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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 |
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2022 Journal Article HUSH, retrotransposon RNA, you're NEXT to decayFaulkner, Geoffrey J. (2022). HUSH, retrotransposon RNA, you're NEXT to decay. Molecular Cell, 82 (9), 1610-1612. doi: 10.1016/j.molcel.2022.04.013 |
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2022 Journal Article Retrotransposons: still mobile in humansFaulkner, Geoffrey J. (2022). Retrotransposons: still mobile in humans. Nature Reviews Genetics, 23 (8), 458-459. doi: 10.1038/s41576-022-00485-6 |
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2022 Journal Article LINE-1 retrotransposon activation intrinsic to interneuron developmentBodea, Gabriela O., Ferreiro, Maria E., Sanchez-Luque, Francisco J., Botto, Juan M., Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H.C., Love, Chloe J., Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2022). LINE-1 retrotransposon activation intrinsic to interneuron development. |
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2022 Book Chapter Locus-specific DNA methylation profiling of human LINE-1 retrotransposonsSanchez-Luque, Francisco J., Kempen, Marie-Jeanne H. C. and Faulkner, Geoffrey J. (2022). Locus-specific DNA methylation profiling of human LINE-1 retrotransposons. Genomic structural variants in nervous system disorders. (pp. 197-227) edited by Christos Proukakis. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2357-2_11 |
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2021 Journal Article The evolving gene regulatory landscape—a tinkerer of complex creaturesFaulkner, Geoffrey J. (2021). The evolving gene regulatory landscape—a tinkerer of complex creatures. Genome Biology, 22 (1) 199, 199. doi: 10.1186/s13059-021-02412-0 |
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2021 Journal Article Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkGrapotte, 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 (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7 |
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2021 Journal Article Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathwaySudhindar, Praveen D., Wainwright, Daniel, Saha, Santu, Howarth, Rachel, McCain, Misti, Bury, Yvonne, Saha, Sweta S., McPherson, Stuart, Reeves, Helen, Patel, Arvind H., Faulkner, Geoffrey J., Lunec, John and Shukla, Ruchi (2021). Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway. Cancers, 13 (20) 5079, 5079. doi: 10.3390/cancers13205079 |
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2021 Journal Article Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genomeTroskie, Robin-Lee, Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. BioEssays, 43 (11) 2100186, 2100186. doi: 10.1002/bies.202100186 |
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2021 Journal Article An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burdenRasmussen, Jay, Ewing, Adam D., Bodea, Liviu‐Gabriel, Bodea, Gabriela O., Gearing, Marla and Faulkner, Geoffrey J. (2021). An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden. Brain Pathology, 32 (3) e13018, e13018. doi: 10.1111/bpa.13018 |
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2021 Journal Article No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencingSmits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports, 36 (7) 109530, 109530. doi: 10.1016/j.celrep.2021.109530 |
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2021 Journal Article Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescenceDrummond, Katherine D., Waring, Michelle L., Faulkner, Geoffrey J., Blewitt, Marnie E., Perry, Christina J. and Kim, Jee Hyun (2021). Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence. Neurobiology of Stress, 15 100367, 1-16. doi: 10.1016/j.ynstr.2021.100367 |
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2021 Journal Article Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics dataMin, Shishi, Li, Zongchang, Shieh, Annie, Giase, Gina, Bao, Riyue, Zhang, Chunling, Kuney, Liz, Kopp, Richard, Asif, Huma, Alliey-Rodriguez, Ney, Qin, Lixia, Craig, David Wesley, Faulkner, Geoffrey J., Gershon, Elliot S., Tang, Beisha, Chen, Chao and Liu, Chunyu (2021). Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data. Neurobiology of Aging, 108, 207-209. doi: 10.1016/j.neurobiolaging.2021.07.010 |
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2021 Other Outputs No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencingSmits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. doi: 10.1101/2021.05.28.446065 |
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2021 Journal Article Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptomeTroskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0 |
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2021 Journal Article Endogenous retroviruses in the origins and treatment of cancerJansz, Natasha and Faulkner, Geoffrey J. (2021). Endogenous retroviruses in the origins and treatment of cancer. Genome Biology, 22 (1) 147, 1-22. doi: 10.1186/s13059-021-02357-4 |
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2020 Journal Article Nanopore sequencing enables comprehensive transposable element epigenomic profilingEwing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024 |
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2020 Conference Publication Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fearDrummond, Katherine, Waring, Michelle, Blewitt, Marnie, Faulkner, Geoffrey, Perry, Christina and Kim, Jee Hyun (2020). Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fear. 75th Annual Scientific Convention and Meeting of the Society-of-Biological-Psychiatry (SOBP), New York, NY, United States, 30 April - 2 May 2020. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.biopsych.2020.02.866 |
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2020 Journal Article Overcoming challenges and dogmas to understand the functions of pseudogenesCheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1 |
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2019 Journal Article Visualization and analysis of RNA-Seq assembly graphsNazarie, Fahmi W., Shih, Barbara, Angus, Tim, Barnett, Mark W., Chen, Sz-Hau, Summers, Kim M., Klein, Karsten, Faulkner, Geoffrey J., Saini, Harpreet K., Watson, Mick, Dongen, Stijn van, Enright, Anton J. and Freeman, Tom C. (2019). Visualization and analysis of RNA-Seq assembly graphs. Nucleic Acids Research, 47 (14), 7262-7275. doi: 10.1093/nar/gkz599 |
