Publications

Faculty – BioRxiv preprint available

1. Daniel S. Park, Son C. Nguyen, Randi Isenhart, Parisha P. Shah, Wonho Kim, R. Jordan Barnett, Aditi Chandra, JenniferM.Luppino, Jailynn Harke, May Wai, Rachel Yang, Yemin Lan, Sora Yoon, Rebecca Yunker, Golnaz Vahedi, Jennifer E. Phillips-Cremins, Rajan Jain, Eric F. Joyce, High-throughput Oligopaint screen identifies druggable regulators of genome folding, BioRxiv 487672 [Preprint]. Available from:  https://doi.org/10.1101/2022.04.08.487672, April 2022.

2. Eduardo A. Maury, Maxwell A. Sherman, Giulio Genovese, Thomas G. Gilgenast, Prashanth Rajarajan, Erin Flaherty, Schahram Akbarian, Andrew Chess, Steven A. McCarroll, Po-Ru Loh, Jennifer E. Phillips-Cremins, Kristen J. Brennand, James T. R. Walters, Michael O’ Donovan, Patrick Sullivan, Psychiatric Genomic Consortium Schizophrenia and CNV workgroup, Brain Somatic Mosaicism Network, Jonathan Sebat, Eunjung A. Lee, Christopher A. Walsh, Schizophrenia-associated somatic copy number variants from 12,834 cases reveal contribution to risk and recurrent, isoform-specific NRXN1 disruptions, MedRxiv 21268385 [Preprint]. Available from: https://doi.org/10.1101/2021.12.24.21268385, January 2022.

3. Linda Zhou, Chunmin Ge, Thomas Malachowski, Ji Hun Kim, Keerthivasan Raanin Channdradoss, Chuanbin Su, Hao Wu, Alejandro Rojas, Owen Wallace, Katelyn R. Titus, Wanfeng Gong, Jennifer E. Phillips-Cremins, Spatially coordinated heterochromatinization of distal short tandom repeats in fragile X syndrome, BioRxiv 441217 [Preprint]. Available from: https://doi.org/10.1101/2021.04.23.44121, April 2021.

4. Genome-Wide Meta-Analysis of Late-Onset Alzheimer’s Disease Using Rare Variant Imputation in 65,602 Subjects Identifies Novel Rare Variant Locu NCK2: The International Genomics of Alzheimer’s Project (IGAP), Adam C. Naj, Ganna Leonenko, Xueqiu Jian, Benjamin Grenier-Boley, ….., Jennifer E. Phillips-Cremins, …. Jean-Charles Lambert, Gerard D. Schellenberg, MedRxiv 21253553 [Preprint]. Available from: https://doi.org/10.1101/2021.03.14.21253553, March 2021.

Faculty – published or in-press

2022

5. Daniel J. Emerson, Peiyao Zhou, Ashley Cook, Kyle Klein, Chunmin Ge, Linda Zhou, Takayo Sasaki, Liyan Yang, Sergey V. Venvev, Johan H. Gibcus, Job Dekker, David M. Gilbert, Jennifer E. Phillips-Cremins, Cohesin-mediated loop anchors confine the location of human replication origins, Nature, in press, April 2022. Available from: https://doi.org/10.1101/2021.01.05.425437BioRxiv 425437 [Preprint].

6. Lesly Calderon, Felix D Weiss, Jonathan A Beagan, Marta S Oliveira, Yi-Fang Wang, Thomas Carroll, Gopuraja Dharmalingam, Wanfeng Gong, Kyoko Tossell, Vincenzo de Paola, Chad Whilding, Mark A Ungless, Amanda G Fisher, Jennifer E. Phillips-Cremins*, Matthias Merkenschlager*, Cohesin-dependence of neuronal gene expression relates to chromatin loop length, eLifein press, April 2022. Available online at https://elifesciences.org/articles/76539 and from: https://doi.org/10.1101/2021.02.24.432639, BioRxiv 432639 [Preprint]. *Co-corresponding last authors

7. Kiran Girhdar, Gabriel Hoffman+, …, Jennifer E. Phillips-Cremins, …, Panos Roussos, Schahram Akbarian, Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains, Nature Neuroscience, 25: 474-483, 2022.

8. 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, Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses in mice, Nature Communications, 13(1): 1-19, 2022

2021

9. Ramita Dewan, Ruth Chia, Jinhui Ding, …. , The NYGenome consortium, *Jennifer E. Phillips-Cremins is an author within the NYGenome consortium, Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis, Neuron, 109(3): 448-460, 2021.

10.  The NeuroLINCs consortium, The NYGenome consortium, *Jennifer E. Phillips-Cremins is an author within the NYGenome consortium, An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients, iScience, 24(11): 103221, 2021.

11.  Kenneth Pham, Alexandria Nikish, Jennifer E. Phillips-Cremins, (See)quence and ye shall find: Higher-order genome folding in situ, Molecular Cell, 81(6): 1130-1132, 2021.

2020

12. 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.

13. 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

14. 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.

15. 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.

16. 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

17. 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.

18. 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

19. 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)

20. 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.

21. 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.

22. 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

23. 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

24. 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

25. 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

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

27. 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

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

29. 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.

30. 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

31. 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.

32. 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

33. 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

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

Postdoctoral

35. 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.

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

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

Doctoral

38. 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.

39. 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.

40. 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.  

41. 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. 

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

43. 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.

44. 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.

45. 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.

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

47. 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.

48. 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

49. 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.