Mapping Memory Through Discovery.

Rohan Patel, Kenneth Pham, Harshini Chandrashekar, Jennifer E. Phillips-Cremins*, FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data, Nature Methods, 22: 1255-1264, 2025. PMCID: PMC12165856. PMID: 40355724. 

*Corresponding last author

Published: https://pubmed.ncbi.nlm.nih.gov/38948824/

**Preprint:  https://doi.org/10.1101/2024.06.18.599627

‍

Bryce-Smith S, Brown AL, Chien MZYJ, Dattilo D, Mehta PR, Mattedi F, Barattucci S, Mikheenko A, Zanovello M, Pellegrini F, El-Agamy SE, Yome M, Kargbo-Hill SE, Qi YA, Sun K, Ryadnov E, Wan Y, NYGC ALS Consortium#, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Wilkins, OG, Ward M, Secrier M, Fratta P, TDP-43 loss induces cryptic polyadenylation in ALS/FTD, Nature Neuroscience, 28(11): 2190-2200, 2025. PMCID: PMC12586162. PMID: 41120751. 

Published: https://doi.org/10.1038/s41593-025-02050-w

**Preprint: https://doi.org/10.1101/2024.01.22.576625

#Phillips-Cremins is a member of the New York Genome Center (NYGC ALS Consortium)

Alekh Paranjapye, Rilli Ahmad, Steven Su, Abraham J. Waldman, Jennifer E. Phillips-Cremins,  Shuo Zhang, Erica Korb, Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons, Genome Research, 35: 2433-2444, 2025. PMCID: PMC12581880. PMID: 41115806. 

Published: doi:10.1101/gr.280698.125

**Preprint:  https://doi.org/10.1101/2025.03.25.645337

‍

Isabel Sierra, Natalie E. Toothacre, Robin H. van der Weide, Claudia D. Lovell, Son C. Nguyen, R. Jordan Barnett, Ashley L. Cook, Han-Seul Ryu, Sarah Pyfrom, Harrison Wang, Daniel Beiting, Jennifer E. Phillips-Cremins, Eric F. Joyce, Montserrat C. Anguera, B cell stimulation changes the structure and higher-order organization of the inactive X chromosome, Cell Reports, 44(3): 115351, 2025. PMCID: PMC11998099. PMID: 40014450.Published: https://doi.org/10.1016/j.celrep.2025.115351
**Preprint: https://doi.org/10.1101/2022.10.19.512821

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

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://pubmed.ncbi.nlm.nih.gov/38106199/

**Preprint: https://doi.org/10.1101/2023.12.04.569731

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

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)

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.E36, 2023. PMCID: PMC10794044. PMID: 38134876.
*Corresponding last author

Published: https://pubmed.ncbi.nlm.nih.gov/38134876/

**Preprint: https://doi.org/10.1101/2021.04.23.441217

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

‍

‍

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

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

‍

‍

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. PMCID: PMC11305015. PMID: 37438531.
Published: https://doi.org/10.1038/s41586-023-06340-w

**Preprint: https://doi.org/10.1101/2022.04.08.487672

‍

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

‍

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)

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

‍

‍

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) 

‍

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

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

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)

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

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) 

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: 10.1016/j.molcel.2021.02.035

‍

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)

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)

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

‍

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

‍

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

‍

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

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, 2020. PMCID: PMC7541666. PMID: 32868908.

Published: https://doi.org/10.1038/s41588-020-0680-8

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

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

‍

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

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)

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

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

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

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

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

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

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

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

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

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

‍

‍

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 AuthorPublished: 10.1002/wsbm.1338

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

‍

‍

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

‍

‍

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.2014.04.00

‍

‍

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

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

‍

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

‍

***Under review

Kenneth Pham, Roy Lee, Isabel Di Rosa, Fangming Jin, Yuki Bradford, Gui-Shuang Ying, JenniferE. Phillips-Cremins, Shefali Setia-Verma, Joan O’Brien, Common tandem repeat variantsassociated with primary open-angle glaucoma risk in individuals of African ancestry, medRxiv 25322489 [Preprint], February 2025. PMCID: PMC11875260. PMID: 40034796.*Preprint:https://doi.org/10.1101/2025.02.19.25322489

***Under review

Kenneth Pham, Thomas Malachowski, Linda Zhou, Ji Hun Kim, Chuanbin Su, Jennifer E Phillips-Cremins, Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity, BioRxiv 644148 [Preprint], March 2025. PMCID: PMC11957133. PMID: 40166285.
*Preprint:  https://doi.org/10.1101/2025.03.19.644148

‍

***Under review

Abraham J. Waldman, Kenneth Pham, Katelyn R. Titus, Alexandria Nikish, Constin Liu, Han-Seul Ryu, Srikar S Muppidi, Keerthivasan Raanin Chandradoss, Peibo Xu, Rohan Patel, Ravi Boya, Jennifer E. Phillips-Cremins*, Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons, BioRxiv 679661 [Preprint], October 2025. *Preprint: https://doi.org/10.1101/2025.09.30.679661

‍

‍

***Under review

Peibo Xu, Keerthivasan Raanin Chandradoss, Bradley Lukasak, Alekh Paranjapye, Abraham J. Waldman, Kenneth Pham, Han-Seul Ryu, Constin Liu, Katelyn R. Titus, Rahul Sureka, Jason D. Shepherd, Erica Korb, Jennifer E. Phillips-Cremins*, Learning induces persistent chromatin loops underlying robust gene expression during memory recall, BioRxiv 678146 [Preprint], October 2025. 

*Preprint: https://doi.org/10.1101/2025.09.30.678146

‍

‍

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

‍

‍

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

‍

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

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

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

‍

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

‍

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

‍

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

‍

‍

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

‍

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

‍

‍

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

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

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

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

‍

‍

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

‍

‍