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CV (December 21, 2020) 1 Braun, Rosemary I Rosemary Braun Curriculum Vitae Education Ph.D. (Physics) University of Illinois, Urbana–Champaign 2004 Dissertation: Molecular Dynamics Studies of Interfacial Effects on Protein Conformation Advisor: Prof. K. Schulten, Physics (Theoretical and Computational Biophysics Group) M.P.H. (Biostatistics) Johns Hopkins–Bloomberg School of Public Health 2006 Thesis: Identifying Differentially Expressed Gene–Pathway Combinations Advisor: Prof. G. Parmigiani, Biostatistics B.Sc. (Physics) Stony Brook University (SUNY Stony Brook) 1996 Honors College Thesis: Binary Pulsar Evolution Advisor: Prof G. E. Brown, Physics (Nuclear Theory Group) Academic Appointments Northwestern University Associate Professor 01/2021—present Molecular BioSciences [primary] Physics & Astronomy [courtesy] Assistant Professor 10/2011—12/2020 Biostatistics, Preventive Medicine [primary] Physics & Astronomy [courtesy] Engineering Sciences & Applied Mathematics [courtesy] Institute and center affiliations: Northwestern Institute on Complex Systems (NICO) R.H. Lurie Comprehensive Cancer Center NSF-Simons Center for Quantitative Biology National Institutes of Health Postdoctoral Fellow, National Cancer Institute 2005–2011 Laboratory of Population Genetics (PI: Ken Buetow) University of Illinois, Urbana-Champaign Postdoctoral Research Associate, Department of Physics 2004–2005 Graduate Research Assistant, Department of Physics 1997–2004 Stony Brook University (SUNY Stony Brook) Undergraduate Research Assistant, Department of Physics 1994–1995 Undergraduate Teaching Assistant, Department of Mathematics 1994–1995 Publications (Chronological) * corresponding author; y Braun lab student/postdoc [1] Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Journal of Computational Physics, 151:190–211, 1999. CV (December 21, 2020) 1 Braun, Rosemary I. [2] Rosemary Braun, Mehmet Sarikaya, and Klaus Schulten. Genetically engineered gold-binding polypeptides: Structure prediction and molecular dynamics. Journal of Biomaterials Science, 13:747–758, 2002. [3] 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. [4] James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781–1802, 2005. [5] 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. [6] Rosemary Braun*, Leslie Cope, and Giovanni Parmigiani. Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics, 9:488, 2008. [7] Ewy A. Mathé, 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. MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clinical Cancer Research, 15:6192–6200, 2009. [8] Rosemary Braun*, William Rowe, Carl Schaefer, Jinghui Zhang, and Kenneth Buetow. Needles in the haystack: Identifying individuals present in pooled genomic data. PLoS Genetics, 5(10):e1000668, 2009. [9] Rosemary Braun* and Kenneth Buetow. Pathways of Distinction Analysis: a new technique for multi-SNP analysis of GWAS data. PLoS Genetics, 7(6):e1002101, 2011. [10] 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. [11] 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 genetic variation and survival in ovarian cancer patients. PLoS One, 8(3):e0055037, 2013. [12] 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. [13] Rosemary Braun*. Systems analysis of high-throughput data. Advances in Experimental Medicine and Biology, 844:153, 2014. [14] Sahil Shahy and Rosemary Braun*. Network methods for pathway analysis of gene expression data. arXiv preprint arXiv:1411.1993, 2014. [15] Michael Kennedy, Rebecca Daugherty, Cecilia Garibay, Camellia Sanford, Jennifer Koerner, Jennifer Lewin, and Rosemary Braun. Science Club: Bridging in-school and out-of-school STEM learning through a collaborative, community-based after-school program. Connected Science Learning, 1(1), 2016. CV (December 21, 2020) 2 Braun, Rosemary I. [16] Sara M Clifton, Rosemary Braun, and Daniel M Abrams. Handicap principle implies emergence of dimorphic ornaments. Proceedings of the Royal Society B: Biological Sciences, 283(1843):20161970, 2016. [17] Nelly A Papalambros, Giovanni Santostasi, Roneil G Malkani, Rosemary Braun, Sandra Weintraub, Ken A Paller, and Phyllis C Zee. Acoustic enhancement of sleep slow oscillations and concomitant memory improvement in older adults. Frontiers in Human Neuroscience, 11:109, 2017. [18] Phan Nguyeny and Rosemary Braun*. Semi-supervised network inference using simulated gene expression dynamics. Bioinformatics, 34(7):1148–1156, 2017. [19] Gary Wilky and Rosemary Braun*. Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer. Nucleic Acids Research, 46(3):1089–1101, 2017. [20] Sara M Clifton, Rosemary Braun, and Daniel M Abrams. Next steps for modelling the evolution of ornamental signals. Animal Behaviour, 2018. [21] NA Papalambros, D Grimaldi, KJ Reid, SM Abbott, RG Malkani, G Santostasi, M Gendy, A Ritger, Rosemary Braun, D Sanchez, et al. Acoustically induced changes in sleep spindle and autonomic activity predict memory consolidation. Sleep, 41(suppl_1):A34–A34, 2018. [22] Patryk Janus, Katarzyna Szołtysek, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Marta Iwanaszkoy, Rosemary Braun, et al. Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes. Cellular Signalling, 46:23–31, 2018. [23] John Wilson IV, Kathryn J Reid, Rosemary Braun, Sabra M Abbott, and Phyllis C Zee. Habitual light exposure relative to circadian timing in delayed sleep-wake phase disorder. Sleep, 41(11):zsy166, 2018. [24] Rosemary Braun*, William L Kath, Marta Iwanaszkoy, Elzbieta Kula-Eversole, Sabra M Abbott, Kathryn J Reid, Phyllis C Zee, and Ravi Allada. Universal method for robust detection of circadian state from gene expression. Proceedings of the National Academy of Sciences, 115(39):E9247–E9256, 2018. [25] Phan Nguyeny and Rosemary Braun*. Time-lagged ordered lasso for network inference. BMC Bioinformatics, 19(1):545, 2018. [26] Gary Wilky and Rosemary Braun*. regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors. PLoS Genetics, 14(12):e1007837, 2018. [27] Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszkoy, Rosemary Braun, Seth J Corey, and Marek Kimmel. Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. PLoS Computational Biology, 15(1):e1006664, 2019. [28] Daniela Grimaldi, Nelly A Papalambros, Kathryn J Reid, Sabra M Abbott, Roneil G Malkani, Maged Gendy, Marta Iwanaszkoy, Rosemary Braun, Daniel J Sanchez, Ken A Paller, et al. Strengthening sleep-autonomic interaction via acoustic enhancement of slow oscillations. Sleep, 2019. [29] Rosemary Braun*, William L Kath, Marta Iwanaszkoy, Elzbieta Kula-Eversole, Sabra M Abbott, Kathryn J Reid, Phyllis C Zee, and Ravi Allada. Reply to Laing et al.: Accurate prediction of circadian time across platforms. Proceedings of the National Academy of Sciences, 116(12):5206–5208, 2019. CV (December 21, 2020) 3 Braun, Rosemary I. [30] Sahil D Shahy and Rosemary Braun*. GeneSurrounder: network-based identification of disease genes in expression data. BMC Bioinformatics, 20:229, 2019. [31] Daniel C Levine, Heekyung Hong, Benjamin J Weidemann, Kathryn M Ramsey, Alison H Affinati, Mark S Schmidt, Jonathan Cedernaes, Chiaki Omura, Rosemary Braun, Choogon Lee, et al. NAD+ controls circadian reprogramming through PER2 nuclear translocation to counter aging. Molecular Cell, 2020. [32] Elan Ness-Cohny, Marta Iwanaszkoy, William L Kath, Ravi Allada, and Rosemary Braun*. TimeTrial: An interactive application for optimizing the design and analysis of transcriptomic times-series data in circadian biology research. J Biol Rhythms, 2020. [33] Daniela Grimaldi, Kathryn J Reid, Nelly A Papalambros, Rosemary Braun, Roneil G Malkani, Sabra M Abbott, Jason C Ong, and Phyllis C Zee. Autonomic dysregulation and sleep homeostasis in insomnia. Sleep, 2020. [34] Matthew B Maas, Marta Iwanaszkoy, Bryan D Lizza, Kathryn J Reid, Rosemary Braun, and Phyllis C Zee. Circadian gene expression rhythms during critical illness. Critical
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