* hopelessly out of date; don't believe a thing.
Content last modified
Tue Sept 3 00:54:13 UTC 2013
I am a physicist with a special interest in computational biophysics and systems biology. In particular, I am interested in computational methods for analyzing high-dimensional genomic data in the context of biological networks, with the goal of revealing the molecular systems that govern the emergence of complex phenotypes (such as cancers).
Here is my CV (PDF, 195KB).
- Assistant Professor of Biostatistics
in the Department
of Preventive Medicine, Northwestern Institute on Complex Systems [NICO] and Robert H. Lurie Comprehensive
Cancer Center at Northwestern
- Postdoc, National Cancer Institute, NIH, 2006-2011. I worked with the Laboratory of Human Carcinogenesis, the Laboratory of Population Genetics and the NCI Center for Biomedical Informatics and Information Technology to develop and apply computational methods for cancer genomics.
- M.P.H., Biostatistics, Johns Hopkins - Bloomberg School of Public Health, 2006.
- Ph.D., Physics, University of Illinois, Urbana Champaign, 2004. My graduate research was conducted in the NIH Resource for Macromolecular Modeling and Bioinformatics under the direction of Klaus Schulten.
- B.S., Physics, Honors College, SUNY Stony Brook, 1996.
- Rosemary Braun. Systems Analysis of High-Throughput Data. In Seth Corey &al., eds, Systems Biology of Blood. Springer-Verlag (in press), 2013.
- Qing-Rong Chen, Rosemary Braun, Ying Hu, Chunhua Yan, Elizabeth M Brunt, Daoud Meerzaman, Arun J Sanyal, and Kenneth Buetow. Multi-SNP analysis of GWAS data identifies pathways associated with nonalcoholic fatty liver disease. PloS One, 8(7):e65982 (2013).
- Rosemary Braun, Richard Finney, Chunhua Yan, Ying Hu, Qing-Rong Chen, Michael Edmonson,
Daoud Meerzaman, and Kenneth Buetow. Discovery Analysis of TCGA Data Reveals Association Between Germline Genotype and Survival in Ovarian Cancer Patients. PLoS One, 8(3):e0055037 (2013).
- Rosemary Braun, Greg Leibon, Scott Pauls, and Daniel Rockmore. Partition Decoupling for Multi-Gene Analysis of Gene Expression Profiling Data. BMC Bioinformatics, 12:497 (2011).
- Rosemary Braun and Ken Buetow. Pathways of Distinction Analysis: A New Technique for Multi-SNP Analysis of GWAS Data.
PLoS Genetics, 7(6):e1002101 (2011).
- Rosemary Braun, William Rowe, Carl Schaefer, Jinghui Zhang, and Ken Buetow. Needles in the Haystack: Identifying Individuals Present in Pooled Genomic Data. PLoS Genetics, 5: e1000668 (2009).
- Ewy A. Mathe, Giang Huong Nguyen, Elise D. Bowman, Yiqiang Zhao, Anuradha Budhu, Aaron J. Schetter, Rosemary Braun, Mark Reimers, Kensuke Kumamoto, Duncan Hughes, Nasser K. Altorki, Alan G. Casson, Chang-Gong Liu, Xin Wei Wang, Nozomu Yanaihara, Nobutoshi Hagiwara, Andrew J. Dannenberg, Masao Miyashita, Carlo M. Croce, and Curtis C. Harris.
MiRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus and associations with survival. Clinical Cancer Research, 15: 6192-6200(2009).
- Rosemary Braun, Leslie Cope, and Giovanni Parmigiani. Identifying Differential Correlation in Gene-Pathway Combinations. BMC Bioinformatics, 9:488 (2008).
- Jordi Cohen, Anton Arkhipov, Rosemary Braun, and Klaus Schulten. Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin. Biophysical Journal, 91:1844-1857 (2006).
- James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802 (2005).
- Rosemary Braun, Donald M. Engelman, and Klaus Schulten. Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices. Biophysical Journal 87, 754-763 (2004).
- Rosemary Braun, Mehmet Sarikaya and Klaus Schulten. Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics. Journal of Biomaterials Science, Polymer Edn. 13, 747-757 (2002).
- Justin R. Gullingsrud, Rosemary Braun, and Klaus Schulten. Reconstrucing Potentials of Mean Force through Time Series Anaylsis of Steered Molecular Dynamics Simulations. Journal of Computational Physics 151 , 190-211 (1999).