Publications

Faculty – BioRxiv preprint available

1. Deborah Y. Kwon, Peng Hu, Ying-Tao Zhao, Jonathan A. Beagan, Jonathan H. Nofziger, Yue Cui, Bing Xu, Daria Zaitseva, Jennifer E. Phillips-Cremins, Julie A. Blendy, Hao Wu, Zhaolan Zhou, Stress-induced epigenetic regulation of transcription in neocortical excitatory neurons drives depression-like behavior, BioRxiv 190280 [Preprint]. Available from: https://doi.org/10.1101/2020.07.06.190280.

Faculty – published or in-press

2020

2. Di Zhang, Thomas G. Gilgenast, Jennifer E. Phillips-Cremins, Ross C. Hardison, Gerd A. Blobel, Alteration of genome folding via contact domain boundary insertion, Nature Genetics, in press, DOI: 10.1038/s41588-020-0680-8, 2020.

3. Lindsey R. Fernandez*, Thomas G. Gilgenast*, and Jennifer E. Phillips-Cremins, 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data, Genome Biology, 21:219, 2020. *Authors contributed equally to this work

4. Jonathan A. Beagan, Elissa D. Pastuzyn, Lindsey R. Fernandez, Michael H. Guo, Kelly Feng, Katelyn R. Titus, Harshini Chandrashekar, Jason D. Shepherd and Jennifer E. Phillips-Cremins, Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression, Nature Neuroscience, 23: 707-717, 2020.

5. Yang Wu, Ting Qi, Huanwei Wang, Futao Zhang, Zhili Zheng, Jennifer E. Phillips-Cremins, Ian J. Deary, Allan F. McRae, Naomi R. Wray, Jian Zeng, Jian Yang, Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data, Nature Communications, 11:2061-2065, 2020.

6. Jonathan A. Beagan, Jennifer E. Phillips-Cremins, On the existence and functionality of topologically associating domains, Invited Review paper, Nature Genetics, 52: 8-16, 2020.

2019

7. Haoyue Zhang, Daniel J. Emerson, Thomas G. Gilgenast, Katelyn R. Titus, Yemin Lan, Peng Huang, Di Zhang, Hongxin Wang, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, Jennifer E. Phillips-Cremins*, Gerd A. Blobel*, Chromatin Structure Dynamics During the Mitosis to G1-Phase Transition, Nature, 576: 158-162, 2019. *Co-corresponding last author.

8. Harvey Huang*, Sunnia T. Chen*, Katelyn R. Titus*, Daniel J. Emerson, Danielle S. Bassett, Jennifer E. Phillips-Cremins, A subset of topologically associating domains fold into mesoscale core-periphery networks. Scientific Reports, 9(1):9526, 2019. *Authors contributed equally to this work

9. Oliver H. Tam, Nikolay V. Rozhkov, Regina Shaw, Duyang Kim, Isabel Hubbard, Samantha Fennessey, Nadia Propp, The NYGC ALS Consortium*, Delphine Fagegaltier, Brent T. Harris, Lyle W. Ostrow, Hemali Phatnani, John Ravits, Josh Dubnau, and Molly Gale Hammell, Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Reports, 29: 1164-1177, 2019. *Jennifer E. Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

10. Ji Hun Kim*, Mayuri Rege*, Jacqueline Valeri, Margaret C. Dunagin, Aryeh Metzger, Katelyn R. Titus, Thomas G. Gilgenast, Wanfeng Gong, Jonathan A. Beagan, Arjun Raj, Jennifer E. Phillips-Cremins, LADL: Light-activated dynamic looping for endogenous gene expression control, Nature Methods, 16(7): 633-639, 2019.

11. Thomas G. Gilgenast and Jennifer E. Phillips-Cremins, Systematic comparison of statistical methods for identifying looping interactions in 5C data. Cell Systems, 8: 197-211, 2019.

12. Anne E. Sizemore, Jennifer E. Phillips-Cremins, Robert Ghrist, Danielle S. Bassett, The importance of the whole: topological data analysis for the network neuroscientist, Network Neuroscience, 0: 1-8, 2019.

2018

13. James H. Sun*, Linda Zhou*, Daniel J. Emerson, Sai A. Phyo, Katelyn R. Titus, Wanfeng Gong, Thomas G. Gilgenast, Jonathan A. Beagan, Beverly L. Davidson, Flora Tassone, Jennifer E. Phillips-Cremins, Disease-associated short tandem repeats co-localize to chromatin domain boundaries, Cell, 175: 1-15, 2018. *Authors contributed equally to this work

14. Ji Hun Kim*, Katelyn R. Titus*, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer 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. *Authors contributed equally to this work

15. Heidi K. Norton*, Daniel J. Emerson*, Jesi Kim, Katelyn R. Titus, Shi Gu, Danielle S. Bassett, Jennifer E. Phillips-Cremins, Detecting the 3D chromatin domain hierarchy with network modularity, Nature Methods, 15(2): 119-122, 2018. *Authors contributed equally to this work

2017

16. Mayuri Rege, Jennifer E. Phillips-Cremins, Dynamic Looping Interactions: Setting the 3D stage for the macrophage, Molecular Cell, 67(6): 901-903, 2017.

17. Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O’Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, Sheng Zhong, 4D Nucleome Network*, The 4D nucleome project, Nature, 549(7671): 219-226, 2017. *Jennifer E. Phillips-Cremins is a member of the 4D Nucleome Network

18. Heidi K. Norton, Jennifer E. Phillips-Cremins, Crossed Wires: 3-D genome misfolding in disease, Journal of Cell Biology, 216(11): 3441-3452, 2017.

19. Jonathan A. Beagan, Michael T. Duong, Katelyn R. Titus, Linda Zhou, Zhendong Cao, Jingjing Ma, Caroline V. Lachanski, Daniel R. Gillis, Jennifer E. Phillips-Cremins, CTCF and YY1 coordinate a 3D genome looping switch during early neurodevelopment, Genome Research, 27:1139-1152, 2017.

20. 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*, Gerd A. Blobel*, The BET protein BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries, Molecular Cell, 66(1): 102-116, 2017. *Co-corresponding last author

2016

21. 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 ReprogrammingCell 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.

22. Jonathan A. Beagan and Jennifer E. Phillips-Cremins, Genome editing throws descriptive 3-D genome folding studies for a loop, WiRes Systems Biology and Medicine, 8: 286-289, 2016.

2015

23. Michael E.G. Sauria, Jennifer .E. Phillips-Cremins, Victor G. Corces, James Taylor, HiFive: a tool suite for easy and efficient HiC and 5C data analysis, Genome Biology, 12:237, 2015.

2014

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

Postdoctoral

25. Jennifer 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.

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

27. Jennifer E. Phillips* and Victor G. Corces, CTCF: Master Weaver of the Genome, Cell, 137(7): 1194-1211, 2009. *Corresponding co-author

Doctoral

28. Jennifer 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.

29. Jennifer 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, 105(34): 12170-12175, 2008.

30. 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.  

31. Jennifer E. Phillips, Robert E. Guldberg, Andres 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. 

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

33. Jennifer 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.

34. Jennifer 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.

35. Rhima M. Coleman, Jennifer E. Phillips, Angela Lin, Barbara D. Boyan, and Robert E. Guldberg, Characterization of a Small Animal Growth Plate Injury Model Using Microcomputed Tomography, Bone, 46(6): 1555-1563, 2010.

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

37. Andres J. Garcia, Robert E. Guldberg, Benjamin A. Byers, Charles A. Gersbach, Jennifer E. Phillips, Genetic Engineering with Runx2/Cbfa1 to Address Cell Sourcing Limitations in Bone Tissue Engineering, IEEE EMB, 22: 65-70, 2003.

38. Robert E. Guldberg, Barbara D. Boyan, Craig L. Duvall, Blaise D. Porter, Jennifer E. Phillips, Analyzing bone, blood, vessels, and biomaterials with microcomputed tomography, IEEE EMB, 22: 77-89, 2003.

Undergraduate

39. 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.