Jennifer E. Phillips-Cremins, Ph.D.

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Assistant Professor of Bioengineering
Department: Bioengineering

Contact information
Lab: 210 South 33rd Street, 515S Skirkanich Hall

Mail: 210 South 33rd Street, Suite 240 Skirkanich Hall

Office: 304 Hayden Hall

Department of Bioengineering
School of Engineering and Applied Sciences
University of Pennsylvania
Philadelphia, PA 19104-6321
Office: 215-898-4121 (office)
Education:
B.S. (Chemical Engineering)
Clarkson University, 1999.
Ph.D. (Biomedical Engineering)
Georgia Institute of Technology, 2007.
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Description of Research Expertise

The Cremins lab investigates the link between three-dimensional organization of genomes and the establishment and maintenance of cellular function. We employ molecular Chromosome-Conformation-Capture technologies and high-throughput sequencing to create high-resolution 3-D genome architecture maps. We also develop and apply computational tools to (1) create 3-D models of chromatin and (2) integrate 3-D architecture maps with genome-wide maps of epigenetic modifications. Current work is focused on understanding the role for higher-order chromatin organization during differentiation of embryonic stem cells into neurons and during reprogramming of somatic cells into induced pluripotent stem cells. We perturb cellular systems using genetic engineering approaches to discover mechanisms regulating chromatin organizing principles. We also use computational and experimental approaches to investigate the link between 3-D architecture, epigenetic modifications, and expression patterns during normal neural development and in models of neurodegenerative disease. Our long-term goal is to engineer and manipulate chromatin structure to control cellular phenotype for regenerative medicine and neurodegenerative disease treatment applications.

Selected Publications

Jonathan Beagan, Jennifer E. Phillips-Cremins: On the existence and functionality of topologically associating domains. Nature Genetics. Nature Genetics, 52(1): 8-16, January 2020.

Adam Huang, Dan Emerson, Thomas Gilgenast, Kate Titus, Jennifer E. Phillips-Cremins*, Gerd Blobel*, *Co-corresponding last author.: Chromatin Structure Dynamics During the Mitosis to G1-Phase Transition. Nature. Nature Publishing Group, 2019 Notes: In Press.

Yang Wu, Ting Qi, Huanwei Wang, Futao Zhang, Zhili Zheng, Jennifer E. Phillips-Cremins, Ian J Deary, Allan F McRae, Naomi R Wray, Jian Zeng, Jian Yang: Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data. BioRxiv 580993 https://doi.org/10.1101/580993. BioRxiv 580993 2019 Notes: https://doi.org/10.1101/580993.

Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, The NYGC ALS Consortium*, Delphine Fagegaltier, Brent T. Harris, Lyle W. Ostrow, Hemali Phatnani, John Ravits, Josh Dubnau, and Molly Gale Hammell: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Reports. Cell Reports, 29: 1164-1177, 2019 Notes: *I am a member of the New York Genome Center (NYGC ALS Consortium)

Sizemore, A. E., Phillips-Cremins, J. E., Ghrist, R., Bassett, D. S.: The importance of the whole: Topological data analysis for the network neuroscientist. Netw Neurosci 3(3): 656-673, 2019.

Kim, J. H., Rege, M., Valeri, J., Dunagin, M. C., Metzger, A., Titus, K. R., Gilgenast, T. G., Gong, W., Beagan, J. A., Raj, A., Phillips-Cremins, J. E.: LADL: light-activated dynamic looping for endogenous gene expression control. Nat Methods 16(7): 633-639, 2019.

Huang, H., Chen, S. T., Titus, K. R., Emerson, D. J., Bassett, D. S., Phillips-Cremins, J. E.: A subset of topologically associating domains fold into mesoscale core-periphery networks. Sci Rep 9(1): 9526, 2019.

Gilgenast, T. G., Phillips-Cremins, J. E.: Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. Cell Syst 8(3): 197-211 e13, 2019.

Lindsey Fernandez, Thomas Gilgenast and Jennifer E. Phillips-Cremins, : 3DeFDR: Classifying dynamic 3D looping interactions across three cellular states. BioRxiv 2018 Notes: Preprint 501056, https://doi.org/10.1101/501056.

Kim, J. H., Titus, K. R., Gong, W., Beagan, J. A., Cao, Z., Phillips-Cremins, J. E.: 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Methods 142: 39-46, 2018.

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Last updated: 02/20/2020
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