1. Jonathan A. Beagan, Michael T. Duong, Katelyn R. Titus, Linda Zhou, Zhendong Cao, Jingjing Ma, Caroline V. Lachanski, Daniel R. Gillis, and Jennifer E. Phillips-Cremins, YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment, Genome Research, in press, 2017.

2. Sarah C. Hsu, Thomas G. Gilgenast, Caroline R. Bartman, Christopher R. Edwards, Aaron J. Stonestrom, Peng Huang, Daniel J. Emerson, Perry Evans, Michael T. Werner, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, Arjun Raj, Jennifer E. Phillips-Cremins, and Gerd A. Blobel, The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries, Molecular Cell, 66:102–116.e7, 2017.

3. Jonathan A. Beagan, Thomas G. Gilgenast, Jesi Kim, Zachary Plona, Heidi K. Norton, Gui Hu, Sarah C. Hsu, Emily J. Shields, Xiaowen Lyu, Effie Apostolou, Konrad Hochedlinger, Victor G. Corces, Job Dekker, and Jennifer E. Phillips-Cremins, Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming, Cell Stem Cell, 18:611-624, 2016.

  • **Highlighted in Kevin Andrew Uy Gonzales and Huck-Hui Ng, Looping around Reprogramming: The Topological Memory of Induced Pluripotency, Cell Stem Cell, 18:557-558, 2016.

4. 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.

5. Jennifer 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.

6. 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.

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

8. J.E. Phillips-Cremins, Michael E. Sauria, Amartya Sanyal, Tatiana Gerasimova, Bryan Lajoie, Joshua Bell, Chintong Ong, Tracy Hookway, Changying Guo, Yuhua Sun, Michael Bland, William Wagstaff, Stephen Dalton, Todd McDevitt, Ranjan Sen, Job Dekker, James Taylor, and Victor G. Corces, Architectural protein subclasses shape 3-D organization of genomes during lineage commitment, Cell, 153(6): 1281-1295, 2013.

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

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

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

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

12. J.E. Phillips, Kellie Burns, Joseph M. Le Doux, Robert E. Guldberg, Andres J. Garcia, Engineering Graded Tissue Interfaces, Proceedings of the National Academy of Sciences USA, 105(34): 12170-12175, 2008.

13. Jennifer E. Phillips and Andres 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.

14. J.E. Phillips, Robert E. Guldberg, Andres 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.

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

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

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

18. 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.

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

20. 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.

21. 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.

22. 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.