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2025 Journal Article A mutant ASXL1-BAP1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemiaDong, Zhen, Sepulveda, Hugo, Arteaga-Vazquez, Leo J., Blouin, Chad, Fernandez, Jenna, Binder, Moritz, Chou, Wen-Chien, Tien, Hwei-Fang, Patnaik, Mrinal M., Faulkner, Geoffrey J., Myers, Samuel A. and Rao, Anjana (2025). A mutant ASXL1-BAP1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia. Proceedings of the National Academy of Sciences, 122 (1) e2413302121. doi: 10.1073/pnas.2413302121 |
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2024 Journal Article Chromatin-based memory as a self-stabilizing influence on cell identityBell, Charles C., Faulkner, Geoffrey J. and Gilan, Omer (2024). Chromatin-based memory as a self-stabilizing influence on cell identity. Genome Biology, 25 (1) 320. doi: 10.1186/s13059-024-03461-x |
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2024 Journal Article Two HUSH complexes connect a direct LINE to innate immunityFaulkner, Geoffrey J. (2024). Two HUSH complexes connect a direct LINE to innate immunity. Molecular Cell, 84 (15), 2801-2803. doi: 10.1016/j.molcel.2024.07.010 |
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2024 Journal Article LINE-1 retrotransposons contribute to mouse PV interneuron developmentBodea, Gabriela O., Botto, Juan M., Ferreiro, Maria E., Sanchez-Luque, Francisco J., de los Rios Barreda, Jose, Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Jansz, Natasha, Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Da Costa Guevara, Darwin J., Cumner, Linda, Bell, Charles C., Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H. C., Love, Chloe J., Saha, Karabi, Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2024). LINE-1 retrotransposons contribute to mouse PV interneuron development. Nature Neuroscience, 27 (7), 1-34. doi: 10.1038/s41593-024-01650-2 |
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2024 Journal Article Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcriptionBell, Charles C., Balic, Jesse J., Talarmain, Laure, Gillespie, Andrea, Scolamiero, Laura, Lam, Enid Y. N., Ang, Ching-Seng, Faulkner, Geoffrey J., Gilan, Omer and Dawson, Mark A. (2024). Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription. Nature Genetics, 56 (6), 1181-1192. doi: 10.1038/s41588-024-01749-z |
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2024 Journal Article Viral genome sequencing methods: benefits and pitfalls of current approachesJansz, Natasha and Faulkner, Geoffrey J. (2024). Viral genome sequencing methods: benefits and pitfalls of current approaches. Biochemical Society Transactions, 52 (3), 1431-1447. doi: 10.1042/bst20231322 |
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2024 Journal Article Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesisMadrid, Lidia I., Hafey, Katelyn, Bandhavkar, Saurabh, Bodea, Gabriela O., Jimenez-Martin, Javier, Milne, Michael, Walker, Tara L., Faulkner, Geoffrey J., Coulson, Elizabeth J. and Jhaveri, Dhanisha J. (2024). Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesis. Development, 151 (1) dev201835, 1-13. doi: 10.1242/dev.201835 |
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2023 Journal Article HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and functionFriedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and Palpant, Nathan J. (2023). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e1. doi: 10.1016/j.devcel.2023.11.012 |
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2023 Journal Article Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic developmentGerdes, Patricia, Chan, Dorothy, Lundberg, Mischa, Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Faulkner, Geoffrey J. and Richardson, Sandra R. (2023). Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Research, 33 (9), 1465-1481. doi: 10.1101/gr.278003.123 |
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2023 Journal Article Transient naive reprogramming corrects hiPS cells functionally and epigeneticallyBuckberry, Sam, Liu, Xiaodong, Poppe, Daniel, Tan, Jia Ping, Sun, Guizhi, Chen, Joseph, Nguyen, Trung Viet, de Mendoza, Alex, Pflueger, Jahnvi, Frazer, Thomas, Vargas-Landín, Dulce B., Paynter, Jacob M., Smits, Nathan, Liu, Ning, Ouyang, John F., Rossello, Fernando J., Chy, Hun S., Rackham, Owen J. L., Laslett, Andrew L., Breen, James, Faulkner, Geoffrey J., Nefzger, Christian M., Polo, Jose M. and Lister, Ryan (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, 620 (7975), 863-872. doi: 10.1038/s41586-023-06424-7 |
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2023 Journal Article Endogenous retroviruses can propagate TDP-43 proteinopathyFerreiro, Maria E. and Faulkner, Geoffrey J. (2023). Endogenous retroviruses can propagate TDP-43 proteinopathy. Trends in Neurosciences, 46 (6), 413-414. doi: 10.1016/j.tins.2023.03.011 |
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2023 Journal Article Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effectFaulkner, Geoffrey J. (2023). Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. Neuron, 111 (5), 610-611. doi: 10.1016/j.neuron.2023.02.007 |
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2023 Journal Article Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genesLi, Zongchang, Min, Shishi, Alliey-Rodriguez, Ney, Giase, Gina, Cheng, Lijun, Craig, David Wesley, Faulkner, Geoffrey J., Asif, Huma, Liu, Chunyu and Gershon, Elliot S. (2023). Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes. Neurobiology of Aging, 123, 222-232. doi: 10.1016/j.neurobiolaging.2022.12.002 |
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2023 Journal Article The complexity of transferring genetic informationStrader, Lucia C., Staller, Max V., Willis, Anne E., Faulkner, Geoffrey J., Beggs, Jean D. and Cech, Thomas R. (2023). The complexity of transferring genetic information. Molecular Cell, 83 (3), 320-323. doi: 10.1016/j.molcel.2023.01.002 |
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2023 Journal Article Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulationZadran, Bassier, Sudhindar, Praveen Dhondurao, Wainwright, Daniel, Bury, Yvonne, Luli, Saimir, Howarth, Rachel, McCain, Misti Vanette, Watson, Robyn, Huet, Hannah, Palinkas, Fanni, Palmini, Rolando Berlinguer, Casement, John, Mann, Derek A., Oakley, Fiona, Lunec, John, Reeves, Helen, Faulkner, Geoffrey J. and Shukla, Ruchi (2023). Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation. British Journal of Cancer, 128 (7), 1236-1248. doi: 10.1038/s41416-023-02154-9 |
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2022 Journal Article Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cellsGerdes, Patricia, Lim, Sue Mei, Ewing, Adam D., Larcombe, Michael R., Chan, Dorothy, Sanchez-Luque, Francisco J., Walker, Lucinda, Carleton, Alexander L., James, Cini, Knaupp, Anja S., Carreira, Patricia E., Nefzger, Christian M., Lister, Ryan, Richardson, Sandra R., Polo, Jose M. and Faulkner, Geoffrey J. (2022). Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nature Communications, 13 (1) 7470, 1-18. doi: 10.1038/s41467-022-35180-x |
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2022 Journal Article Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y |
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2022 Book Chapter Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic ModificationsSmits, Nathan and Faulkner, Geoffrey J. (2022). Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications. Transposable Elements: Methods and Protocols. (pp. 151-171) New York, NY United States: Springer. doi: 10.1007/978-1-0716-2883-6_9 |
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2022 Journal Article Endogenous retrovirus expression during fruitfly metamorphosis enhances adult viral immunityBotto, Juan M. and Faulkner, Geoffrey J. (2022). Endogenous retrovirus expression during fruitfly metamorphosis enhances adult viral immunity. Nature Genetics, 54 (12), 1765-1767. doi: 10.1038/s41588-022-01209-6 |
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2022 Journal Article Somatic retrotransposition in the developing rhesus macaque brainBillon, Victor, Sanchez-Luque, Francisco J, Rasmussen, Jay, Bodea, Gabriela O, Gerhardt, Daniel J, Gerdes, Patricia, Cheetham, Seth W, Schauer, Stephanie N, Ajjikuttira, Prabha, Meyer, Thomas J, Layman, Cora E, Nevonen, Kimberly A, Jansz, Natasha, Garcia-Perez, Jose L, Richardson, Sandra R, Ewing, Adam D, Carbone, Lucia and Faulkner, Geoffrey J (2022). Somatic retrotransposition in the developing rhesus macaque brain. Genome Research, 32 (7), gr.276451.121-1314. doi: 10.1101/gr.276451.121 |
