1. T.G. Gilgenast, J.E. Phillips-Cremins, Systematic evaluation of statistical methods for identifying looping interactions  in 5C data, Cell Systems, in press, 2019. BioRxiv preprint here:

2. 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,

3. 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.

4. M. Rege*, JH. Kim*, J. Valeri, M. Dunagin, A. Metzger, W. Gong, J. Beagan, A. Raj, J.E. Phillips-Cremins, LADL: Light-activated dynamic looping for endogenous gene expression control, Biorxiv, 2018.

5. 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.

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

7. 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.

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

9. 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.

10. H.K. Norton, J.E. Phillips-Cremins, Crossed wires: 3D genome misfolding in human disease, The Journal of Cell Biology, 2017.

11. 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.

12. 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.

13. 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.

14. 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, 8:286–299, 2016.

15. 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.

16. 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, 12:237, 2015.

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

18. 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.

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

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

21. 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.

22. 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.

23. 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.

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

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

26. 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.

27. 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.

28. 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.

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. 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.

31. 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.

32. 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.