Publications

1. J.A. Beagan, J.E. Phillips-Cremins, On the existence and functionality of topologically associating domains, Nature Genetics , Invited Review paper, in press, final decision, October 2019.

2. H. Zhang, D.J. Emerson, T.G. Gilgenast, K.R. Titus, Y. Lan, P. Huang, D. Zhang, H. Wang, C.A. Keller, B. Giardine, R.C. Hardison, J.E. Phillips-Cremins*, and G.A. Blobel*, Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition, Nature, in press, 2019. https://www.biorxiv.org/content/10.1101/604355v1 *co-corresponding last author

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

4. 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. *co-first author

5. 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. *co-first author

6. 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.

7. 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

8. 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. *co-first author

9. 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. *co-first author

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

11. 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. *co-first author

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

13. 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.

14. 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.

15. 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.

16. 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. *co-corresponding last author

17. 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.

18. 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.

19. 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.

20. 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.

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

22. 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.

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

24. 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.

25. 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.

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

27. 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.

28. 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.

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

30. 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.

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

32. 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.

33. 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.

34. 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.

35. 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.

36. 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.