DEPARTMENT OF PHYSICS AND ASTRONOMY

Living systems are governed by a complex network of molecular interactions involving hundreds of thousands of interacting elements. These systems are finely tuned to produce precise biological effects, robust enough to tolerate intrinsic and extrinsic variability, and flexible enough to adapt to environmental changes.

The Braun Lab develops and applies powerful mathematical and computational techniques to investigate living systems at multiple scales — from the atomic level, to the gene level, to the systems level, to the tissue/organismal level, and finally to the population level — and apply these methods in close collaboration with experimentalists and clinicians to address pressing biomedical questions, from circadian disruption to cancer. Working at the intersection between mathematics, computation, and biology, we advance our understanding of how macroscopic phenotypes emerge from the complex interplay of microscopic interactions.

Selected Publications

• Elan Ness-Cohn*, Marta Iwanaszko*, William L Kath, Ravi Allada, Rosemary Braun. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Times-Series Data in Circadian Biology Research. Journal of Biological Rhythms, 2020.
• 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, Charles Brenner, Clara Bien Peek, Joseph Bass.
• NAD⁺ Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging. Molecular Cell, 78(5):805-807, 2020.
• Sahil D Shah* and Rosemary Braun. GeneSurrounder: network-based identification of disease genes in expression data. BMC Bioinformatics, 20:229, 2019.
• Rosemary Braun, William L Kath, Marta Iwanaszko*, 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.
• Daniela Grimaldi, Nelly A Papalambros, Kathryn J Reid, Sabra M Abbott, Roneil G Malkani, Maged Gendy, Marta Iwanaszko*, Rosemary Braun, Daniel J Sanchez, Ken A Paller, et al. Strengthening sleep-autonomic interaction via acoustic enhancement of slow oscillations. Sleep, 2019.
• Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko*, 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.
• Gary Wilk* and Rosemary Braun. regQTLs: Single nucleotide polymorphisms that modulate microrna regulation of gene expression in tumors. PLoS Genetics, 14(12):e1007837, 2018.
• Phan Nguyen* and Rosemary Braun. Time-lagged ordered lasso for network inference. BMC Bioinformatics, 19(1):545, 2018.

* Indicates Braun Lab Student/Postdoc