Mary Allen
Research Associate Professor • Faculty Director, Responsible Conduct of Research Education Programs, CU Boulder • Associate Director of the Crnic Institute Boulder Branch
BioFrontiers Institute
Office: JSCBB A420


Mary Ann Allen engages experimental and computational methods to investigate the function of RNA in propagating disease. Dr. Allen holds a B.A. in biochemistry from Spring Arbor University, an M.S. in cellular and molecular biology from University Wisconsin-Madison, and a Ph.D. in molecular, cellular and developmental biology from the University of Colorado Boulder. During her graduate training, Dr. Allen focused on trans-splicing in C. elegans. She saw the importance of computation in biological research and pursued opportunities in the growing field of bioinformatics. This led her to join Dr. Robin Dowell’s (MCDB) laboratory as a postdoc in 2010. With the Dowell lab, Dr. Allen undertook an ambitious project to investigate gene regulation by p53, a transcription factor and known tumor suppressor. Using Global Run-On deep-sequencing (GRO-seq), Dr. Allen clearly demonstrated p53 is a transcriptional activator. The role of p53 as a transcriptional activator or suppressor was highly contended, and Dr. Allen leveraged computational techniques to answer this longstanding biological question.

While investigating p53, Dr. Allen uncovered a class of novel non-coding RNAs called eRNAs. These small RNAs are correlated with enhancer function, and Dr. Allen is currently investigating how eRNAs are altered in disease. Dr. Allen focuses heavily on Down syndrome, studying transcriptional dysregulation and the role of eRNAs in producing disease phenotypes. She seeks to advance sequencing technology on both experimental and computational scales and has collaborated with Manuel Lladser (APPM) to analyze GRO-seq data. Dr. Allen improved the GRO-seq protocol to make it feasible for human studies and will use this to determine how chromosome duplication affects global transcription in Down syndrome cells. Through bioinformatics, Dr. Allen works to make an impact on human health. Dr. Allen’s dedication to innovative methodology drives her work forward and leads other researchers to discovery as well.

Dr. Allen currently serves as a Research Assistant Professor and the Faculty Director of the Responsible Conduct of Research Education Program. She is dedicated to creating educational tools and ensuring all scientists at the BioFrontiers Institute are trained to conduct research responsibly. Dr. Allen is also devoted to training biologists in bioinformatics and has developed an annual two-week workshop on short read sequencing analysis. Dr. Allen pursues collaborative projects and encourages researchers across BioFrontiers to engage in thoughtful data analysis. As a scientist and mentor, Mary Allen is bringing computational biology to the forefront of the BioFrontiers Institute. Dr. Allen is committed to understanding transcription and improving human health through multidisciplinary investigation.