Bioinformatics & Health Data Science

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We are a multidisciplinary group with diverse expertise, backgrounds and skills ranging from biology, genetics, medicine, health informatics, clinical bioinformatics, genetic epidemiology, public health, epidemiology, computational biology, to data science, computer science, engineering, Artificial Intelligence, machine learning, big data, statistics and mathematics collaborating to address important questions in medical sciences.

Theme Centres

Centre for Health Data Science

The Centre for Health Data Science, led by Professor Georgios Gkoutos and Professor Krishnarajah Nirantharakumar  includes clinicians and academics that cover expertise in digital epidemiology, clinical bioinformatics, learning health systems, and artificial intelligence for health. With research and training at the core of our Centre, we aim to harness the full potential of Birmingham’s health data science capabilities to develop regional, national, and global leadership in the field of health data science.

Centre for Environmental Research and Justice (CERJ) 

The Centre for Environmental Research and Justice (CERJ) (Deputy Director: Professor Georgios Gkoutos) brings together academic expertise across three university colleges – Life and Environmental Sciences, Arts and Law, Medical and Dental Sciences – with an ambitious mission to help remedy harm to human health and the environment caused by pollution.

Theme Lead

Professor Georgios Gkoutos

Professor Georgios Gkoutos

Director - Centre for Health Science 

Deputy Director - Centre for Environmental Research and Justice 

Chair of Clinical Bioinformatics 

View Professor Gkoutos' profile

Research groups 

PIResearch Interests

Dr Animesh Acharjee, Assistant Professor of Integrative Analytics and AI

Multi-modal Integration, Diagnostics, Network Biology, Microbiomics
Dr Roland Arnold, Group Leader Bioinformatics analyses of transcription in cancer
Dr Deena Gendoo, Associate Professor of Computational Biology Bioinformatics characterization of preclinical disease models and their applications in therapy
Professor Georgios V. Gkoutos, Chair of Clinical Bioinformatics Clinical Bioinformatics, Health Data Science, Precision Medicine, Translational Phenomics
Dr Marc Haber, Associate Professor of Population Genetics, University of Birmingham Dubai Population Genetics
Dr Mohamed El-Hadidi, Associate Professor of Bioinformatics, University of Birmingham Dubai Bioinformatics
Dr Andreas Karwath, Associate Professor of Health Data Science Artificial intelligence and machine learning for health
Dr Anas Rana, Lecturer Statistical method development, ML methods
Dr Mamunur Rashid, Assistant Professor of Bioinformatics Bioinformatics
Dr Karin Slater, Assistant Professor of Biomedical Semantics Ontology, Semantics, Text mining, NLP, Artifical Intelligence
Dr Csilla Várnai Structural Bioinformatics

Teaching and Education

The members of our section are responsible for the following programmes

In addition, we deliver a number of standalone modules for various programmes:

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.  Computational pharmacogenomic screen identifies drugs that potentiate the anti-breast cancer activity of statins. Nat Commun 13, 6323 (2022).

MVA-specific drug network fusion diagram


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. 

COVID cancer study image for Computational Biology as described below

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. Artificial intelligence to enhance clinical value across the spectrum of cardiovascular healthcare. doi: 10.1093/eurheartj/ehac758

Gut (2023). Karamitopoulou E, Wenning AS, Acharjee A, et al. Spatially restricted tumour-associated and host-associated immune drivers correlate with the recurrence sites of pancreatic cancer. doi:10.1136/gutjnl-2022-329371  

JAMA Netw Open 5:e220130 (2022). Varnai C, C Palles, R Arnold, HM Curley, K Purshouse, VWT Cheng, . . . J-B Cazier, The UKCCMP Team. Mortality Among Adults With Cancer Undergoing Chemotherapy or Immunotherapy and Infected With COVID-19.

Cell Rep Med. (2022).Irvine HJ, Acharjee A, Wolcott Z, et al. Hypoxanthine is a pharmacodynamic marker of ischemic brain edema modified by glibenclamide. doi:10.1016/j.xcrm.2022.100654 

Bioinformatics. (2022).Xu Y, Nash K, Acharjee A, Gkoutos GV. CACONET: a novel classification framework for microbial correlation networks.  doi:10.1093/bioinformatics/btab879 

JAMA Psychiatry (2022), Williams JA, Burgess S, Suckling J, Lalousis PA, Batool F, Griffiths SL, Palmer E, Karwath A, Barsky A, Gkoutos GV, Wood S, Barnes NM, David AS, Donohoe G, Neill JC, Deakin B, Khandaker GM, Upthegrove R; PIMS Collaboration. Inflammation and Brain Structure in Schizophrenia and Other Neuropsychiatric Disorders: A Mendelian Randomization Study., May 1;79(5):498-507. doi: 10.1001/jamapsychiatry.2022.0407.

Lancet 398:1427-1435 (2021). Karwath A, KV Bunting, SK Gill, O Tica, S Pendleton, F Aziz, . . .GV Gkoutos, D Kotecha, The cadrdAlc group and the Beta-blockers in Heart Failure Collaborative Group. Redefining beta-blocker response in heart failure patients with sinus rhythm and atrial fibrillation: a machine learning cluster analysis.

Cell 184:4612-4625 e4614 (2021). Almarri MA, M Haber, RA Lootah, P Hallast, S Al Turki, HC Martin, . . . C Tyler-Smith. The genomic history of the Middle East

American J Human Genetics 107:149-157 (2020)Haber M, J Nassar, MA Almarri, T Saupe, L Saag, SJ Griffith, . . . C Tyler-Smith. A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.

EClinicalMedicine (2021), Malik NS, Chernbumroong S, Xu Y, Vassallo J, Lee J, Moran CG, Newton T, Arul GS, Lord JM, Belli A, Keene D, Foster M, Hodgetts T, Bowley DM, Gkoutos GV., Paediatric major incident triage: UK military tool offers best performance in predicting the need for time-critical major surgical and resuscitative intervention. Aug 23;40:101100. doi: 10.1016/j.eclinm.2021.101100. eCollection 2021 Oct.

Nat Commun 11:1825 (2020). Chung PED, DMA Gendoo, R Ghanbari-Azarnier, JC Liu, Z Jiang, J Tsui, . . . E Zacksenhaus. Modeling germline mutations in pineoblastoma uncovers lysosome disruption-based therapy.

Am J Hum Genet 107:149-157 (2020). Haber M, J Nassar, MA Almarri, T Saupe, L Saag, SJ Griffith, . . . C Tyler-Smith. A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.

Lancet Oncol 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.


More Publications

EClinicalMedicine (2021), Malik NS, Chernbumroong S, Xu Y, Vassallo J, Lee J, Bowley DM, Hodgetts T, Moran CG, Lord JM, Belli A, Keene D, Foster M, Gkoutos GV. The BCD Triage Sieve outperforms all existing major incident triage tools: Comparative analysis using the UK national trauma registry population, May 15;36:100888. doi: 10.1016/j.eclinm.2021.100888.

Comput Biol Med. (2021).Bisht V*, Acharjee A*, Gkoutos GV. NFnetFu: A novel workflow for microbiome data fusionComput Biol Med. 2021;135:104556. doi:10.1016/j.compbiomed.2021.104556 

Front Genet 11:669 (2020). Mountford HS, P Villanueva, MA Fernandez, L Jara, Z De Barbieri, LG Carvajal-Carmona, . . . JB Cazier, DF Newbury. The Genetic Population Structure of Robinson Crusoe Island, Chile.

Sci Rep 9:17405 (2019). Althubaiti S, A Karwath, A Dallol, A Noor, SS Alkhayyat, R Alwassia, . . . GV Gkoutos, R Hoehndorf. Ontology-based prediction of cancer driver genes.

Sci Data. (2019). Bravo-Merodio L, Acharjee A, Hazeldine J, …, Gkoutos GV, Lord J Machine learning for the detection of early immunological markers as predictors of multi-organ dysfunction.  doi:10.1038/s41597-019-0337-6

PLoS Comput Biol 15:e1006596 (2019)Gendoo DMA, RE Denroche, A Zhang, N Radulovich, GH Jang, M Lemire, . . . B Haibe-Kains. Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.

J Transl Med (2019). Bravo-Merodio L, Williams JA, Gkoutos GV, Acharjee A. Omics biomarker identification pipeline for translational medicine. doi:10.1186/s12967-019-1912-5