[Research] [Supervision] [Biography][CVLink opens in a new window][Impact][Software][Publications][Teaching]

Research

My passion lies in interdisciplinary, project-oriented work, collaborating with scientists and engineers from fields such as infrastructure, genomics, biochemistry, microscopy, neuroscience, ecology, public health, and medicine. As a statistical data scientist with a foundation in probability and ergodic theory, I see each data analysis challenge as an opportunity to develop general methods applicable to similar situations.

I am particularly interested in modeling uncertainty in novel high-throughput measurement processes, such as spatially distributed structural monitoring sensors (in bridges or train tracks), genome-scale transcriptomics, and wearable devices. Insights from these technologies can support health monitoring—of both engineered structures and people—and drive scientific discoveries.

Methodologically, my recent research projects have involved spatial statistics, ensemble prediction techniques, extended regression models, signature theory, high-dimensional data quality assessment and normalization, topological data analysis, decision algorithms, and subjective and objective approaches to risk and uncertainty.

I have also been leading I am leading the WIHEA-funded WUSTLink opens in a new window project. We develop an online toolbox facilitating students taking more control of their academic success while simultaneously providing learning-by-applying opportunities for a wide range of skills.

Supervision

I currently have the capacity for PhD supervision and welcome inquiries about research projects. I tend to design projects linked to real-world applications and select methodologies that best fit the challenges defined by the data and the research objectives.

8 of my PhD students have graduated and I am currently (co-)supervising 4. I have also supervised about 60 Master level projects primarily at Warwick (MMORSE, MMathStat, MSc Statistics) and a few in other institutions (Masters in Statistics, Masters in Epidemiology). I have also supervised 7 third-year Data Science projects.

Previously supervised topics have spanned a wide range of domains, including behavioral decision-making under risk and uncertainty (e.g., medical treatment, financial investment, admissions), genomics, image data (e.g., X-ray, microscopy, brain imaging), medical statistics (e.g., cancer screening, survival predictors, trial design), and infrastructure projects (e.g., project data analysis, health monitoring of engineered structures).

Short biography

I am a Reader at the Department of Statistics at the University of Warwick where I previously worked as an Associate (2010-2021) and Assistant Professor (2007-2010). I am an Alumna Fellow of the Alan Turing InstituteLink opens in a new window, the UK's National Institute for Data Science and AI. I am in the core team of the Health SpotlightLink opens in a new window, one of six recently launched Interdisciplinary Research Initiatives,Link opens in a new window and I lead the Health & Technology team. I am a Senior Fellow of the Higher Education Academy (SFHEA) and a Fellow of the Warwick International Higher Education Academy (WIHEALink opens in a new window).

Previously, I held a joint appointment as an Assistant Professor at the Departments of Math/Stats and of Community Health/Epidemiology & Cancer Research Institute, Queen's University, Canada. I was a visiting Assistant Professor and Research Statistician at the Department of Statistics at the University of California at Berkeley, USA. I held a Postdoctoral Fellowship in Computational Biology at Eurandom at the TU Eindhoven in the Netherlands.

My PhD (2001) was in Mathematics, with a thesis on large deviations in statistical mechanics models, supervised by Prof. H. Föllmer, Humboldt University Berlin, Germany. I got a Master's degree in Mathematics with a thesis about measure-valued diffusions and quasilinear Dirichlet problems supervised by Prof. H. Föllmer and minor qualifications in Computer Sciences and Psychology, at the University of Bonn, Germany.

Impact and wider dissemination

Press release Shift workers 'can't all adjust to night shift': new research relating to our July 2022 eBioMedicine publication: Digital circadian and sleep health in individual hospital shift workers: a cross-sectional telemonitoring studyLink opens in a new window

Brettschneider J
Quality assessment for high-throughput genomic data in research and clinical practice
Impact Case Study for REF2014
Unit of assessment: Mathematical Sciences, Summary impact type: Technological, REF2014Link opens in a new window
Available at REF website

Software

DetectorCheckerWebApp is an interactive WebApp for analysing pixel damage in CT scanners using the associated R-package DetectorChecker. Both have been developed jointly with The Alan Turing Institute and Prof Wilfrid Kendall. The project emerged from our EPSRC inside-out blog. Initial versions of the software were issued on 29.3.2019 and new versions were released on 30.6.2020.

Recent publications and manuscripts

E Knight, H Balzter, TD Breeze, J Brettschneider, RD Girling, A Hagen-Zanker, M Image, CG Johnson, C Lee, A Lovett, S Petrovskiy, A Varah, M Whelan, S Yang, E Gardner
Adapting genetic algorithms for multifunctional landscape decisions: a theoretical case study on wild bees and farmers in the UK
Methods in Ecology and Evolution (2024), issue TBA, early view link

J Brettschneider, G Burro, V Henderson 17(2), pp.302-337.
Make hay while the sun shines: an empirical study of maximum price, regret and trading decisions
Published in Journal of the European Economic Association (2024):jvae028Link opens in a new window, also available at WRAPLink opens in a new window

Y Shen, N Brookes, L Lattuf, J Brettschneider
Data Analytics for Project Delivery: Unlocking the Potential of an Emerging Field
International Journal of Managing Projects in Business (2024), 17(2), pp.302-337Link opens in a new window based on this preprintLink opens in a new window

J Brettschneider, B Morrison, D Jenkinson, K Freeman, J Walton, A Sitch, O Kearins, S Pinder, R Given-Wilson, L Wilkinson, M Wallis, S Cheung, S Taylor-Phillips
Development and Quality Appraisal of a new English Breast Screening linked dataset as part of the Age, test Threshold and frequency of Mammography screening (ATHENA-M) study
British Journal of Radiology, 97, no. 1153 (2024)Link opens in a new window

HF Williamson, J Brettschneider, M Caccamo et al
Data management challenges for artificial intelligence in plant and agricultural research
Link opens in a new windowF1000Research 2023, 10:324Link opens in a new window 

Y Shen, V Locke, J Brettschneider, N Brookes
Using Machine Learning to Predict Construction Project Cost and Duration: A Systematic Literature Review
Submitted

Y Ma, J Brettschneider, JF Collingwood
A systematic review and meta-analysis of cerebrospinal fluid amyloid and tau levels identifies Mild Cognitive Impairment patients progressing to Alzheimer’s Disease
Biomedicines 2022, 10(7), 1713Link opens in a new window

Y Zhang, E Cordina-Duverger, S Komarzynski, A Attari, Q Huang, A Aristizabal, B Faraut, D Léger, R Adam, P Guénel, J Brettschneider, B Finkenstädt, and F Lévi
Digital circadian and sleep health in individual hospital shift workers: a cross sectional telemonitoring study 
eBioMedicine, Vol 81, July 2022Link opens in a new window

J Brettschneider, G Burro, V Henderson
Wide Framing Disposition Effect: an empirical study
Journal of Economic Behaviour and Organisation, Volume 185, May 2021Link opens in a new window, available at WRAPLink opens in a new window

P Guénel, E Cordina-Duverger, B Faraut, J Brettschneider, B Finkenstädt, D Léger, Y Zhang, A Aristizabal, R Adam, F Lévi, and A Attari
RF-103 Determinants of sleep patterns in health care professionals working permanent night shifts or rotating day shifts: a multivariate analysis based on one-week sleep diaries and sensor data 
Occupational and Environmental Medicine 2021;78:A142Link opens in a new window

J Brettschneider, G Burro, V Henderson
Not in my mind: the disposition effect is in the eyes of the beholder
Available at SSRNLink opens in a new window

JA Brettschneider, OT Giles, WS Kendall, T Lazauskas
DetectorChecker: analyzing patterns of defects in detector screens
Journal of Open Source Software, 2020, 5(56), 2474Link opens in a new window

F Lévi, S Komarzynski, Q Huang, T Young, Y Ang, C Fuller, M Bolborea, J Brettschneider, B Finkenstädt, J Fursse, DP White, and PF Innominato
Actionable determinants of circadian and sleep disruption identified from tele-monitoring of cancer patients during daily life
Cancers, 2020, 12(7), 1938Link opens in a new window

M Christodoulou, J Brettschneider, D Steinsaltz
Erosion of representativeness in a cohort study
Available at MedArXivLink opens in a new window Link opens in a new window

S Rajan, J Brettschneider, JF Collingwood
Segmentation of the corpus callosum in diffusion tensor images - methodology comparison in a study of healthy ageing and mild cognitive impairment
Journal of Neuroscience Methods (2020):108870Link opens in a new window

M Palma, S Tavakoli, J Brettschneider, T Nichols
Quantifying uncertainty in brainpredicted age using scalar-on-image quantile regression
NeuroImage (2020): 116938Link opens in a new window

JA Brettschneider
Perspectives on decision trees
Manuscript, presented at SPUDM Amsterdam 2019

M McFarlane, JA Brettschneider, A Gelsthorpe, S James, D Snead, K Gopalakrishnan, H Mehenna, J Jankowski, R Arasaradnam, C Nwokolo
An assessment of candidate genes to assist prognosis in gastric cancer
J Gastrointest Oncol. 2018 Apr; 9(2): 303–310

FM Nixon, TR Honnor, NI Clarke, GP Starling, AJ Beckett, AM Johansen, JA Brettschneider, IA Prior, SJ Royle
Microtubule organization within mitotic spindles revealed by serial block face scanning EM and image analysis
Journal of Cell Science, April 2017, 15;130(10):1845-1855. doi: 10.1242/jcs.203877Link opens in a new window

JA Brettschneider, M Burgess
Using a frailty model to measure the effect of covariates on the disposition effect
CRiSM Working Paper Series No. 17-05, 2017

S Cheung, JL Hutton, JA Brettschneider
Review of sojourn time calculation models used in breast cancer screening
CRiSM Working Paper Series No. 17-04, 2017

TR Honnor, AM Johansen, JA Brettschneider
A nonparametric test for dependency between estimated local bulk movement patterns
CRiSM Working Paper Series No. 17-03, 2017

JA Brettschneider, JW Warnett, TE Nichols, WS Kendall
Higher level spatial analysis of dead pixels on detectors based on local grid geometry
CRiSM Working Paper Series No. 17-02, 2017

TR Honnor, JA Brettschneider, AM Johansen
Differences in spatial point patterns with applications to subcellular biological structures
CRiSM Working Paper Series No. 17-01, 2017

Kueh A, Warnett JM, Gibbons GJ, Brettschneider J, Nichols TE, Williams MA, & Kendall WS
Modelling the Penumbra in Computed Tomography
Journal of X-ray science and technology, 24 (4), 2016, 583-97 (Gold Access) 

J Brettschneider
Practical uses of quality assessment for high-dimensional gene expression data
in Aston et al (Eds): UK Success Stories in Industrial Mathematics, Chapter 29, Springer, 2016.
Preliminary version

Brettschneider J, Thornby J, Nichols TE and Kendall WS
Spatial analysis of dead pixels
CRiSM Working Paper Series No. 14-24, 2014

Brettschneider J
Decision­ making in adjuvant cancer treatment choices based on complex information, including genomic recurrence risk scores, Abstract, Decision Making Bristol 2014, September 2014

Brettschneider J
On uniform convergence in ergodic theorems for a class of skew product transformations
Discrete and Continuous Dynamical Systems - A, 29 (3), March 2011, 873-891
Download here (Journal website) or from arXiv

Foster CJ, Farmer P, Baetz T, Brettschneider J, Feilotter HE and LeBrun DP
Differential expression of cell cycle regulatory proteins defines distinct classes of follicular lymphoma
Human Pathology, Volume 42, Issue 7, July 2011, 972-982Link opens in a new window

Guan SH, Bonnett L, and Brettschneider J
Using gene subsets in the assessment of microarray data quality for time course experiments
CRISM research paper 09-24, May 2009

Hickey JG, Myers SM, Tian X, Zhu SJ, Shaw JLV, Andrew SD, Richardson DS, Brettschneider J and Mulligan LM
RET-dependent gene expression patterns distinguish RET isoforms but not oncogenic mutants
Genes, Chromosomes and Cancer, 48(5), 429-440, May 2009Link opens in a new window

Brettschneider J, Collin F, Bolstad BM, and Speed TP
Quality assessment for short oligonucleotide arrays (with 5 commentaries and rejoinder)
Technometrics, 50(3): 241-264 (article), 279-283 (rejoinder), Aug 2008Link opens in a new window

Magalhaes T, Feilotter H and Brettschneider J
Comparison of five prominent expression measures and quality assessment and control for affymetrix microarrays
Work in progress

Brettschneider J
Shannon-McMillan type theorems for random fields along curves and lower bounds for surface-order large deviations
Probability Theory and Related Fields, 142 (3), 443-473, Nov 2007Link opens in a new window

Guan SH, Zheng J, and Brettschneider J
Microarray data quality assessment for developmental time series
In: Barber S, Baxter PD, and Mardia KV (eds.)
Systems Biology & Statistical Bioinformatics, LASR Proceedings, Leeds University Press, July 2007 Link opens in a new window

Barrier A, Lemoine A, Boelle PY, Tse C, Brault D, Chiappini F, Brettschneider J, Lacaine F, Houry S, Huguier M, Van der Laan MJ, Speed TP, Debuire B, Flahault A and Dudoit S
Colon cancer prognosis prediction by gene expression profiling
Oncogene, 24(40): 6155-6164, Sep 2005Link opens in a new window

Bolstad BM, Collin F, Brettschneider J, Cope L, Simpson K, Irizarry RA, and Speed TP
Quality assessment of affymetrix genechip data
In Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S (eds.)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer, New York, 2005 Link opens in a new window

Marciano PG, Brettschneider J, Manduchi E, Davis JE, Eastman S, Raghupathi R, Saatman KE, Speed TP, Stoeckert CJ, Jr., Eberwine JH and McIntosh TK
Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury
Journal of Neuroscience, Mar 2004, 24(12): 2866-76Link opens in a new window

Teaching

Introduction to Statistical Modelling (ST117)
Module for first-year MORSE, Mathstat, and Data Science students, Warwick University, Module development and lead in 2023 and 2024 (Term 2)

ST912 Statistical Frontiers, PhD students, 2022, 2019, 2022, 2023 (Term 2)

Games, Decision and Behaviour (ST222)
Module for second-year MORSE, MathStat and Maths students, Warwick University, Module development and lead in 2014, 2015, 2016, 2017 (Term 1)

Advanced Topics in Biostatistics (ST414)
Statistical methods for large data sets
Module for 4th year and MSc students, Warwick University, 2015 (Term 2)

Statistical Laboratory (ST104)
Module for first-year MORSE and MathStat students, Warwick University, Module co-development and lead 2014 (Term 3)

Introduction to the Practice of Statistics (ST952)
Module for MSc students, Warwick University, 2013 (Term 1)

Probability A/B (ST111/ST112)
Module for first Math year students, Warwick University, 2011, 2012 (Tem 2)

Advanced Topics in Biostatistics (ST416)
Statistical methods for large biological data sets
Module for 4th year and MSc students, Warwick University, 2011, 2012 (Term 2)

Probability A (ST111)
Module for first-year Math and MORSE and MathStat students, Warwick University, 2010 (Term 1)

Games and Decisions (ST114)
Module for first-year students, Warwick University, 2008 (Term 1)

Introduction to the Practice of Statistics (ST952) (with Dr Heather Turner)
Module for MSc students, Warwick University, Module co-development and lead Fall term 2007

Some recent presentations

LunchtimeLink opens in a new window

Briefing session 1.11.2022 IM projectsLink opens in a new window

Talk 26.10.2022

(keynote version)

Talk 7.7.2022Link opens in a new window

Talk 13.6.2022Link opens in a new window

Talk 14.2.2022Link opens in a new window

Talk 1.12.2021Link opens in a new window

Talk 3.3.2020 CDT (ST912) Decision theory inspired by applications

Talk at Probabilistic Coupling and Geometry December 2019Link opens in a new window

Talk about Sampling Biases (Newton Institute workshop (UQ) March 8, 2018)

Asru talk

Short Talk slides

opendaytalkslides slides2

PosterJune2017

ResearchSpotlights_pdf

ResearchSpotlights_key

Tue1Link opens in a new window TueLink opens in a new window2Link opens in a new window MonLink opens in a new window

Welcome BioInference Day1Link opens in a new window

Email:

Contact:

Room 1.19, Statistics Department in the Mathematical Sciences Building (MSB), University of Warwick
Coventry, CV4 7AL