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Dr Julia Brettschneider

Office hours week 10 (term 2): Tuesday 11-12, Wednesday 10-11, 12-13, Friday 10-11.

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

Research interests

* Statistical methodology for genomic data (e.g. gene expression profiles, microscopic images)
* Quality assessment for high-dimensional data (e.g. microarrays, additive layer manufacturing)
* Spatial modelling
* Modeling decision-making processes involving genomic cancer recurrence risk
* Intuitive and normative concepts of probability, risk and uncertainty

Supervision

Topics typically come from applied statistics such as from the areas listed below. 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.

* High-dimensional gene expression data quality assessment and improvement
* Cancer treatment decision making involving complex genomic information
* Subjective perception of risk and randomness
* Behavioral finance
* Colocalisation of proteins in fluorescent confocal microscopy images
* Additive layer manufacturing

PhD projects

Giovanni Burrow (Bridges programme) started in October 2016 on a project jointly supervised with Dr Vicky Henderson about regret theory applied to individual trader data; Ella Kaye (OxWaSP) started in October 2016 on a project jointly supervised with Dr Anastasia Papavasiliou and Dr David Steinsaltz about multi-level methods for complex social data; Sherman Ip (OxWaS) started in October 2016 on a project jointly supervised with Prof Tom Nichols about modelling noise in computed tomography; Matthew Burgess started October 2013 on a project about empirical challenges in behavioural finance; Tom Honnor started in October 2012 on a project jointly supervised with Dr Adam Johanson, about measurement of protein colocalisation tracked by fluorescent confocal microscopy images and videos; Chui Shan Cheung started in January 2012 on a project jointly supervised with Prof Jane Hutton, about statistical aspects of large breast cancer screening data sets.

Master dissertations

Jack Carter (MMORSE 2015/16 in progress), Prajay Avlani (MMORSE 2015/16 in progress), Nikesh Lad (MMathStat 2014/15), Liam Mohan (MMORSE 2013/14), Iain Barrett (MMORSE 2013/14), Emily Smith (MMORSE 2013/14), Tom Suchen Jin (MMORSE 2013/14), Hiren Patel (MSc 2011/12), Mitya Moitra (MSc 2011/12), Nurgul Batyrbekova (MMORSE 2013/14), Catherine Hunter (MMORSE 2011/12), Gergana Ivanova (MMORSE 2011/12), Solange Moniquette (MMORSE 2011/12), Mark Streather (MMORSE 2011/12), Shin Yip (MMORSE 2011/12), Joanna Chan (MSc 2010/11), Wendy Nga-ching Yeung (MMORSE 2010/11), James Thomas (MMORSE 2010/11), Parit Shah (MMORSE 2012/11), Magdalena Roszczuk (MSc 2009/10), Tom D Hargreaves (MMORSE 2007/08), Laura J Bonnett (MMORSE 2007/08)

Supervision in previous institutions

Jing Jin: Master's thesis in epidemiology, Dept of Community Health and Epidemiology at Queen's, 2006-2009; Shiqin Helen Guan: Master's thesis in statistics, Dept of Mathematics and Statistics at Queen's, 2006/07; Peng Wu: Master's thesis in statistics, Dept of Mathematics and Statistics at Queen's, 2006/07

Short biography

* UG in Mathematics (with Computer Sciences and Psychology) in Bonn, Germany
* PhD (2000) in Mathematics, Supervisor Prof. H. Foellmer, 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, United States
* Ass Prof, Dept Math/Stats & Dept Community Health/Epidemiology, Queen's University, Canada
* Ass Prof (2007-2010), Assoc Prof (since 2010), Dept Stats, University of Warwick, United Kingdom

Recent publications and manuscripts

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

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)

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
Download from here (CRISM)

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
Preprint

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)

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

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

Asru talk

Short Talk slides

opendaytalkslides slides2

Dr Julia Brettschneider large

Email:

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Contact:

Rm C1.11, Department of Statistics
Mathematics & Statistics Building
University of Warwick
Coventry, CV4 7AL