Computational and molecular biology

• 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

• Somatic retrotransposition in the developing rhesus macaque brain

  Billon, 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

• HUSH, retrotransposon RNA, you're NEXT to decay

  Faulkner, 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

• Retrotransposons: still mobile in humans

  Faulkner, Geoffrey J. (2022). Retrotransposons: still mobile in humans. Nature Reviews Genetics, 23 (8), 458-459. doi: 10.1038/s41576-022-00485-6

• Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

  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 (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

• The evolving gene regulatory landscape—a tinkerer of complex creatures

  Faulkner, 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

• Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway

  Sudhindar, 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. doi: 10.3390/cancers13205079

• Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome

  Troskie, 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

• An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden

  Rasmussen, 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

• No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

  Smits, 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

• 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

  Min, 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

• Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence

  Drummond, 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

• Endogenous retroviruses in the origins and treatment of cancer

  Jansz, 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

• Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

  Troskie, 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

• Nanopore sequencing enables comprehensive transposable element epigenomic profiling

  Ewing, 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

• LINE-1 Evasion of epigenetic repression in humans

  Sanchez-Luque, Francisco J., Kempen, Marie-Jeanne H.C., Gerdes, Patricia, Vargas-Landin, Dulce B., Richardson, Sandra R., Troskie, Robin-Lee, Jesuadian, J. Samuel, Cheetham, Seth W., Carreira, Patricia E., Salvador-Palomeque, Carmen, García-Cañadas, Marta, Muñoz-Lopez, Martin, Sanchez, Laura, Lundberg, Mischa, Macia, Angela, Heras, Sara R., Brennan, Paul M., Lister, Ryan, Garcia-Perez, Jose L., Ewing, Adam D. and Faulkner, Geoffrey J. (2019). LINE-1 Evasion of epigenetic repression in humans. Molecular Cell, 75 (3), 590-604.e12. doi: 10.1016/j.molcel.2019.05.024

• L1 mosaicism in mammals: extent, effects, and evolution

  Faulkner, Geoffrey J. and Garcia-Perez, Jose L. (2017). L1 mosaicism in mammals: extent, effects, and evolution. Trends in Genetics, 33 (11), 802-816. doi: 10.1016/j.tig.2017.07.004

• Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells

  Klawitter, Sabine, Fuchs,Nina V., Upton, Kyle R., Munoz-Lopez, Martin, Shukla, Ruchi, Wang, Jichang, Garcia-Canadas, Marta, Lopez-Ruiz, Cesar, Gerhardt, Daniel J., Sebe, Attila, Grabundzija, Ivana, Merkert, Sylvia, Gerdes, Patricia, Pulgarin, J. Andres, Bock, Anja, Held, Ulrike, Witthuhn, Anett, Haase, Alexandra, Sarkadi, Balazs, Lower, Johannes, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltan, Izsvak, Zsuzsanna, Garcia-Perez, Jose L., Faulkner, Geoffrey J. and Schumann, Gerald G. (2016) Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nature Communications, 7 1-14. doi:10.1038/ncomms10286

• Ubiquitous L1 mosaicism in hippocampal neurons

  Upton, Kyle R., Gerhardt, Daniel J., Jesuadian, J. Samuel, Richardson, Sandra R., Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Salvador-Palomeque, Carmen, van der Knaap, Mario S., Brennan, Paul M., Vanderver, Adeline and Faulkner, Geoffrey J. (2015) Ubiquitous L1 mosaicism in hippocampal neurons. Cell, 161 2: 228-239. doi:10.1016/j.cell.2015.03.026

• L1 retrotransposons and somatic mosaicism in the brain

  Richardson, Sandra R., Morell, Santiago and Faulkner, Geoffrey J. (2014) L1 retrotransposons and somatic mosaicism in the brain. Annual Review of Genetics, 48 1-27. doi:10.1146/annurev-genet-120213-092412

• Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

  Shukla, Ruchi, Upton, Kyle R., Muñoz-Lopez, Martin, Gerhardt, Daniel J., Fisher, Malcolm E., Thu Nguyen, Brennan, Paul M., Baillie, J. Kenneth, Collino, Agnese, Ghisletti, Serena, Sinha, Shruti, Iannelli, Fabio, Radaelli, Enrico, Dos Santos, Alexandre, Rapoud, Delphine, Guettier, Catherine, Samuel, Didier, Natoli, Gioacchino, Carninci, Piero, Ciccarelli, Francesca D., Luis Garcia-Perez, Jose, Faivre, Jamila and Faulkner, Geoffrey J. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153 1: 101-111. doi:10.1016/j.cell.2013.02.032

• Somatic retrotransposition alters the genetic landscape of the human brain

  Baillie, J. Kenneth, Barnett, Mark W., Upton, Kyle R., Gerhardt, Daniel J., Richmond, Todd A., De Sapio, Fioravante, Brennan. Paul M., Rizzu, Patrizia, Smith, Sarah, Fell, Mark, Talbot, Richard T., Gustincich, Stefano, Freeman, Thomas C., Mattick, John S., Hume, David A., Heutink, Peter, Carninci, Piero, Jeddeloh, Jeffrey A. and Faulkner, Geoffrey J. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479 7374: 534-537. doi:10.1038/nature10531

• The regulated retrotransposon transcriptome of mammalian cells

  Faulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009) The regulated retrotransposon transcriptome of mammalian cells. Nature genetics, 41 5: 563-571. doi:10.1038/ng.368

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