On Study Leave in Terms 1, 2 & 3 2012-13 - 3rd year students looking into dissertations topics for next year are welcome to email me with questions. I'll answer by email first, but we can also set up a skype or phone call to discuss your questions (I'm currently overseas).

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

Research interests

Current
* Statistical methodology for molecular biological (e.g. microarrays, microscopic images)
* Quality assessment for high-dimensional data
* Assessment and communication of genomic cancer recurrence risk
* Medical decision-making in situations with both intuitive and normative concepts of probability

Past
* Large deviations for random fields
* Ergodic properties of skew products

Read more...

Short biography

* 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
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.)

Posters

W N Yeung, J Thomas and Julia Brettschneider, "Mathematical and intuitive concepts of probability in decisions under uncertainty in the context of cancer", ISI, Dublin, August 2011.

M Rogers, TAF Long, J Brettschneider and A Chippindale, Does intersexual co-evolution drive rapid population divergence? Evidence from population crosses and the Drosophila transcriptome, 11th Meeting of the European Society for the Study of Evolutionary Biology, Uppsala, August 2007, and 1st General Meeting of the Canadian Society for the study of Ecology and Evolution, Toronto, May 2007.

Recently taught courses

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

Advanced Topics in Biostatistics (ST416)
Component 1: Statistical methods for large biological data sets - Module resource page for this component
Module for 4th year and MSc students, Warwick University, Fall term 2011

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

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

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

Introduction to the Practice of Statistics (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

Supervision

Hiren Patel: Master's of science in statistics, Warwick, 2011/12 (completed)

Mitya Moitra: Master's of science in statistics, Warwick, 2011/12 (completed)

Nurgul Batyrbekova: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Catherine Hunter: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Gergana Ivanova: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Solange Moniquette: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Mark Streather: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Shin Yip: Master's thesis in statistics (MMORSE), Warwick, 2011/12 (completed)

Joanna Chan: Master's of science in statistics, Warwick, 2009/10 (completed)

Wendy Nga-ching Yeung: Master's thesis in statistics (MMORSE), Warwick, 2010/11 (completed)

James Thomas: Master's thesis in statistics (MMORSE), Warwick, 2010/11 (completed)

Parit Shah: Master's thesis in statistics (MMORSE), Warwick, 2010/11 (completed)

Magdalena Roszczuk: Master's of science in statistics, Warwick, 2009/10 (completed)

Jing Jin: Master's thesis in epidemiology, Queen's, 2006-2009 (completed)

Tom D Hargreaves: Master's thesis in statistics (MMORSE), Warwick, 2007/08 (completed)

Laura J Bonnett: Master's thesis in statistics (MMORSE), Warwick, 2007/08 (completed)

Shiqin Helen Guan: Master's thesis in statistics, Queen's, 2006/07 (completed)

Peng Wu: Master's thesis in statistics, Queen's, 2006/07 (completed)

Research description

Presently, Dr. Brettschneider's primary research area is the development
of statistical methods for high dimensional biological data. The quest for
understanding of biological processes on the molecular level has become
a central task in current scientific research. Applications are manifold,
including the study of biological processes such as the cell cycle, the
development of organisms or the circadian clock on a molecular level.
Applications in medical research are mainly in the etiology and treatment
of complex genetic diseases.

Novel technologies for the measurement of the biochemical productivity
of genes have lead to a dramatic change in modern laboratories. What
used to be done on a one-by-one basis can now be processed simultaneously
for tens of thousands of genes using microarrays. The resulting data sets are
high-dimensional, correlated and noisy, and the development of suitable
statistical models is still work in progress. Statistical tasks include image
analysis, normalization, quality assessment and control, and selection of
statistically relevant genes or gene sets.

Jointly with Dr. Collin, Dr. Bolstad and Prof. Speed, Dr. Brettschneider has
worked out a framework for statistical quality assessment for microarray
experiments and to the development of several specific quality measures
for the current industrial standard microarray platform. So far, the measures
have been applied to experimental data sets showing very promising results.
Future work should include the study of the statistical properties of these
measures using mathematical approaches and simulations. Furthermore,
they need to be linked to concepts such as reliability coefficients. Their
generalization to other high-dimensional measurement technologies should
also be explored. Dr. Brettschneider has further been working on microarray
data quality for the special case of time series and on spatial biases.

More recently, the new molecular technologies have been used in clinical
practice for cancer prognosis prediction on individual patients. This triggers
new interdisciplinary research questions regarding the educational
background of the medical community and the patients with respect to
genomics, the implications of uncertainty with regard to the data quality for
prognosis on individual patients and the justification of prediction methods
while the molecular basis of the disease etiology is still work in progress.
Dr. Brettschneider has initiated a project with the cognitive psychologist
Dr. Deb Feldman-Stewart and the radiation oncologist Dr. Mike Brundage
about risk communication for new genomic tests in cancer. As a first step,
they have completed survey instrument to elicit the attitudes of oncologists
regarding the use of these new tests.

Dr. Brettschneider has further been working on large deviations for
random fields and on ergodic theory for skew products. A long time ago,
she has done some work on measure-valued diffusions and applications
to quasi linear partial differential equations.

Contact:

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

Tel: +44 (0)24 7657 3904
Fax: +44 (0)24 7652 4532

Email:

Alternative email address to be used if the above doesn't seem to work:

jabrettschneider"at"me.com

Frequently used Warwick links