Rosemary Braun

About me

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, 85KB).

Trajectory

• Assistant Professor of Biostatistics in the Department of Preventive Medicine and Robert H. Lurie Comprehensive Cancer Center at Northwestern University, 2011-date.
• 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, 1995.

Publications

• 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).

More information

• I can be reached in email via firstname dot lastname at gmail.com.
• Here is a collection of potentially useful biophysics links; and my personal website, of which it is part.