curley, K Purshouse, VWT Cheng, . . . J-B Cazier, The UKCCMP Team. .
Cancer Med Online: doi: 10.1002/cam4.4941 (2022). Bahcivanci B, R Shafiha, GV Gkoutos and A Acharjee. .
Lancet 398:1427-1435 (2021). Karwath A, KV Bunting, SK Gill, O Tica, S Pendleton, F Aziz, . . .GV Gkoutos, D Kotecha, .
Cell 184:4612-4625 e4614 (2021). Almarri MA, M Haber, RA Lootah, P Hallast, S Al Turki, HC Martin, . . . C Tyler-Smith. .
mSystems 6:e0034621 (2021). Benkwitz-Bedford S, M Palm, TY Demirtas, V Mustonen, A Farewell, J Warringer, . . . D Moradigaravand. .
Eur J Obstet Gynecol Reprod Biol 261:211-216 (2021). Craciunas L, O Pickering, J Chu, M Choudhary, J Zurauskiene and A Coomarasamy. .
Cancers 13:2779 (2021). Dragomir I, A Akbar, JW Cassidy, N Patel, HW Clifford and G Contino. .
mSphere 6 e00738-20 (2021). Murphy R, M Palm, V Mustonen, J Warringer, A Farewell, L Parts and D Moradigaravand. .
American J Human Genetics 107:149-157 (2020). Haber M, J Nassar, MA Almarri, T Saupe, L Saag, SJ Griffith, . . . C Tyler-Smith. .
Nat Commun 11:1825 (2020). Chung PED, DMA Gendoo, R Ghanbari-Azarnier, JC Liu, Z Jiang, J Tsui, . . . E Zacksenhaus. .
Am J Hum Genet 107:149-157 (2020). Haber M, J Nassar, MA Almarri, T Saupe, L Saag, SJ Griffith, . . . C Tyler-Smith. .
Lancet Oncol 21:1309-1316 (2020). Lee LYW, JB Cazier, T Starkey, SEW Briggs, R Arnold, V Bisht, . . . UKCCMP Team. .
Cancer Cell 38:306-307 (2020). Lee LYW, T Hill, O Topping, M Tilby, M Baker, J Greig, . . . UKBCCC- Project. .
Front Genet 11:669 (2020). Mountford HS, P Villanueva, MA Fernandez, L Jara, Z De Barbieri, LG Carvajal-Carmona, . . . JB Cazier, DF Newbury. .
Sci Rep 9:17405 (2019). Althubaiti S, A Karwath, A Dallol, A Noor, SS Alkhayyat, R Alwassia, . . . GV Gkoutos, R Hoehndorf. .
PLoS Comput Biol 15:e1006596 (2019). Gendoo DMA, RE Denroche, A Zhang, N Radulovich, GH Jang, M Lemire, . . . B Haibe-Kains. .
PLoS Comput Biol 14:e1006258 (2018). Moradigaravand D, M Palm, A Farewell, V Mustonen, J Warringer and L Parts. .
Genome Med 9:119 (2017). Moradigaravand D, T Gouliouris, B Blane, P Naydenova, C Ludden, C Crawley, . . . SJ Peacock. .
BMC Bioinformatics 17:140 (2016). Zurauskiene J and C Yau. .
Nat Commun 5:3756 (2014). Cazier JB, SR Rao, CM McLean, AK Walker, BJ Wright, EE Jaeger, . . . FC Hamdy. .