Jennifer E. Phillips-Cremins, Ph.D.

Associate Professor Dean's Faculty Fellow in Bioengineering and Genetics

University of Pennsylvania
The School of Engineering and Applied Sciences
Department of Bioengineering
Lab:  515 Skirkanich Hall
Office: 304 Hayden Hall
210 South 33rd Street
Philadelphia, PA 19104

215-898-4121
Website
Lab Website

Research Interest

Epigenomics and Systems Neurobiology Lab: The Cremins Lab investigates the link between three-dimensional organization of genomes and the establishment and maintenance of neural cell function. We employ systems level experimental and computational approaches to (1) create high-resolution 3-D genome architecture maps and (2) integrate 3-D architecture maps with genome-wide maps of epigenetic modifications and gene expression. Current work is focused on understanding the role for higher-order chromatin organization during differentiation of embryonic stem cells into neurons, during reprogramming of neurons into induced pluripotent stem cells and in models of neurodegenerative disease.

Lab Members

FIRST NAME:LAST NAME:TITLE:EMAIL:
JenniferPhillips-CreminsPIjcremins@seas.upenn.edu
MichaelGuoResident (PGY-2), Department of Neurologymduong@sas.upenn.edu
WanfengGongResearch Specialistwanfeng@seas.upenn.edu
HarshiniChandrashekarComputational Scientist Ihchand@seas.upenn.edu
MiriamMinskUndergraduate Studentmminsk@seas.upenn.edu
DanielEmersonComputational Scientist Idemerson368@gmail.com
RaviBoyaPostdoctoral Associatebravi.uohyd@gmail.com
HeesunChoiPostdoctoral Associatehschoi@seas.upenn.edu
KateTitusGraduate Studentkatetitus1@gmail.com
LindaZhouMD/Ph.D. Graduate StudentLinda.Zhou@uphs.upenn.edu
ChuanbinSuPostdoctoral Associatechuanbin@seas.upenn.edu
ChunminGeResearch Specialistcmge@seas.upenn.edu
FranklinBrianRotation Studentbrian.franklin1@pennmedicine.upenn.edu
Keerthivasan RaaninChandradosPostdoc Researcherrckeerthivasan@gmail.com
KennethPhamMD Ph.D. MS1 first yearkenneth.pham@columbia.edu
RohanPatelPh.Drohanpat@seas.upenn.edu
ThomasMalachowskiPh.Dtmalach@seas.upenn.edu
AbrahamWaldmanPh.Dabrahamjwaldman@gmail.com

Publications

  • Neuronal YY1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress. Kwon DY, Xu B#, Hu P#, Zhao Y-T, Beagan JA, Nofziger JH, Cui Y, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z*. Nature Communications 13: 55. doi.org/10.1038/s41467-021-27571-3, 2022.
  • Wu Y, Wang H, Zhang F, Zheng Z, Phillips-Cremins JE, Deary IJ, McRae AF, Wray NR, Zeng J, Yang J. Nat Commun. 2020;11(1):2061. doi: 10.1038/s41467-020-15587-0. PMID: 32345984
  • Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremis JE. Nat Neurosci. 2020;23(6):707-717. doi: 10.1038/s41593-020-0634-6. PMID: 32451484
  • Fernandez LR, Gilgenast TG, Phillips-Cremins JE. Genome Biology. 2020;21(1):219. doi: 10.1186/s13059-020-02061-9. PMID: 32859248
  • Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA. Nat Genet. 2020 Aug 31. doi: 10.1038/s41588-020-0680-8. PMID: 32868908
  • Beagan J, Phillips-Cremins JE. Nat Genet. 2020;52(1):8-16. doi: 10.1038/s41588-019-0561-1. PMID: 31925403
  • Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA. Nature. 2019;576:158-162. doi: 10.1038/s41586-019-1778-y. PMID: 31776509
  • Huang H, Chen ST, Titus KR, Emerson DJ, Bassett DS, Phillips-Cremins JE. Sci Rep. 2019 Jul 2;9(1):9526. doi: 10.1038/s41598-019-45457-9. PMID:31266973
  • LADL: light-activated dynamic looping for endogenous gene expression control. Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE. Nat Methods. 2019 Jul;16(7):633-639. doi: 10.1038/s41592-019-0436-5. Epub 2019 Jun 24. PMID:31235883

  • 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE. Methods. 2018 Jun 1;142:39-46. doi: 10.1016/j.ymeth.2018.05.005. Epub 2018 May 24.

  • Detecting hierarchical genome folding with network modularity. Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE. Nat Methods. 2018 Feb;15(2):119-122. doi: 10.1038/nmeth.4560. Epub 2018 Jan 15. PMID: 29334377
  • Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries. 2017 Sept 20.  James Sun, Linda Zhou, Daniel J Emerson, Thomas G. Gilgenast, Katelyn Titus, Jonathan A. Beagan, Jennifer E. Phillips-Cremins.  DOI: 10.1101/191213
  • YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE.  Genome Res. 2017 Jul;27(7):1139-1152.
  • Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan JA1, Gilgenast TG1, Kim J1, Plona Z1, Norton HK1, Hu G1, Hsu SC2, Shields EJ2, Lyu X3, Apostolou E4, Hochedlinger K4, Corces VG3, Dekker J5, Phillips Cremins JE6. Cell Stem Cell. 2016 May 5; 18(5):611-24. doi: 10.1016/j.stem.2016.04.004