Publications

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

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

3. T.G. Gilgenast, J.E. Phillips-Cremins, Systematic evaluation of statistical methods for identifying looping interactions  in 5C data, Cell Systems, 8(3):197-211, 2019. 

4. L.R. Fernandez, T.G. Gilgenast, J.E. Phillips-Cremins, 3DeFDR: Identifying cell type-specific looping interactions with empirical false discovery rate guided thresholdingBiorxiv, under review, 2019, https://www.biorxiv.org/content/10.1101/501056v1

5. J.H. Sun*, L. Zhou*, D.J. Emerson, S.A. Phyo, K.R. Titus, W. Gong, T.G. Gilgenast, J.A. Beagan, B.L. Davidson, F. Tassone, J.E. Phillips-Cremins, Disease-associated short tandem repeats co-localize to chromatin domain boundaries, Cell, 175(1):224-238, 2018.

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

7. J.E. Phillips-Cremins, The Author File: Jennifer Phillips-Cremins, Nature Methods, 15(2):93, 2018.

8. H.K. Norton*, D.J. Emerson*, H. Huang, J. Kim, K.R. Titus, S. Gu, D.S. Bassett, J.E. Phillips-Cremins, Detecting hierarchical 3-D genome domain reconfiguration with network modularity, Nature Methods, 15(2):119–122, 2018.

9. M. Rege, J.E. Phillips-Cremins, Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage, Molecular Cell, 67(6):901-903, 2017.

10. J. Dekker, A.S. Belmont, M. Guttman, V.O. Leshyk, J.T. Lis, S. Lomvardas, L.A. Mirny, C.C. O’Shea, P.J. Park, B. Ren, J.C.R. Politz, J. Shendure, S. Zhong, 4D Nucleome Network, The 4D nucleome project, Nature, 549(7671):219-226, 2017.

11. H.K. Norton, J.E. Phillips-Cremins, Crossed wires: 3D genome misfolding in human disease, The Journal of Cell Biology, 216(11):3441-3452, 2017.

12. J.A. Beagan, M.T. Duong, K.R. Titus, L. Zhou, Z. Cao, J. Ma, C.V. Lachanski, D.R. Gillis, and J.E. Phillips-Cremins, YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment, Genome Research, 27(7):1139-1152, 2017.

13. S.C. Hsu, T.G. Gilgenast, C.R. Bartman, C.R. Edwards, A.J. Stonestrom, P. Huang, D.J. Emerson, P. Evans, M.T. Werner, C.A. Keller, B. Giardine, R.C. Hardison, A. Raj, J.E. Phillips-Cremins, and G.A. Blobel, The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries, Molecular Cell, 66(1):102–116.e7, 2017.

14. J.E. Phillips-Cremins, The Path to My Lab’s First Paper: Rong Lu, Alvaro Rada-Iglesias, and Jennifer Phillips-Cremins, Cell Stem Cell, 19(6):683-685, 2016.

15. J.A. Beagan and J.E. Phillips-Cremins, CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop, WIREs Systems Biology and Medicine, 8(4):286–299, 2016.

16. J.A. Beagan, T.G. Gilgenast, J. Kim, Z. Plona, H.K. Norton, G. Hu, S.C. Hsu, E.J. Shields, X. Lyu, E. Apostolou, K. Hochedlinger, V.G. Corces, J. Dekker, and J.E. Phillips-Cremins, Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming, Cell Stem Cell, 18(5):611-624, 2016.

  • **Highlighted in K.A. Gonzales and H. Ng, Looping around Reprogramming: The Topological Memory of Induced Pluripotency, Cell Stem Cell, 18:557-558, 2016.

17. M.E. Sauria, J.E. Phillips-Cremins, V.G. Corces, J. Taylor, HiFive: a tool suite for easy and efficient HiC and 5C data analysis, Genome Biology, 16:237, 2015.

18. J.E. Phillips-Cremins, Unraveling architecture of the pluripotent genome, Current Opinion Cell Biology, 28:96-104, 2014.

19. J.E. Phillips-Cremins, M.E. Sauria, A. Sanyal, T. Gerasimova, B. Lajoie, J. Bell, C. Ong, T. Hookway, C. Guo, Y. Sun, M. Bland, W. Wagstaff, S. Dalton, T. McDevitt, R. Sen, J. Dekker, J. Taylor, and V.G. Corces, Architectural protein subclasses shape 3-D organization of genomes during lineage commitment, Cell, 153(6): 1281-1295, 2013.

  • **Highlighted in M.S. Bodner and D.L. Spector, Chromatin Meets its Organizers, Cell, 153(6): 1187-1189, 2013.
  • **Highlighted in T. Sexton and G. Cavalli, The 3D genome shapes up for pluripotency, Cell Stem Cell, 13(1): 3-4, 2013.

20. J.E. Phillips-Cremins and V.G. Corces, Chromatin Insulators: Linking genome organization to cellular function, Molecular Cell, 50(4): 461-74, 2013.

21. R.M. Coleman, J.E. Phillips, A. Lin, B.D. Boyan, and R.E. Guldberg, Characterization of a Small Animal Growth Plate Injury Model Using Microcomputed Tomography, Bone, 46(6): 1555-1563, 2010.

22. J.E. Phillips, T. Petrie, F.P. Creighton, A.J. Garcia, Human mesenchymal stem cell differentiation on self-assembled monolayers presenting different surface chemistries, Acta Biomaterialia, 6(1): 12-20, 2010.

23. J.E. Phillips* and V.G. Corces, CTCF: Master Weaver of the Genome, Cell, 137(7): 1194-1211, 2009.

24. J.E. Phillips, K. Burns, J.M. Le Doux, R.E. Guldberg, A.J. Garcia, Engineering Graded Tissue Interfaces, Proceedings of the National Academy of Sciences USA, 105(34): 12170-12175, 2008.

25. Jennifer E. Phillips and A.J. Garcia, Retroviral-mediated gene therapy for the differentiation of primary cells into a mineralizing osteoblastic phenotype, Methods in Molecular Biology, 434: 333-354, 2008.

26. C.A. Gersbach, J.E. Phillips, A.J. Garcia, Gene Therapy for Musculoskeletal Regeneration, Annual Reviews in Biomedical Engineering, 9: 87-119, 2007.

27. J.E. Phillips, R.E. Guldberg, A.J. Garcia, Dermal Fibroblasts Genetically Modified to Express Runx2/Cba1 as a Mineralizing Cell Source for Bone Tissue Engineering, Tissue Engineering, 13(8): 2029-2040, 2007.

28. J.E. Phillips, C.A. Gersbach, A.J. Garcia, Virus-based gene therapy strategies for bone regeneration, Biomaterials, 28: 211-229, 2007.

29. J.E. Phillips, C.A. Gersbach, A.J. Garcia, Glucocorticoid-Induced Osteogenesis is Negatively Regulated by Runx2/Cbfa1 Phosphorylation, Journal of Cell Science, 119: 581-591, 2006.

30. J.E. Phillips, R.E. Guldberg, A.J. Garcia, Mineralization capacity of tissue engineered constructs containing Runx2-expressing fibroblasts is scaffold dependent, Biomaterials, 27: 5535-5545, 2006.

31. Andres J. Garcia, R.E. Guldberg, B.A. Byers, C.A. Gersbach, J.E. Phillips, Genetic Engineering with Runx2/Cbfa1 to Address Cell Sourcing Limitations in Bone Tissue Engineering, IEEE EMB, 22: 65-70, 2003.

32. R.E. Guldberg, B.D. Boyan, C.L. Duvall, B.D. Porter, J.E. Phillips, Analyzing bone, blood, vessels, and biomaterials with microcomputed tomography, IEEE EMB, 22: 77-89, 2003.

33. A.L. Halverson, W.L., Barrett, P. Bahnot, J.E. Phillips, A.R. Iglesias, L.K. Iglesias, L.K. Jacobs, J.M. Sackier, Intraabdominal adhesion formation after pre-peritoneal dissection in the murine model, Surgical Endoscopy, 13: 14-16, 1999.