Faculty – BioRxiv preprint available and/or under review
1. Isabel Sierra, Son C. Nguyen, R. Jordan Barnett, Ashley L. Cook, Han-Seul Ryu, Zachary T. Beethem, Jennifer E. Philips-Cremins, Eric F. Joyce, Montserrat C. Anguera, Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation, BioRxiv 512821 [Preprint]. Available from: https://doi.org/10.1101/2022.10.19.512821, November 2022. *In Revision
2. 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. *In Revision
3. 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. *In Revision
4. Linda Zhou, Chunmin Ge, Thomas Malachowski, Ji Hun Kim, Keerthivasan Raanin Chandradoss, Chuanbin Su, Hao Wu, Alejandro Rojas, Owen Wallace, Katelyn R. Titus, Wanfeng Gong, Jennifer E. Phillips-Cremins*, Spatially coordinated heterochromatinization of autosomal short tandem repeats in fragile X syndrome, BioRxiv 441217 [Preprint]. Available from: https://doi.org/10.1101/2021.04.23.44121, April 2021. *In Revision
5. Adam C. Naj, Ganna Leonenko, Xueqiu Jian, Benjamin Grenier-Boley, ….., Jennifer E. Phillips-Cremins, …. Jean-Charles Lambert, Gerard D. Schellenberg, Genome-Wide Meta-Analysis of Late-Onset Alzheimer’s Disease Using Rare Variant Imputation in 65,602 Subjects Identifies Novel Rare Variant Locus NCK2: The International Genomics of Alzheimer’s Project (IGAP), MedRxiv 21253553 [Preprint]. Available from: doi: https://doi.org/10.1101/2021.03.14.21253553, March 2021. *In Revision
Faculty – published or in-press
2022
6. Anna-Leigh Brown, Oscar G. Wilkins, Matthew J. Keuss, Sarah E. Hill, Matteo Zanovello, …., NYGC ALS Consortium, et al. Michael E. Ward, Pietro Fratta, TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A, Nature, 603: 131-137, 2022. *JEPC is a member of the New York Genome Center (NYGC ALS Consortium)
7. Sara Cappelli, Alida Spalloni, Fabian Feiguinn, Giulia Visani, Ursa Susnjar, Anna-Leigh Brown, …., NYGC ALS Consortium, Marco De Bardi, Giovanna Borsellino, Maria Secrier, Hemali Phatnani, Maurizio Romano, Pietro Fratta, Patrizia Langone, Emanuele Buratti, NOS1AP is a novel molecular target and critical factor in TDP-43 pathology, Brain Communications, 4(5): 2022.*JEPC is a member of the New York Genome Center (NYGC ALS Consortium)
8. Spencer A. Haws, Zoltan Simandi, R. Jordan Barnett, Jennifer E. Phillips-Cremins*, 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome, Cell, 185(15): 2690-2707, 2022.
9. Daniel J. Emerson, Peiyao A. Zhao, Ashley L. Cook, R. Jordan Barnett, Kyle N. Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltan Simandi, Miriam K. Minsk, Katelyn R. Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, Sergey V. Venev, Johan H. Gibcus, Hongbo Yang, Takayo Sasaki, Masato T. Kanemaki, Feng Yue, Job Dekker, Chun-Long Chen, David M. Gilbert, Jennifer E. Phillips-Cremins, Cohesin-mediated loop anchors confine the location of human replication origins, Nature, 606: 812–819, 2022.
10. 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, eLife, 11: e76539, 2022. *Co-corresponding last author
11. Celine Bellenguez, Fahri Kucukali, Iris E. Kleineidam, Sonia Moreno-Grau, Najaf Amin, Adam C. Naj, …., Alzheimer’s Disease Genetics Consortium (ADGC), et al. Alfredo Ramirez, Jean-Charles Lambert, New insights into the genetic etiology of Alzheimer’s disease and related dementias, Nature Genetics, 54: 412-436, 2022.
*JEPC is a member of the Alzheimer’s Disease Genetics Consortium (ADGC)
12. Kiran Girdhar, 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.
13. 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 Ying Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses in mice, Nature Communications, 13(1): 1-19, 2022.
2021
14. 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.
15. 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.
16. 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
17. 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, 52: 1076–1087, 2020.
18. 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
19. 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.
20. 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.
21. 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
22. 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.
23. 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
24. 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)
25. 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.
26. 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.
27. 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
28. 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
29. 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
30. 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
31. Mayuri Rege, Jennifer E. Phillips-Cremins, Dynamic Looping Interactions: Setting the 3D stage for the macrophage, Molecular Cell, 67(6): 901-903, 2017.
32. 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
33. Heidi K. Norton, Jennifer E. Phillips-Cremins, Crossed Wires: 3-D genome misfolding in disease, Journal of Cell Biology, 216(11): 3441-3452, 2017.
34. 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.
35. 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
36. 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.
37. 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
38. 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
39. Jennifer E. Phillips-Cremins, Unraveling architecture of the pluripotent genome, Current Opinion Cell Biology, 28:96-104, 2014.
Postdoctoral
40. 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.
41. Jennifer E. Phillips-Cremins and Victor G. Corces, Chromatin Insulators: Linking genome organization to cellular function, Molecular Cell, 50(4): 461-74, 2013.
42. Jennifer E. Phillips* and Victor G. Corces, CTCF: Master Weaver of the Genome, Cell, 137(7): 1194-1211, 2009. *Corresponding co-author
Doctoral
43. 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.
44. 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.
45. 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.
46. 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.
47. Jennifer E. Phillips, Charles A. Gersbach, Andres J. Garcia, Virus-based gene therapy strategies for bone regeneration, Biomaterials, 28: 211-229, 2007.
48. 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.
49. 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.
50. 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.
51. Charles A. Gersbach, Jennifer E. Phillips, Andres J. Garcia, Gene Therapy for Musculoskeletal Regeneration, Annual Reviews in Biomedical Engineering, 9: 87-119, 2007.
52. 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.
53. 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
54. 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.