Faculty – BioRxiv preprint available and under review

  1. 4D Nucleome Consortium, Job Dekker, Betul Akgol Oksuz, Yang Zhang, Ye Wang, Miriam K Minsk, Shuzhen Kuang, Liyan Yang, Johan H Gibcus, Nils Krietenstein, Oliver Rando, Jie Xu, Derek H Janssens, Steven Henikoff, Alexander Kukalev, Andrea Willemin, Warren Winick-Ng, Rieke Kempfer, Ana Pombo, Miao Yu, Pradeep Kumar, Liguo Zhang, Andrew S Belmont, Takayo Sasaki, Tom van Schaik, Laura Brueckner, Daan Peric-Hupkes, Bas van Steensel, Ping Wang, Haoxi Chai, Minji Kim, Yijun Ruan, Ran Zhang, Sofia A Quinodoz, Prashant Bhat, Mitchell Guttman, Wenxin Zhao, Shu Chien, Yuan Liu, Sergey V Venev, Dariusz Plewczynski, Ibai Irastorza Azcarate, Dominik Szabo, Christoph J Thieme, Teresa Szczepinska, Mateusz Chilinski, Kaustav Sengupta, Mattia Conte, Andrea Esposito, Alex Abraham, Ruochi Zhang, Yuchuan Wang, Xingzhao Wen, Qiuyang Wu, Yang Yang, Jie Liu, Lorenzo Boninsegna, Asli Yildirim, Yuxiang Zhan, Andrea Maria Chiariello, Simona Bianco, Lindsay Lee, Ming Hu, Yun Li, R Jordan Barnett, Ashley L Cook, Daniel J Emerson, Claire Marchal, Peiyao Zhao, Peter Park, Burak H Alver, Andrew Schroeder, Rahi Navelkar, Clara Bakker, William Ronchetti, Shannon Ehmsen, Alex Veit, Nils Gehlenborg, Ting Wang, Daofeng Li, Xiaotao Wang, Mario Nicodemi, Bing Ren, Sheng Zhong, Jennifer E Phillips-Cremins*, David M Gilbert*, Katherine S Pollard*, Frank Alber*, Jian Ma*, William S Noble*, Feng Yue*, An integrated view of the structure and function of the human 4D nucleome, BioRxiv 613111 [Preprint], September 2024.
    *Co-corresponding last author
    **Preprint: https://doi.org/10.1101/2024.09.17.613111
    ***Under review – received reviews and invitation to revise and resubmit November 2024
  2. Chuanbin Su, Ken Chandradoss, Thomas Malachowski, Ravi Boya, Han-Seul Ryu, Kristen J. Brennand, Jennifer E. Phillips-Cremins*, MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with Sequencing, BioRxiv 591790 [Preprint], April 2024.
    *Corresponding last author
    **Preprint:  https://doi.org/10.1101/2024.04.29.591790
    ***Resubmitted – December 2024
  3. Raphaela Nativio, Y Lan, Greg Donahue, O Shcherbakova, Noah Barnett, Katelyn R Titus, Harshini Chandrashekar, Jennifer E. Phillips-Cremins, Nancy M. Bonini, Shelley L. Berger, The chromatin conformation landscape of Alzheimer’s disease, BioRxiv 588722 [Preprint], April 2024.
    *Corresponding last author
    **Preprint: https://doi.org/10.1101/2024.04.09.588722
    ***Submitted – January 2025
  4. Harshini Chandrashekar, Zoltan Simandi, Heesun Choi, Han-Seul Ryu, Abraham J. Waldman, Alexandria Nikish, Srikar S. Muppidi, Wanfeng Gong, Dominik Paquet, Jennifer E. Phillips-Cremins*, A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer’s disease mutations, BioRxiv 582395 [Preprint], February 2024.
    *Corresponding last author
    **Preprint: https://doi.org/10.1101/2024.02.27.582395
    ***Under review – received reviews and invitation to revise and resubmit June 2024
  5. 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

Faculty – Peer-Review Completed & Published To Date

2025

  1. Rohan Patel, Kenneth Pham, Harshini Chandrashekar, Jennifer E. Phillips-Cremins*, FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data, BioRxiv 599627 [Preprint], June 2024.
    *Corresponding last author
    **Preprint:  https://doi.org/10.1101/2024.06.18.599627
    ***Accepted in Principle, in press, Nature Methods – January 2025
  2. 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
    ***Accepted, in press, Cell Reports – February 2025
  3. Michael H. Guo, Wan-Ping Lee, Badri N. Vardarajan, Gerard D. Schellenberg, Jennifer E. Phillips-Cremins*, Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease, Nature Communications, 16(1): 1126, 2025. PMCID: PMC11775329. PMID: 39875385.
    *Corresponding last author
    Published: 10.1038/s41467-025-56400-0
    **Preprint: https://doi.org/10.1101/2023.11.16.23298623

2024

  1. Katelyn R. Titus, Zoltan Simandi, Harshini Chandrashekar, Jennifer E. Phillips-Cremins, Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation, Cell Genomics, 4(8): 100606, 2024. PMCID: PMC11406193. PMID: 38991604.
    *Corresponding last author
    Published: https://doi.org/10.1016/j.xgen.2024.100606
    **Preprint: https://doi.org/10.1101/2023.12.04.569731
  2. Ahmed Elhussein, Ulugbek Baymuradov, NYGC ALS Consortium#, Noemie Elhadad, Karthik Natarajan, Gamze Gursoy, A framework for sharing of clinical and genetic data for precision medicine applications, Nature Medicine, 30(12): 3578-3589, 2024. PMCID: PMC11645287. PMID: 39227443.
    Published: https://doi.org/20.2038/s41591-024-03239-5
    #Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)
  3. Allison Coté, Aoife O’Farrell, Ian Dardani, Margaret Dunagin, Chris Coté, Yihan Wan, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, Rohan Patel, Kenneth Pham, Edward S. Boyden, Shelley Berger, Jennifer Phillips-Cremins, L. Stirling Churchman, Arjun Raj, Post-transcriptional splicing can occur in a slow-moving zone around the gene, eLife, 12: RP91357, 2023. PMCID: PMC10997330. PMID: 38577979.
    Published: https://doi.org/10.7554/eLife.91357.1
    **Preprint: https://doi.org/10.1101/2020.04.06.028092
  4. Yogindra Raghav, Allison A Dilliott, Tiziana Petrozziello, Spencer E Kim, James D Berry, Merit E Cudkowicz, Khashayar Vakili, NYGC ALS Consortium#, Ernest Fraenkel, Sali MK Farhan, Ghazaleh Sadri‐Vakili, Identification of gene fusions associated with amyotrophic lateral sclerosis, Muscle & Nerve, 69(4): 477-489, 2024. PMID: 38305586.
    Published: https://doi.org/10.1002/mus.28043
    **Preprint: https://doi.org/10.1101/2022.06.04.22275962
    #Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

2023

  1. Thomas Malachowski, Keerthivasan Raanin Chandradoss, Ravi Boya, Linda Zhou, Ashley L. Cook, Chuanbin Su, Kenneth Pham, Spencer A. Haws, Ji Hun Kim, Han-Seul Ryu, Chunmin Ge, Jennifer M. Luppino, Son C. Nguyen, Katelyn R. Titus, Wanfeng Gong, Owen Wallace, Eric F. Joyce, Hao Wu, Luis Alejandro Rojas, Jennifer E. Phillips-Cremins*, Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome, Cell, 186(26): 5840-5858, 2023. PMCID: PMC10794044. PMID: 38134876.
    *Corresponding last author
    Published: https://doi.org/10.1016/j.cell.2023.11.019
    **Preprint: https://doi.org/10.1101/2021.04.23.441217
  2. 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, 83(17): 3064-3079, 2023. PMCID: PMC10529333. PMID: 37552993.
    Published: https://doi.org/10.1016/j.molcel.2023.07.009
  3. 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, Anastassia 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. PMCID: PMC10528254.
    Published: 10.1016/j.molcel.2023.06.018
  4. Eduardo A. Maury, Maxwell A. Sherman, Giulio Genovese, Thomas G. Gilgenast, Tushar Kamath, S. J. Burris, Prashanth Rajarajan, Erin Flaherty, Schahram Akbarian, Andrew Chess, Steven A. McCarroll, Po-Ru Loh, Jennifer E. Phillips-Cremins, Kristen J. Brennand, Evan Z. Macosko, 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 recurrent NRXN1 and ABCB11 disruptions, Cell Genomics, 3(8): 100356, 2023. PMCID: PMC10435376. PMID: 37601975.
    Published: https://doi.org/10.1016/j.xgen.2023.100356
    **Preprint: https://doi.org/10.1101/2021.12.24.21268385
  5. 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, Patrick J. Walsh, Richard J. Abdill, Rachel Yang, Yemin Lan, Sora Yoon, Rebecca Yunker, Masato T. Kanemaki, Golnaz Vahedi, Jennifer E. Phillips-Cremins, Rajan Jain, Eric F. Joyce, High-throughput Oligopaint screen identifies druggable 3D genome regulators, Nature, 620 (7972): 209-217, 2023. PubMed PMID: 37438531. PMID: 37438531.
    Published: https://doi.org/10.1038/s41586-023-06340-w
    **Preprint: https://doi.org/10.1101/2022.04.08.487672

2022

  1. 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, The 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. PMCID: PMC8891020. PMID: 35197628.
    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)
  2. 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. PMCID: PMC10225251. PMID: 35868274. 
    *Corresponding last author
    Published: 10.1016/j.cell.2022.06.052
  3. Sara Cappelli, Alida Spalloni, Fabian Feiguin, Giulia Visani, Ursa Susnjar, Anna-Leigh Brown, The 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. PMCID: PMC9576154. PMID: 36267332.
    Published: https://doi.org/10.1093/braincomms/fcac242
    #Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)
  4. Daniel J. Emerson, Peiyao A. Zhou, 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. Venvev, 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 locations of human replication origins, Nature, 606: 812-819, 2022. PMCID: PMC9217744. PMID: 35676475.
    *Corresponding last author
    Published: https://doi.org/10.1038/s41586-022-04803-0
    **Preprint: https://doi.org/10.1101/2021.01.05.425437
  5. Lesly Calderon, Felix D. Weiss, Jonathan A. Beagan, Marta S. Oliveira, Radina Georgieva, Yi-Fang Wang, Thomas S. 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. PMCID: PMC9106336. PMID: 35471149.
    *Co-corresponding last author
    Published: https://doi.org/10.7554/eLife.76539
    **Preprint: https://doi.org/10.1101/2021.02.24.432639
  6. Céline Bellenguez, Fahri Küçükali, Iris E. Jansen, Luca Kleineidam, Sonia Moreno-Grau, Najaf Amin, Adam C. Naj, Rafael Campos-Martin, Benjamin Grenier-Boley, Victor Andrade, Peter A. Holmans, Anne Boland, Vincent Damotte, Sven J. van der Lee, Marcos R. Costa, Teemu Kuulasmaa, Qiong Yang, Itziar de Rojas, Joshua C. Bis, Amber Yaqub, Ivana Prokic, Julien Chapuis, Shahzad Ahmad, Vilmantas Giedraitis, Dag Aarsland, Pablo Garcia-Gonzalez, Carla Abdelnour, Emilio Alarcón-Martín, Daniel Alcolea, Montserrat Alegret, Ignacio Alvarez, Victoria Álvarez, Nicola J. Armstrong, Anthoula Tsolaki, Carmen Antúnez, Ildebrando Appollonio, Marina Arcaro, Silvana Archetti, Alfonso Arias Pastor, Beatrice Arosio, Lavinia Athanasiu, Henri Bailly, Nerisa Banaj, Miquel Baquero, Sandra Barral, Alexa Beiser, Ana Belén Pastor, Jennifer E. Below, Penelope Benchek, Luisa Benussi, Claudine Berr, Céline Besse, Valentina Bessi, Giuliano Binetti, Alessandra Bizarro, Rafael Blesa, Mercè Boada, Eric Boerwinkle, Barbara Borroni, Silvia Boschi, Paola Bossù, Geir Bråthen, Jan Bressler, … , Alzheimer’s Disease Genetics Consortium (ADGC)#, CHARGE, Lindsay A. Farrer, Bruce M. Psaty, Mohsen Ghanbari, Towfique Raj, Perminder Sachdev, Karen Mather, Frank Jessen, M. Arfan Ikram, Alexandre de Mendonça, Jakub Hort, Magda Tsolaki, Margaret A. Pericak-Vance, Philippe Amouyel, Julie Williams, Ruth Frikke-Schmidt, Jordi Clarimon, Jean-François Deleuze, Giacomina Rossi, Sudha Seshadri, Ole A. Andreassen, Martin Ingelsson, Mikko Hiltunen, Kristel Sleegers, Gerard D. Schellenberg, Cornelia M. van Duijn, Rebecca Sims, Wiesje M. van der Flier, Agustín Ruiz, Alfredo Ramirez & Jean-Charles Lambert, New insights into the genetic etiology of Alzheimer’s disease and related dementias, Nature Genetics, 54: 412-436, 2022. PMCID: PMC9005347. PMID: 35379992.
    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)
  7. 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, Vahram 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. PMCID: PMC8989650. PMID: 35332326.
    Published: https://doi.org/10.1038/s41593-022-01032-6
    **Preprint: https://doi.org/10.1101/2021.06.02.446728
  8. Ursa Susnjar, Neva Skrabar, Anna-Leigh Brown, Yasmine Abbassi, Anna-Leigh Brown, Hemali Phatnani, The NYGC ALS Consortium#, Andrea Cortese, Cristina 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. PMCID: PMC8983780. PMID: 35383280.
    Published: https://doi.org/10.1038/s42003-022-03253-8
    #Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)
  9. Deborah Y. Kwon, Bing Zhu, 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 to chronic stress in mice, Nature Communications, 13(1): 1-19, 2022. PMCID: PMC8748737. PMID: 35013139.
    Published: https://doi.org/10.1038/s41467-021-27571-3
    **Preprint: https://doi.org/10.1101/2020.07.06.190280

2021

  1. Ramita Dewan, Ruth Chia, Jinhui Ding, Richard A. Hickman, Thor D. Stein, Yevgeniya Abramzon, Sarah Ahmed, Marya S. Sabir, Makayla K. Portley, Arianna Tucci, Kristina Ibáñez, F N U Shankaracharya, Pamela Keagle, Giacomina Rossi, Paola Caroppo, Fabrizio Tagliavini, Maria L. Waldo, Per M. Johansson, Christer F. Nilsson, American Genome Center (TAGC), FALS Sequencing Consortium, Genomics England Research Consortium, International ALS/FTD Genomics Consortium (iAFGC), International FTD Genetics Consortium (IFGC), International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium#; PROSPECT Consortium; James B. Rowe, Luisa Benussi, Giuliano Binetti, Roberta Ghidoni, Edwin Jabbari, Coralie Viollet, Jonathan D. Glass, Andrew B. Singleton, Vincenzo Silani, Owen A. Ross, Mina Ryten, Ali Torkamani, Toshiko Tanaka, Luigi Ferrucci, Susan M. Resnick, Stuart Pickering-Brown, Christopher B. Brady, Neil Kowal, John A. Hardy, Vivianna Van Deerlin, Jean Paul Vonsattel, Matthew B. Harms, Huw R. Morris, Raffaele Ferrari, John E. Landers, Adriano Chiò, J. Raphael Gibbs, Clifton L. Dalgard, Sonja W. Scholz, Bryan J. Traynor, Pathogenic Huntingtin repeat expansions in patients with frontotemporal dementia and amyotrophic lateral sclerosis, Neuron, 109(3): 448-460, 2021. PMCID: PMC7864894. PMID: 33242422.
    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)
  2. NeuroLINCS Consortium; Jonathan Li, Ryan G. Lim, Julia A. Kaye, Victoria Dardov, Alyssa N. Coyne, Jie Wu, Pamela Milani, Andrew Cheng, Terri G. Thompson, Loren Ornelas, Aaron Frank, Miriam Adam, Maria G Banuelos, Malcolm Casale, Veerle Cox, Renan Escalante-Chong, J Gavin Daigle, Emilda Gomez, Lindsey Hayes, Ronald Holewenski, Susan Lei, Alex Lenail, Leandro Lima, Berhan Mandefro, Andrea Matlock, Lindsay Panther, Natasha Leanna Patel-Murray, Jacqueline Pham, Divya Ramamoorthy, Karen Sachs, Brandon Shelley, Jennifer Stocksdale, Hannah Trost, Mark Wilhelm, Vidya Venkatraman, Brook T. Wassie, Stacia Wyman, Stephanie Yang, The NYGenome consortium#,, Jennifer E. Van Eyk, Thomas E. Lloyd, 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. PMCID: PMC8554488. PMID: 34746695.
    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)
  3. 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. PMCID: PMC9295612.
    *Corresponding last author
    Published: https://doi.org/10.1016/j.molcel.2021.02.035

2020

  1. Di Zhang, Peng Huang, Malini Sharma, Cheryl A. Keller, Belinda Giardine, Haoyue 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(10):1076-1087. PMCID: PMC7541666. PMID: 32868908.
    Published: https://doi.org/10.1038/s41588-020-0680-8
  2. 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. PMCID: PMC7496221. PMID: 32859248.
    *Corresponding last author
    Published: https://doi.org/10.1186/s13059-020-02061-9
    **Preprint: https://doi.org/10.1101/501056
  3. Jonathan Beagan, Jennifer E. Phillips-Cremins*, On the existence and functionality of topologically associating domains, Nature Genetics,52:8-16, 2020. PMCID: PMC7567612. PMID: 31925403.
    *Corresponding last author
    Published: https://doi.org/10.1038/s41588-019-0561-1
  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. PMCID: PMC7558717. PMID: 32451484.
    *Corresponding last author
    Published: https://doi.org/10.1038/s41593-020-0634-6
  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. PMCID: PMC7188843. PMID: 32345984.
    Published: https://doi.org/10.1038/s41467-020-15587-0
    **Preprint: https://doi.org/10.1101/580993

2019

  1. Haoyue Zhang, 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. PMCID: PMC6895436. PMID: 31776509.
    *Co-Corresponding last author
    Published: https://doi.org/10.1038/s41586-019-1778-y
    **Preprint: https://doi.org/10.1101/604355
  2. 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. PMCID: PMC6606598. PMID: 31266973.
    *Corresponding last author
    Published: https://doi.org/10.1038/s41598-019-45457-9
  3. 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. PMCID: PMC6866666. PMID: 31665631.
    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)
  4. 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. PMCID: PMC6599567. PMID: 31235883.
    *Corresponding last author
    Published: https://doi.org/10.1038/s41592-019-0436-5
    **Preprint: https://doi.org/10.1101/349340
  5. 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. PMCID: PMC6696950. PMID: 30904376.
    *Corresponding last author
    Published: https://doi.org/10.1016/j.cels.2019.02.006
    **Preprint: https://doi.org/10.1101/201681
  6. 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. PMCID: PMC6663305.
    Published: 10.1162/netn_a_00073
    **Preprint: https://doi.org/10.48550/arXiv.1806.05167

2018

  1. 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. PMCID: PMC6175607. PMID: 30173918.
    *Corresponding last author
    Published: 10.1016/j.cell.2018.08.005
    **Preprint: https://doi.org/10.1101/191213
  2. 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. PMCID: PMC5993643. PMID: 29772275.
    *Corresponding last author
    Published: 10.1016/j.ymeth.2018.05.005
    **Preprint: https://doi.org/10.1101/244285
  3. Heidi K. Norton, Daniel J. Emerson, Harvey Huang, Jesi Kim, Katelyn R. Titus, Shi Guo, Danielle S. Bassett, Jennifer E. Phillips-Cremins*, Detecting hierarchical genome folding with network modularity, Nature Methods, 15(2):119-122, 2018. PMCID: PMC6029251. PMID: 29334377.
    *Corresponding last author
    Published: https://doi.org/10.1038/nmeth.4560
    **Preprint: https://doi.org/10.1101/089011

2017

  1. Heidi K. Norton, Jennifer E. Phillips-Cremins*, Crossed Wires: 3-D genome misfolding in disease, Journal of Cell Biology, 216(11):3441-3452, 2017. PMCID: PMC5674879.
    *Corresponding last author
    Published: 10.1083/jcb.201611001
  2. Mayuri Rege, Jennifer E. Phillips-Cremins*, Dynamic Looping Interactions: Setting the 3D stage for the macrophage, Molecular Cell, 67(6): 901-903, 2017. PMCID: PMC7564868.
    *Corresponding Author      
    Published: 10.1016/j.molcel.2017.09.011
  3. 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. PMCID: PMC5617335.
    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
  4. 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. PMCID: PMC5495066. PMID: 28536180.
    *Corresponding last author
    Published: 10.1101/gr.215160.116
  5. 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. PMCID: PMC5393350. PMID: 28388437.
    *Co-corresponding last authors
    Published: 10.1016/j.molcel.2017.02.027

2016

  1. 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. PMCID: PMC4859942. PMID: 27152443.
    *Corresponding last author
    Published: 10.1016/j.stem.2016.04.004
  2. 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. PMCID: PMC7564889. PMID: 27265842.
    *Corresponding Author
    Published: 10.1002/wsbm.1338

2015

  1. 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. PMCID: PMC5410870.
    Published: 10.1186/s13059-015-0806-y
    **Preprint: https://doi.org/10.1101/009951

2014

  1. Jennifer E. Phillips-Cremins*, Unraveling architecture of the pluripotent genome, Current Opinion Cell Biology, 28:96-104, 2014. PMID: 24813689.
    *Corresponding last author
    Published: https://doi.org/10.1016/j.ceb.2014.04.006

Postdoctoral – Peer-Reviewed & Published

  1. Jennifer E. Phillips-Cremins and Victor G. Corces, Chromatin Insulators: Linking genome organization to cellular function, Molecular Cell, 50(4): 461-74, 2013. PMCID: PMC3670141.
    Published: https://doi.org/10.1016/j.molcel.2013.04.018
  2. 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. PMCID: PMC3712340.
    Published: https://doi.org/10.106/j.cell.2013.04.053
  3. Jennifer E. Phillips* and Victor G. Corces, CTCF: Master Weaver of the Genome, Cell, 137(7):1194-1211, 2009. PMCID: PMC3040116. *Co-Corresponding last author
    Published: 10.1016/j.cell.2009.06.001

Graduate School – Peer-Reviewed & Published

  1. 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. PMID: 20176156.
    Published:  10.1016/j.bone.2010.02.017
  2. 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. PMCID: PMC2787851.
    Published:  10.1016/j.actbio.2009.07.023
  3. 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. PMCID: PMC2527884.
    Published:  https://doi.org/10.1073/pnas.0801988105
  4. 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. PubMed PMID: 18679633.
    Published:   10.1007/978-1-59745-237-3_20
  5. 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. PMID: 17516856.
    Published:  10.1089/ten.2006.0041
  6. Jennifer E. Phillips, Charles A. Gersbach, Andres J. Garcia, Virus-based gene therapy strategies for bone regeneration, Biomaterials, 28:211-229, 2007. PMID: 16928397.
    Published:  10.1016/j.biomaterials.2006.07.032
  7. Charles A. Gersbach, Jennifer E. Phillips, Andres J. Garcia, Gene Engineering for Skeletal Regenerative Medicine, Annual Reviews in Biomedical Engineering, 9:87-119, 2007. PMID: 17425467.
    Published: 10.1146/annurev.bioeng.9.060906.151949
  8. 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. PMID: 16857257.
    Published:  10.1016/j.biomaterials.2006.06.019
  9. 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. PMID: 16443755.
    Published:  10.1242/jcs.02758
  10. 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. PMID: 14699938.
    Published: https://doi.org/10.1109/memb.2003.1256274
  11. 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. PMID: 14699940.
    Published: 10.1109/memb.2003.1256276

Undergraduate

  1. 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. PMID: 9869680.
    Published: https://doi.org/10.1007/s004649900888