Faculty
Jennifer E. Phillips-Cremins, Ph.D.

Associate Professor of Genetics
Department: Genetics
Graduate Group Affiliations
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
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)
Email:
jcremins@seas.upenn.edu
jcremins@seas.upenn.edu
Publications
Education:
B.S. (Chemical Engineering)
Clarkson University, 1999.
Ph.D. (Biomedical Engineering)
Georgia Institute of Technology, 2007.
Permanent linkB.S. (Chemical Engineering)
Clarkson University, 1999.
Ph.D. (Biomedical Engineering)
Georgia Institute of Technology, 2007.
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
Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins JE.: Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer's disease. Nat Commun 16: 1126, Jan 2025.4D Nucleome Consortium; Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F.: An integrated view of the structure and function of the human 4D nucleome. bioRxiv Oct 2024.
Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE.: Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation. Cell Genom 4: 100606, Aug 2024.
Patel R, Pham K, Chandrashekar H, Phillips-Cremins JE.: FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data. bioRxiv Jun 2024.
Su C, Chandradoss KR, Malachowski T, Boya R, Ryu HS, Brennand KJ, Phillips-Cremins JE.: MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing. bioRxiv May 2024.
Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A.: Post-transcriptional splicing can occur in a slow-moving zone around the gene. Elife 12: RP91357, Apr 2024.
Chandrashekar H, Simandi Z, Choi H, Ryu HS, Waldman AJ, Nikish A, Muppidi SS, Gong W, Paquet D, Phillips-Cremins JE.: A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations. bioRxiv Feb 2024.
Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE.: Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. bioRxiv Dec 2023.
Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE.: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Cell 186: 5840-5858, Dec 2023.
Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins J.: Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease. medRxiv Nov 2023.
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