[Research] [Supervision] [Biography][Publications] [Teaching]

Research interests

• Statistical methodology for high-dimensional data (e.g. gene expression profiles)
• Quality assessment and improvement for high-dimensional data (e.g. microarrays, X-ray detectors, additive layer manufacturing)
• Spatial modelling (e.g. microscopic images, colocalisation of proteins, dead pixels)
• Modeling decision-making processes involving complex information (cancer recurrence risk, biographic profiles)
• Intuitive versus normative concepts of probability, risk and uncertainty and implications on decision making (e.g. in behaviour finance)

Supervision

I have supervised supervised 31 Master level projects (MMORSE, MMathStat, Masters in Statistics, Masters in Epidemiology) at Warwick and Queen's University and am currently supervising 2 such projects. 3 of my PhD students have graduated in the last two years and I am currently (co-)supervising 5 PhD projects.

Topics include methods for statistical analysis of high-dimensional data from genomics, spatial analysis using image data (e.g. X-ray, microscopy), medical statistics (e.g. cancer screening, predictors for survival, questions related to trial design), perception of randomness and behavioural decision theory (e.g. medical treatment decision, finance, admissions).

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

* UG in Mathematics (with Computer Sciences and Psychology) in Bonn, Germany
* PhD (2001) in Mathematics, Supervisor Prof. H. Föllmer, Humboldt University Berlin, Germany
* Postdoctoral fellow in Computational Biology at Eurandom, Netherlands
* Vis Ass Prof and Research Statistican, Dept of Stats at University of California at Berkeley, US
* Ass Prof, Dept Math/Stats & Dept Community Health/Epidemiology & Cancer Research Institute, Queen's University, Canada
* Ass Prof (2007-2010), Assoc Prof (since 2010), Dept Stats, University of Warwick, UK

Recent publications and manuscripts

JA Brettschneider
Perspectives on decision trees
Manuscript, August 2018

M McFarlane, JA Brettschneider, Adrian 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

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

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.203877

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
Quality assessment for high-throughput genomic data in research and clinical practice, Impact Statement REF2014, Unit of assessment: Mathematical Sciences, Summary impact type: Technological. Download here (REF website)

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, 972-982

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 2009
Abstract and download from here (Wiley)

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 2008
Download from here (ASA)

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 2007
Downlaod from here (Springer) or from arXiv

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, Leeds University Press, July 2007
Download abstract from LASR Proceedings here

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 2005
Abstract and download from here (nature)

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
Description of the book is here (Springer)

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): 2866-76
Abstract and download from here (J. Neurosci.)

Recently taught courses

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 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/B (ST111/ST112)
Module for first year Math students, Warwick University, Winter 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

Topics in Applied Statistics (with Dr David Steinsaltz)
Seminar course for graduate students, Queen's University, Winter term 2007

Statistics for Genomics
Lecture course for forth year students, Queen's University, Fall term 2006

Some recent presentations

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

Asru talk

Short Talk slides

opendaytalkslides slides2

PosterJune2017

ResearchSpotlights_pdf

ResearchSpotlights_key

Email:

Contact:

Rm 1.19, Department of Statistics
Note: We moved to a new building called Mathematical Sciences Building connected to the old one via a Bridge.
University of Warwick
Coventry, CV4 7AL