I am a statistician with an interest in bioinformatics. In particular, I am interested in the analysis and interpretation of microarray data. DNA Microarrays (or gene chips) exist for many organisms - animals, plants, and humans. They are used to measure the extent to which many genes (humans have about 30,000 protein coding genes) are “turned on” at any given time. Researchers are interested in measuring gene expression to study which genes are associated with a particular condition such as cancer.
Genes are influenced by many things: external factors that an organism is subjected to (e.g., drought for plants or disease for humans) but genes and proteins also influence each other in a complicated network. Is it possible to identify genes that are up or down regulated by other genes or by proteins in time course microarray data? This question is investigated using a state space model for gene regulation in my thesis [pdf].
- Harsh Bhatia, Attila G. Gyulassy, Valerio Pascucci, Martina Bremer, Mitchell T. Ong, Vincenzo Lordi, Erik W. Draeger, John E. Pask, and Peer-Timo Bremer. Interactive Exploration of Atomic Trajectories Through Relative-Angle Distribution and Associated Uncertainties [pdf]. In Proceedings of the 9th IEEE Pacific Visualization Symposium, pp. 120–127, Taipei, Taiwan. Apr. 19–22, 2016.
- M. Bremer, R.W. Doerge, Using R at the Bench - Step-by-Step Data Analytics for Biologists, Cold Spring Harbor Press, 2015.
- T. Nguyen, D. Ravindra, B. Kwong, S. Waheed, N. Tarlton, R. Ferguson, M. Bremer, T. Abramson, Differential expression of alpha 4 integrins on effector memory cells during Bordetella infections. Delayed responses in B. pertussis. PLOS One, December 2012, Vol 7, Issue 12.
- S. Yadegarnynia, A. Pham, A. Ng, D. Nguyen, T. Lialiutska, A. Bortolazzo, V. Syvriuk, M. Bremer, J.B. White, Profiling Flavonoid Cytotoxicity in Human Breast Cancer Cell Lines: Determination of Structure-Function Relationships. Natural Product Communications, 7 (10), 2012.
- N.J. Tarlton, C.M. Green, N.H. Lazarus, L. Rott, A.P. Wong, O.N. Abramson, M. Bremer, E.C. Butcher, T. Abramson, Plasmablast frequency and trafficking receptor expression are altered in pediatric ulcerative colitis. Inflammatory Bowel Diseases, April 5, 2012.
- J. Park, P.L. Knezevich, W. Wung, S.N. O’Hanlon, A. Goyal, K.L. Benedetti, B.J. Barsi-Rhyne, M. Raman, N. Mock, M. Bremer, M.K. VanHoeven, A conserved juxtacrine signal regulates synaptic partner recognition in Caenorhabditis elegans, Neural Development, 6:28, 2011.
- A.Madlung, M. Bremer, E. Himelblau, A. Tullis, A Study Assessing the Potential of Negative Effects in Interdisciplinary Math-Biology Education, CBE - Life Sciences Education, Vol 10, 43 - 54, Spring 2011.
- M. Bremer & R.W. Doerge, Statistics at the Bench: A Step-by-Step Handbook for Biologists, Cold Spring Harbor Press, 2010
- M. Bremer, E. Himelblau, A. Madlung, Introduction to the Statistical Analysis of Two-Color Microarray Data (book chapter) in Bang, H, Zhou, XK, Van Epps, H, Mazumdar, M. (Editors) Statistical Methods in Molecular Biology. Humana Press. 2010.
- M. Bremer & R.W. Doerge, The KM-Algorithm identifies regulated genes in time series expression data, Advances in Bioinformatics, 2009