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

Research

As a statistical data scientist with initial training in probability and ergodic theory, I see every data analysis as an opportunity to derive general methods for a class of similar situations. My passion is in interdisciplinary project oriented work, operating closely with experts from domains including genomics, microscopy, neuroscience, medicine, epidemiology, wearable devices, manufacturing, complex projects monitoring, ecology, and crop management.

I develop methods to asses and optimise data quality, to maximise information and knowledge gained from experiments, and to model joint and individual decision processes from axiomatic/rational as well as subjective/descriptive perspectives. I have a particular interest in explicit modelling of uncertainty in high-throughput scientific measurement processes.

Supervision

4 of my PhD students have graduated and I am currently (co-)supervising 6. I have supervised 38 Master level projects (MMORSE, MMathStat, Masters in Statistics, Masters in Epidemiology) at Warwick and Queen's University and am currently supervising 4 such projects. I have further supervised 3 third year Data Science project and am currently supervising 4.

Topics are about methods for statistical analysis of data from a wide range of domains including genomics (e.g. data quality), image data (e.g. X-ray, microscopy, brain images), medical statistics (e.g. cancer screening, predictors for survival, statistical questions of trial design), music streaming (e.g. Spotify playlists), concepts of probability (e.g. perception of randomness) and decision making (e.g. medical treatment, financial investment, admissions, crop management).

Students with an interest in a suitable topic of their choice, whether included in the list or not, are encouraged to contact me for this to be considered.

Short biography

• Reader (since 2021), Associate Professor (2010-2021), Assistant Professor (2007-2010), Dept of Statistics, University of Warwick, UK
• Assistant Professor, Dept of Math/Stats & Dept of Community Health/Epidemiology & Cancer Research Institute, Queen's University, Canada
• Visiting Assistant Professor and Research Statistician, Dept of Statistics at University of California at Berkeley, USA
• Postdoctoral fellow in Computational Biology at Eurandom, Netherlands
• PhD (2001) in Mathematics, thesis supervisor Prof. H. Föllmer, Humboldt University Berlin, Germany
• Masters in Mathematics (with Computer Sciences and Psychology), thesis supervisor Prof. H. Föllmer, University Bonn, Germany

Impact

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, REF2014
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 as a spin off 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

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
2022, under review

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 2022

H F Williamson, JA Brettschneider, M Caccamo, RP Davey, C Goble, PJ Kersey,... & S Leonelli
Data management challenges for artificial intelligence in plant and agricultural research
F1000Research, 10(324), 324Link 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 2021, Pages 330-347, available at SSRNLink 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
Submitted, 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
Under revision, available at MedArXivLink opens in a new window

J Brettschneider, G Burro, V Henderson
Make hay while the sun shines: an empirical study of maximum price, regret and trading decisions
Submitted, available at SSRNLink 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):108870

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 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

ST912 CDT 9.3.2022

ST912 CDT 16.3.2022Link opens in a new window

Games, Decision and Behaviour (ST222)
Module for second year MORSE, MathStat and Maths students, Warwick University, Fall term 2014, Fall term 2015, Fall term 2016, Fall term 2017

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

Statistical Laboratory (ST104)
Module for first year MORSE and MathStat students, Warwick University, Summer term 2014

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

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

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

Probability A (ST111)
Module for first year Math and MORSE and MathStat students, Warwick University, Winter term 2010

Games and Decisions (ST114)
Module for first year students, Warwick University, Winter term 2008

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

Some recent presentations

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

Test

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Contact:

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