Biostatistics

James Doecke
Team Leader
Biostatistics

At the heart of all great papers lies a keen biostatistician who has meticulously screened the data, identified the best statistical model to use for analyses, and then devised an analytical plan to get the headline result that we see in all good publications. These analyses are only as good as the data; our team has expertise in quality database design to ensure that data is stored and accessible for all who need to use it.

Our Science
The Biostatistics team’s major focus is on the statistical analyses of biomarkers related to Alzheimer’s disease (AD) pathology. Collaborating with both national and international groups, the majority of research is conducted deriving and applying benchmark statistical methodologies to elucidate the complex relationships between biomarkers and disease pathology. For all projects, the quality of the data is first and foremost important. Team members set up databases, accessing and aligning data from multiple disparate data sources into one easy place for people to download. The major challenge is to define a panel of blood-based biomarkers that can predict disease pathology status prior to the onset of clinical symptoms, with greater than 90% accuracy. Other challenges include working with geographically dispersed groups to align and analyse data from multiple collaborative groups, and validation of statistical models for the prediction of disease status.

Impact on the Health System
The derivation of an easy blood-based biomarker test as a screening tool for the early identification of AD will allow treatment strategies to take effect prior to the onset of clinical symptoms. Such treatment strategies are likely to reduce the ever-increasing burden from dementia on the Australian healthcare system.

Our Solutions
Statistical analyses of large amounts of data from well curated databases to define a blood-based biomarker test as a screening tool for the early identification of AD.

 

Case Studies

 

Team Members:

James Doecke

Marcela Cespedes

Ibrahima Diouf

Amir Fazlollahi

Saba Momeni

 

 

 

 

 

Parnesh Raniga

Julie Trinder

Michael Vacher

 

 

 

 

 

 

James Doecke
Team Leader, a senior research scientist and a biostatistician whose main research focus lies within identifying biomarkers of Alzheimer’s disease.
CSIRO Profile

Marcela Cespedes
Biostatistician research scientist with a focus on applying and developing statistical methods in order to better understand the biology behind Alzheimer’s disease dementia. Her research includes combining demographic, lifestyle, biomarkers and neuroimaging information in order to provide insight into brain degeneration due to healthy ageing or progression towards Alzheimer’s disease.
CSIRO Profile

Ibrahima Diouf
Experimental Scientist, collaborating with the Florey Institute on MRI and CSF-based biomarkers for predicting neuro-degeneration.
CSIRO Profile

Amir Fazlollahi
Postdoctoral Fellow, improving an iron-sensitive MRI biomarker for predicting neuro-degeneration, and had a paper in a high impact journal (11>).
CSIRO Profile

Saba Momeni
PhD Student, developing machine learning techniques to improve the detection of brain lesions.

Parnesh Raniga
Research scientist with a background in medical imaging (MRI & PET), neuroscience and biomedical informatics. Parnesh works on the AIBL and PISA projects, also has a strong interest in the neuroscience of dementia, especially Alzheimer’s disease and on applying informatics tools and principals to do reproducible science and reuse data.
CSIRO Profile

Julie Trinder
Research Assistant, working on data management for Medical and Clinical Imaging Teams, including the development and implementation of the bioinformatics platform and standard operating procedures (SOPs) for the team.
CSIRO Profile

Michael Vacher
Postdoctoral Fellow, developing computational approaches for integrating and analysing heterogenous data to facilitate the early detection of Alzheimer’s disease.
CSIRO Profile

Publications 

  1. Biesiekierski J, Newnham E, Irving P, Barrett J, Haines M, Doecke JD, Shepherd S, Muir J, Gibson P. Gluten causes gastrointestinal symptoms in subjects without Coeliac Disease: A double blind, randomised placebo controlled trial.
  2. Doecke JD, Laws SM, Faux NG, Wilson W, Burnham SC, Lam CP, Mondal A, Bedo J, Bush AI, Brown B, De Ruyck K, Ellis KA, Fowler C, Gupta VB, Head R, Macaulay SL, Pertile K, Rowe CC, Rembach A, Rodrigues M, Rumble R, Szoeke C, Taddei K, Taddei T, Trounson B, Ames D, Masters CL, Martins RN; for the Alzheimer’s Disease Neuroimaging Initiative and Australian Imaging Biomarker and Lifestyle Research Group. Blood-Based Protein Biomarkers for Diagnosis of Alzheimer Disease.
  3. Simms LA, Doecke JD, Walsh MD, Huang N, Fowler EV, and Radford-Smith GL. Reduced alpha-defensin expression is associated with inflammation and not NOD2 mutation status in ileal Crohn’s disease.
  4. Ferreira RC, Guo H, Coulson RM, Smyth DJ, Pekalski ML, Burren OS, Cutler AJ, Doecke JD, Flint S, McKinney EF, Lyons PA, Smith KG, Achenbach P, Beyerlein A, Dunger DB, Wicker LS, Todd JA, Bonifacio E, Wallace C, Ziegler AG. A type I interferon transcriptional signature precedes autoimmunity in children genetically at-risk of type 1 diabetes.
  5. Ramm GA , Shepherd RW, Hoskins AC, Greco SA, Ney AD, Pereira TN, Bridle KR, Doecke JD, Meikle PJ, Turlin B, Lewindon PJ. Fibrogenesis in Pediatric Cholestatic Liver Disease: Role of Taurocholate and Hepatocyte-Derived Monocyte Chemotaxis Protein-1 in Hepatic Stellate Cell Recruitment.
  6. Cheng L, Doecke JD, Sharples R, Villemagne VL, Fowler CJ, Rembach A, Martins RN, Rowe C, Macaulay SL, Masters CL, Hill AF. Prognostic serum miRNA biomarkers associated with Alzheimer’s disease shows concordance with neuropsychological and neuroimaging assessment.
  7. Fowler EV, Doecke JD, Simms LA, Zhao ZZ, Webb PM, Hayward NK, Whiteman DC, Florin TH, Montgomery GW, Cavanaugh JA, Radford-Smith GL. ATG16L1 T300A Shows Strong Associations With Disease Subgroups in a Large Australian IBD Population: Further Support for Significant Disease Heterogeneity.
  8. Doecke JD, Zhao ZZ, Pandeya N, Sadeghi S, Stark M, Green AC, Hayward NK, Webb PM, Whiteman DC. Polymorphisms in MGMT and DNA repair genes and the risk of esophageal adenocarcinoma.
  9. Squitti R, Simonelli I, Ventriglia M, Siotto M, Pasqualetti P, Doecke JD, Rembach A, Bush AI. Meta-analysis of serum Non-ceruloplasmin copper in Alzheimer’s disease.
  10. Herath NI, Doecke JD, Spanevello MD, Leggett BA, Boyd AW. Epigenetic silencing of EphA1 expression in colorectal cancer is correlated with poor survival.
  11. Burnham SC, Faux NG, Wilson W, Laws SM, Ames D, Bedo J, Bush AI, Doecke JD, Ellis KA, Head R, Jones G, Kiiveri H, Martins RN, Rembach A, Rowe CC, Salvado O, Macaulay SL, Masters CL, Villemagne VL; Alzheimer’s Disease Neuroimaging Initiative; Australian Imaging, Biomarkers and Lifestyle Study Research Group. A blood-based predictor for neocortical Aβ burden in Alzheimer’s disease: results from the AIBL study.
  12. Croft A, Walsh A, Doecke JD, Cooley R, Howlett M, Radford-Smith G. Outcomes of salvage therapy for steroid-refractory acute severe ulcerative colitis: ciclosporin vs. infliximab.
  13. Doecke JD, Day CJ, Stephens ASJ, Carter SL, van Daal A, Kotowicz MA, Nicholson GC, Morrison NA. Outcomes of salvage therapy for steroid-refractory acute severe ulcerative colitis: ciclosporin vs. infliximab.
  14. Simms, L.A, Doecke JD, Roberts, R.L, Fowler, E.V, Zhao, Z.Z, McGuckin, M.A, Huang, N, Hayward, N.K, Webb, P.M, Whiteman, D.C, Cavanaugh, J.A, McCallum, R, Florin, T.H.J, Barclay, M.L, Gearry, R.R, Merriman, T.R. KCNN4 gene variant is associated with ileal Crohn’s disease in the Australian and New Zealand Population.
  15. Gray P, Kirby J, Smith MT, Cabot PJ, Williams B, Doecke JD, Cramond T. Pregabalin in severe burn injury pain: A double-blind, randomised placebo-controlled trial.
  16. Hume GE, Fowler EV, Doecke JD, Simms LA, Huang N, Palmieri O, Griffiths LR, Florin THJ, Annese V, Radford-Smith GL. Novel NOD2 haplotype strengthens the association between TLR4 Asp299Gly and Crohn’s disease in an Australian population.
  17. Neale RE, Doecke JD, Pandeya N, Sadhegi S, Green AC, Webb PM, Whiteman DC. Does type 2 diabetes influence the risk of oesophageal adenocarcinoma?
  18. Nakamura A, Kaneko N, Villemagne VL, Kato T, Doecke JD, Doré V, Fowler C, Li QX, Martins R, Rowe C, Tomita T, Matsuzaki K, Ishii K, Ishii K, Arahata Y, Iwamoto S, Ito K, Tanaka K, Masters CL, Yanagisawa K. Does type 2 diabetes influence the risk of oesophageal adenocarcinoma?
  19. Nakamura A, Kaneko N, Villemagne VL, Kato T, Doecke J, Doré V, Fowler C, Li QX, Martins R, Rowe C, Tomita T, Matsuzaki K, Ishii K, Ishii K, Arahata Y, Iwamoto S, Ito K, Tanaka K, Masters CL, Yanagisawa K. Complex expression patterns of Eph receptor tyrosine kinases and their ephrin ligands in colorectal carcinogenesis.
  20. Doecke JD, Zhao ZZ, Stark MS, Green AC, Hayward NK, Montgomery GW, Webb PM, Whiteman DC. Single nucleotide polymorphisms in obesity-related genes and the risk of esophageal cancers.