Publications – Cremins Laboratory

Preprint available & 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], November 2022.
**Preprint: https://doi.org/10.1101/2022.10.19.512821
*In revision, Nature Communications

2. 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], April 2021. *Corresponding last author
**Preprint: https://doi.org/10.1101/2021.04.23.44121
*In revision, Cell

3. Adam C. Naj, Ganna Leoneko, Xueqiu Jian, Benjamin Grenier-Boley, Maria C. Dalmasso, Celine Belleguez, Jin Sha, Yi Zhao, Sven J. van der Lee, Rebecca Sims, Vincent Chouraki, Joshua C. Bis, Brian W. Kunkle, Peter Holmans, Yuk Yee Leung, John J. Farrell, Alessandra Chesi, Hung Hsin Chen, Badri Vardarajan, Penelope Benchek, Sandral Barral, Chien Yueh Lee, Pavel Kuksa, Jacob Haut, Edward B. Lee, Mingyao Li, Yuanchao Zhang, Struan Grant, Jennifer E. Phillips-Cremins, Hata Comic, Achilleas Pitsillides, Rui Xia, Kara L. Hamilton Nelson, Amanda Kuzma, Otto Valladares, Brian Fulton-Howard, Josee Dupuis, Will S. Bush, Li-San Wang, Jennifer E. Below, Lindsay A Farrer, Cornelia can Duijn, Richard Mayeux, Jonathan L. Haines, Anita L. DeStefano, Margaret A. Pericak Vance, Alfredo Ramirez, Sudha Seshadri, Philippe Amouyel, Julie Williams, 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], March 2021.
**Preprint: https://doi.org/10.1101/2021.03.14.21253553
*In revision

Faculty Peer-Reviewed & Published

2023

4. Phillip Wulfridge, Qingqing Yan, Nathaniel Rell, John Doherty, Skye Jacobson, Sarah Offley, Sandra Deliard, Kelly Feng, Jennifer E. Phillips-Cremins, Alessandro Gardini, Kavitha Sarma, G-quadraplexes associated with R-loops promote CTCF binding, Molecular Cell, available online August 7, 2023.
Published: https://doi.org/10.1016/j.molcel.2023.07.009

5. Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G Bruneau, Andrew S Belmont, Lacramioara Bintu, Alistair Boettiger, Riccardo Calandrelli, Christine M Disteche, David M Gilbert, Thomas Gregor, Anders S Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina S Leslie, Wenbo Li, Yun Li, Jian Ma, William S Noble, Peter J Park, Jennifer E Phillips-Cremins, Katherine S Pollard, Susanne M Rafelski, Bing Ren, Yijun Ruan, Yaron Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio-De Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong, Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project, Molecular Cell, 83(15):2624-2640.
Published: 10.1016/j.molcel.2023.06.018

6. 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, Cell Genomics, 3: 100356, 2023.
Published: https://doi.org/10.1016/j.xgen.2023.100356
**Preprint: https://doi.org/10.1101/2021.12.24.21268385

7. Daniel S. Park, Son C. Nguyen, Randi Isenhart, Parisha P. Shah, Wonho Kim, R. Jordan Barnett, Aditi Chandra, Jennifer M. 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, Nature, 620: 209-217, 2023.
Published: https://doi.org/10.1038/s41586-023-06340-w
**Preprint: https://doi.org/10.1101/2022.04.08.487672

2022

8. Anna-Leigh Brown, Oscar G. Wilkins, Matthew J. Keuss, Sarah E. Hill, Matteo Zanovello, Weaverly Colleen Lee, Alexander Bampton, Flora C. Y. Lee, Laura Masino, Yue A. Qi, Sam Bryce-Smith, Ariana Gatt, Martina Hallegger, Delphine Fagegaltier, Hemali Phatnani, NYGC ALS Consortium#, Jia Newcombe, Emil K. Gustavsson, Sahba Seddinghi, Joel F. Reyes, Steven L. Coon, Daniel Ramos, Giampietro Schiavo, Elizabeth M.C. Fisher, Towfique Raj, Maria Secrier, Tammaryn Lashley, Jernei Ule, Emanuele Buratti, Jack Humphrey, Michael E. Ward, Pietro Fratta, TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A, Nature, 603: 131-137, 2022.
Published: https://doi.org/10.1038/s41586-022-04436-3
**Preprint: https://doi.org/10.1101/2021.04.02.438170
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

9. 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. *Corresponding last author
Published: 10.1016/j.cell.2022.06.052.

10. 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.
Published: https://doi.org/10.1093/braincomms/fcac242
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

11. 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 origins, Nature, 606: 812-819, 2022. *Corresponding last author
Published: https://doi.org/10.1038/s41586-022-04803-0
**Preprint: https://doi.org/10.1101/2021.01.05.425437

12. 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 authors
Published: https://doi.org/10.7554/eLife.76539
**Preprint: https://doi.org/10.1101/2021.02.24.432639

13. Celine Bellenguez, Fahri Kucukali, Iris E. Kleineidam, Sonia Moreno-Grau, Najaf Amin, Adam C. Naj, …., Alzheimer’s Disease Genetics Consortium (ADGC)#, …, Alfredo Ramirez, Jean-Charles Lambert, New insights into the genetic etiology of Alzheimer’s disease and related dementias, Nature Genetics, 54: 412-436, 2022.
Published: https://doi.org/10.1038/s41588-022-01024-z
**Preprint: https://doi.org/10.1101/2020.10.01.20200659
#Phillips-Cremins is a member of the Alzheimer’s Disease Genetics Consortium (ADGC)

14. Kiran Girdhar, Gabriel Hoffman+, Jaroslav Bendl, Samir Rahman, Pengfei Dong, Will Liao, Mads E. Hauberg, Laura Sloofman, Leanne Brown, Olivia Devillers, Bibi S. Kassim, Jennifer R. Wiseman, Royce Park, Elizabeth Zharovsky, Rivky Jacobov, Elie Flatow, Alexey Kozlenkov, Thomas Gilgenast, Jessica S. Johnson, Lizette Couto, Mette A. Peters, Jennifer E. Phillips-Cremins, Chang-Gyu Hahn, Raquel E. Gur, Carol A. Tamminga, David A. Lewis, Vvahram Haroutunnian, PsychENCODE Consortium, Stella Dracheva, Barbara K. Lipska, Stefano Marenco, Marija Kundakovic, John F. Fullard, Yan Jiang, 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.
Published: https://doi.org/10.1038/s41593-022-01032-6
**Preprint: https://doi.org/10.1101/2021.06.02.446728

15. Ursa Susnjar, Neva Skrabar, Anna-Leigh Brown, Yasmine Abbassi, Anna-Leigh Brown, Hemali Phatnani, NYGC ALS Consortium#, Andrea Cortese, Cristinna Cereda, Enrico Bugiardini, Rosanna Cardani, Giovanni Meola, Michela Ripolone, Maurizio Moggio, Maurizio Romano, Maria Secreier, Pietro Fratta, Emanuele Buratti, Cell environment shapes TDP-43 function with implications in neuronal and muscle disease, Communications Biology, 5(1): 314, 2022.
Published: https://doi.org/10.1038/s42003-022-03253-8
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

16. Deborah Y. Kwon, Bing Xu, Peng Hu, Ying-Tao Zhao, Jonathan A. Beagan, Jonathan H. Nofziger, Yue Cui, 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.
Published: https://doi.org/10.1038/s41467-021-27571-3
**Preprint: https://doi.org/10.1101/2020.07.06.190280

2021

17. Jinhui Ding, Richard A. Hickman, Thor D. Stein, Yevgeniya Abramzon, Sarah Ahmed, Marya S. Sabir, Makayla K. Portley, Arianna Tucci, Kristina Ibanez, …, The NYGenome consortium#, …, Raffaele Ferrari, John E. Landers, Adriano Chio, J. Raphael Gibbs, Clifton L. Dalgard, Bryan J. Traynor, Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis, Neuron, 109(3): 448-460, 2021.
Published: https://doi.org/10.1016/j.neuron.2020.11.005
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

18. Jonathan Li, Ryan G. Lim, Julia A. Kaye, Victoria Dardov, Alyssa N. Coyne, Jie Wu, Pamela Milani, Andrew Chang, Terri G. Thompson, Loren Ornelas, Aaron Frank, Miriam Adam, Maria G. Ganuelos, Malcolm Casele, …, The NYGenome consortium#, …, Steven Finkbeiner, Ernest Fraenkel, Jeffrey D. Rothstein, Dhruv Sareen, Clive N. Svendsen, Leslie M. Thompson, An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients, iScience, 24(11): 103221, 2021.
Published: https://doi.org/10.1016/j.isci.2021.103221
**Preprint: https://doi.org/10.1101/2020.11.01.362269
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

19. 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. *Corresponding last author
Published: 10.1016/j.molcel.2021.02.035

2020

20. Di Zhang, Thomas Gilgenast, Jennifer E. Phillips-Cremins, Ross Hardison, Gerd Blobel, Alteration of genome folding via contact domain boundary insertion, Nature Genetics, 52(10):1076-1087.
Published: https://doi.org/10.1038/s41588-020-0680-8

21. 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. *Corresponding last author
Published: https://doi.org/10.1186/s13059-020-02061-9
**Preprint: https://doi.org/10.1101/501056

22. Jonathan Beagan, Jennifer E. Phillips-Cremins*, On the existence and functionality of topologically associating domains, Nature Genetics,52:8-16, 2020. *Corresponding last author
Published: https://doi.org/10.1038/s41588-019-0561-1

23. Jonathan A. Beagan, Elissa Pastuzyn, Lindsey Fernandez, Michael Guo, Kelly Feng, Harshini Chandrashekar, Jason Shepherd, and Jennifer E. Phillips-Cremins*, 3D genome restructuring across timescales of activity-induced neuronal gene expression, Nature Neuroscience, 23:707-717, 2020. *Corresponding last author
Published: https://doi.org/10.1038/s41593-020-0634-6

24. 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.
Published: https://doi.org/10.1038/s41467-020-15587-0
**Preprint: https://doi.org/10.1101/580993

2019

25. Haoyue Zhuang, Daniel J. Emerson, Thomas G. Gilgenast, Katelyn R. Titus, Yemin Lan, Peng Huang, Di Zhang, Hongxin Wang, Cheryl A. Keller, Belinda Gerardine, Ross C. Hardison, Jennifer E. Phillips-Cremins*, Gerd Blobel*, Chromatin Structure Dynamics During the Mitosis to G1-Phase Transition, Nature, 576:158-162, 2019. *Co-Corresponding last authors
Published: https://doi.org/10.1038/s41586-019-1778-y
**Preprint: https://doi.org/10.1101/604355

26. Harvey Huang, Sunnia Chen, Katelyn R. Titus, Daniel Emerson, Danielle Bassett, Jennifer E. Phillips-Cremins*, A subset of topologically associating domains fold into mesoscale core-periphery networks. Scientific Reports, 9(1):9526, 2019. *Corresponding last author
Published: https://doi.org/10.1038/s41598-019-45457-9

27. 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.
Published: https://doi.org/10.1016/j.celrep.2019.09.066
**Preprint: https://doi.org/10.1101/574509
#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

28. Ji Hun Kim, Mayuri Rege, Jacqueline Valeri, Margaret Dunagin, Aryeh Metzger, Wanfeng Gong, Jonathan Beagan, Arjun Raj, Jennifer E. Phillips-Cremins*, LADL: Light-activated dynamic looping for endogenous gene expression control, Nature Methods, 16(7):633-639, 2019. *Corresponding last author
Published: https://doi.org/10.1038/s41592-019-0436-5
**Preprint: https://doi.org/10.1101/349340

29. Thomas Gilgenast and Jennifer E. Phillips-Cremins*, Systematic comparison of statistical methods for identifying looping interactions in 5C data.Cell Systems, 8:197-211, 2019. *Corresponding last author
Published: https://doi.org/10.1016/j.cels.2019.02.006
**Preprint: https://doi.org/10.1101/201681

30. Anne 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.
Published: 10.1162/netn_a_00073
**Preprint: https://doi.org/10.48550/arXiv.1806.05167

2018

31. 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):224-238, 2018. *Corresponding last author
Published: 10.1016/j.cell.2018.08.005
**Preprint: https://doi.org/10.1101/191213

32. 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. *Corresponding last author
Published: 10.1016/j.ymeth.2018.05.005
**Preprint: https://doi.org/10.1101/244285

33. Heidi K. Norton, Daniel Emerson, Jesi Kim, Shi Guo, Danielle Bassett, Jennifer E. Phillips-Cremins*, Detecting the 3D chromatin domain hierarchy with network modularity, Nature Methods, 15(2):119-122, 2018. *Corresponding last author
Published: https://doi.org/10.1038/nmeth.4560
**Preprint: https://doi.org/10.1101/089011

2017

34. Jonathan A. Beagan, Michael T. Duong, Katelyn R. Titus, Linda Zhou, Zhendong Cao, Jingjing Ma, Caroline Lachanski, Daniel R. Gillis, Jennifer E. Phillips-Cremins*, CTCF and YY1 orchestrate a 3D genome looping switch during early neural lineage commitment, Genome Research, 27:1139-1152, 2017. *Corresponding last author
Published: 10.1101/gr.215160.116

35.Sarah Hsu, Caroline Bartman, Thomas Gilgenast, Arjun Raj, Jennifer E. Phillips-Cremins*, Gerd Blobel*, The BET protein BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries, Molecular Cell, 66(1):102-116, 2017. *Co-corresponding last authors
Published: 10.1016/j.molcel.2017.02.027

36. 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.
Published: https://doi.org/10.1038/nature23884
**Preprint: https://doi.org/10.1101/103499
#Phillips-Cremins is a member of the NIH Common Fund’s 4DN Consortium

37. Heidi K. Norton, Jennifer E. Phillips-Cremins*, Crossed Wires: 3-D genome misfolding in disease, Journal of Cell Biology, 216(11):3441-3452, 2017. *Corresponding last author
Published: 10.1083/jcb.201611001

38. Mayuri Rege, Jennifer E. Phillips-Cremins*, Dynamic Looping Interactions: Setting the 3D stage for the macrophage, Molecular Cell, 67(6): 901-903, 2017. *Corresponding Author
Published: 10.1016/j.molcel.2017.09.011

2016

39. 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. *Corresponding last author
Published: 10.1016/j.stem.2016.04.004

40. Jonathan Beagan and Jennifer E. Phillips-Cremins*, CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop, WiRes Systems Biology and Medicine, 8:286-289, 2016. *Corresponding Author
Published: 10.1002/wsbm.1338

2015

41. M.E. Sauria, Jennifer 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.
Published: 10.1186/s13059-015-0806-y
**Preprint: https://doi.org/10.1101/009951

2014

42. Jennifer E. Phillips-Cremins*, Unraveling architecture of the pluripotent genome, Current Opinion Cell Biology, 28:96-104, 2014. *Corresponding last author
Published: https://doi.org/10.1016/j.ceb.2014.04.006

Postdoctoral Peer-Reviewed & Published

43. Jennifer E. Phillips-Cremins and Victor G. Corces, Chromatin Insulators: Linking genome organization to cellular function, Molecular Cell, 50(4): 461-74, 2013.
Published: https://doi.org/10.1016/j.molcel.2013.04.018

44. 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.
Published: https://doi.org/10.106/j.cell.2013.04.053

45. Jennifer E. Phillips* and Victor G. Corces, CTCF: Master Weaver of the Genome, Cell, 137(7):1194-1211, 2009. *Co-Corresponding last author
Published: 10.1016/j.cell.2009.06.001

Graduate School Peer-Reviewed & Published

46. 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.
Published: 10.1016/j.bone.2010.02.017

47. 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.
Published: 10.1016/j.actbio.2009.07.023

48. 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.
Published: https://doi.org/10.1073/pnas.0801988105

49. 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.
Published: 10.1007/978-1-59745-237-3_20

50. Jennifer E. Phillips, Robert E. Guldberg, Andres J. Garcia, Fibroblasts Genetically Modified to Express Runx2/Cba1 as a Mineralizing Cell Source for Bone Tissue Engineering, Tissue Engineering, 13(8): 2029-2040, 2007.
Published: 10.1089/ten.2006.0041

51. Jennifer E. Phillips, Charles A. Gersbach, Andres J. Garcia, Virus-based gene therapy strategies for bone regeneration, Biomaterials, 28:211-229, 2007.
Published: 10.1016/j.biomaterials.2006.07.032

52. Charles A. Gersbach, Jennifer E. Phillips, Andres J. Garcia, Gene Engineering for Skeletal Regenerative Medicine, Annual Reviews in Biomedical Engineering, 9:87-119, 2007.
Published: 10.1146/annurev.bioeng.9.060906.151949

53. 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.
Published: 10.1016/j.biomaterials.2006.06.019

54. 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.
Published: 10.1242/jcs.02758

55. Andres J. Garcia, Robert E. Guldberg, Benjamin A. Byers, Charles A. Gersbach, Jennifer E. Phillips, Addressing Cell Sourcing Limitations with Gene Therapy, IEEE EMB, 22:65-70, 2003.
Published: 10.1109/memb.2003.1256274

56. 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.
Published: 10.1109/memb.2003.1256276

Undergraduate Peer-Reviewed & Published

57. 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.
Published: https://doi.org/10.1007/s004649900888