The University of Queensland

Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications

Smits, 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

Locus-specific DNA methylation profiling of human LINE-1 retrotransposons

Sanchez-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

Analysis of somatic LINE-1 insertions in neurons

Sanchez-Luque, Francisco J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2017). Analysis of somatic LINE-1 insertions in neurons. Genomic mosaicism in neurons and other cell types. (pp. 219-251) edited by José María Frade and Fred H. Gage. New York, United States: Humana Press. doi: 10.1007/978-1-4939-7280-7_12

Neuronal genome plasticity: retrotransposons, environment and disease

Kempen, Marie-Jeanne H. C., Bodea, Gabriela O. and Faulkner, Geoffrey J. (2017). Neuronal genome plasticity: retrotransposons, environment and disease. Human retrotransposons in health and disease. (pp. 107-125) edited by Gael Cristofari. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-48344-3_5

Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans

Sanchez-Luque, Francisco J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans. Transposons and retrotranspons: methods and protocols. (pp. 47-77) edited by Jose L. Garcia-Pérez. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-3372-3_4

Setting CAGE tags in a genomic context

Faulkner, G. J. and Grimmond, S. M. (2009). Setting CAGE tags in a genomic context. Cap- Analysis Gene Expression (Cage): The Science of Decoding Gene Transcription. (pp. 93-100) edited by Carninci, P. Singapore: Pan Stanford Publishing. doi: 10.4032/9789814241359

Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesis

Madrid, 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. (2023). Stimulation of the muscarinic receptor M4 regulates neural precursor cell proliferation and promotes adult hippocampal neurogenesis. Development, 151 (1) dev201835. doi: 10.1242/dev.201835

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

Friedman, 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

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

Gerdes, 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

Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Buckberry, 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

Endogenous retroviruses can propagate TDP-43 proteinopathy

Ferreiro, 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

Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect

Faulkner, 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

Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes

Li, 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

The complexity of transferring genetic information

Strader, 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

Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation

Zadran, 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

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

Gerdes, 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

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

Endogenous retrovirus expression during fruitfly metamorphosis enhances adult viral immunity

Botto, 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

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

LINE-1 retrotransposon activation intrinsic to interneuron development

Bodea, 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.

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

Overcoming challenges and dogmas to understand the functions of pseudogenes

Cheetham, 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

Visualization and analysis of RNA-Seq assembly graphs

Nazarie, 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

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

Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation

Salvador-Palomeque, Carmen, Sanchez-Luque, Francisco J., Fortuna, Patrick R. J., Ewing, Adam D., Wolvetang, Ernst J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2019). Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Molecular and Cellular Biology, 39 (7) e00499-18, 1-19. doi: 10.1128/mcb.00499-18

Erratum to: Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Nature Communications, (2016), 7, 1, (10286), 10.1038/ncomms10286)

Klawitter, Sabine, Fuchs, Nina V., Upton, Kyle R., Muñoz-Lopez, Martin, Shukla, Ruchi, Wang, Jichang, Garcia-Cañadas, 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, Balázs, Löwer, Johannes, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltán, Izsvák, Zsuzsanna, Garcia-Perez, Jose L., Faulkner, Geoffrey J. and Schumann, Gerald G. (2018). Erratum to: Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Nature Communications, (2016), 7, 1, (10286), 10.1038/ncomms10286). Nature Communications, 9 (1) 5398, 5398. doi: 10.1038/s41467-018-07917-0

Retrotransposon-induced mosaicism in the neural genome

Bodea, Gabriela O., McKelvey, Eleanor G. Z. and Faulkner, Geoffrey J. (2018). Retrotransposon-induced mosaicism in the neural genome. Open Biology, 8 (7) 180074, 180074. doi: 10.1098/rsob.180074

L1 retrotransposition in the soma: a field jumping ahead

Faulkner, Geoffrey J. and Billon, Victor (2018). L1 retrotransposition in the soma: a field jumping ahead. Mobile DNA, 9 (1) 22, 22. doi: 10.1186/s13100-018-0128-1

Heritable L1 retrotransposition events during development: understanding their origins: examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions

Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). Heritable L1 retrotransposition events during development: understanding their origins: examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions. BioEssays, 40 (6) 1700189, e1700189. doi: 10.1002/bies.201700189

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

Schauer, Stephanie N., Carreira, Patricia E., Shukla, Ruchi, Gerhardt, Daniel J., Gerdes, Patricia, Sanchez-Luque, Francisco J., Nicoli, Paola, Kindlova, Michaela, Ghisletti, Serena, Santos, Alexandre Dos, Rapoud, Delphine, Samuel, Didier, Faivre, Jamila, Ewing, Adam D., Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Research, 28 (5), 639-653. doi: 10.1101/gr.226993.117

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

Baillie, J. Kenneth, Bretherick, Andrew, Haley, Christopher S., Clohisey, Sara, Gray, Alan, Neyton, Lucile P. A., Barrett, Jeffrey, Stahl, Eli A., Tenesa, Albert, Andersson, Robin, Brown, J. Ben, Faulkner, Geoffrey J., Lizio, Marina, Schaefer, Ulf, Daub, Carsten, Itoh, Masayoshi, Kondo, Naoto, Lassmann, Timo, Kawai, Jun, IIBDGC Consortium, Mole, Damian, Bajic, Vladimir B., Heutink, Peter, Rehli, Michael, Kawaji, Hideya, Sandelin, Albin, Suzuki, Harukazu, Satsangi, Jack, Wells, Christine A. ... Hume, David A. (2018). Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PL o S Computational Biology, 14 (3) e1005934, e1005934. doi: 10.1371/journal.pcbi.1005934

L1 retrotransposon heterogeneity in ovarian tumor cell evolution

Nguyen, Thu H. M., Carreira, Patricia E., Sanchez-Luque, Francisco J., Schauer, Stephanie N., Fagg, Allister C., Richardson, Sandra R., Davies, Claire M., Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Troskie, Robin-Lee, James, Cini, Beaven, Elizabeth A., Wallis, Tristan P., Coward, Jermaine I. G., Chetty, Naven P., Crandon, Alexander J., Venter, Deon J., Armes, Jane E., Perrin, Lewis C., Hooper, John D., Ewing, Adam D., Upton, Kyle R. and Faulkner, Geoffrey J. (2018). L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Reports, 23 (13), 3730-3740. doi: 10.1016/j.celrep.2018.05.090

FANTOM5 CAGE profiles of human and mouse samples

Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter ... Hayashizaki, Yoshihide (2017). FANTOM5 CAGE profiles of human and mouse samples. Scientific Data, 4 (1) 170112, 170112. doi: 10.1038/sdata.2017.112

On the role of H3.3 in retroviral silencing

Wolf, Gernot, Rebollo, Rita, Karimi, Mohammad M., Ewing, Adam D., Kamada, Rui, Wu, Warren, Wu, Brenda, Bachu, Mahesh, Ozato, Keiko, Faulkner, Geoffrey J., Mager, Dixie L., Lorincz, Matthew C. and Macfarlan, Todd S. (2017). On the role of H3.3 in retroviral silencing. Nature, 548 (7665), E1-E6. doi: 10.1038/nature23277

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

Richardson, Sandra R., Gerdes, Patricia, Gerhardt, Daniel J., Sanchez-Luque, Francisco J., Bodea, Gabriela-Oana, Muñoz-Lopez, Martin, Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Carreira, Patricia E., Jeddeloh, Jeffrey A., Garcia-Perez, Jose L., Kazazian Jr., Haig H., Ewing, Adam D. and Faulkner, Geoffrey J. (2017). Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Research, 27 (8), 1395-1405. doi: 10.1101/gr.219022.116

Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18

Rava, M., D'Andrea, A., Doni, M., Kress, T. R., Ostuni, R., Bianchi, V., Morelli, M. J., Collino, A., Ghisletti, S., Nicoli, P., Recordati, C., Iascone, M., Sonzogni, A., D'Antiga, L., Shukla, R., Faulkner, G. J., Natoli, G., Campaner, S. and Amati, B. (2017). Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18. Hepatology, 65 (5), 1708-1719. doi: 10.1002/hep.28942

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

Baillie, J. Kenneth, Arner, Erik, Daub, Carsten, De Hoon, Michiel, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Faulkner, Geoffrey J., Wells, Christine A., Rehli, Michael, Pavli, Paul, Summers, Kim M., Hume, David A. and FANTOM Consortium (2017). Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genetics, 13 (3) e1006641, 1-36. doi: 10.1371/journal.pgen.1006641

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

TET enzymes: double agents in the transposable element-host genome conflict

Gerdes, Patricia, Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). TET enzymes: double agents in the transposable element-host genome conflict. Genome Biology, 17 (1) 259. doi: 10.1186/s13059-016-1124-8

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

Carreira, Patricia E., Ewing, Adam D., Li, Guibo, Schauer, Stephanie N., Upton, Kyle R., Fagg, Allister C., Morell, Santiago, Kindlova, Michaela, Gerdes, Patricia, Richardson, Sandra R., Li, Bo, Gerhardt, Daniel J., Wang, Jun, Brennan, Paul M. and Faulkner, Geoffrey J. (2016). Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mobile DNA, 7 (1) 21, 1-14. doi: 10.1186/s13100-016-0076-6

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service

Gerdes, Patricia, Richardson, Sandra R., Mager, Dixie L. and Faulkner, Geoffrey J. (2016). Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biology, 17 (1) 100. doi: 10.1186/s13059-016-0965-5

Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant

Li, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001

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) 10286, 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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Arner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, J. Kenneth, Beckhouse, Anthony, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E. ... Hayashizaki, Yoshihide (2015). Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 (6225), 1010-1014. doi: 10.1126/science.1259418

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

Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis

Upton, Kyle R. and Faulkner,Geoffrey J. (2014). Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis. Mobile DNA, 5 (1) 15, 15. doi: 10.1186/1759-8753-5-15

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

Pascarella, Giovanni, Lazarevic, Dejan, Plessy, Charles, Bertin, Nicolas, Akalin, Altuna, Vlachouli, Christina, Simone, Roberto, Faulkner, Geoffry J., Zucchelli, Silvia, Kawai, Jun, Daub, Carsten O., Hayashizaki, Yoshihide, Lenhard, Boris, Carninci, Piero and Gustincich, Stefano (2014). NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience, 8 (FEB) 41, 41. doi: 10.3389/fncel.2014.00041

A promoter-level mammalian expression atlas

Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab ... Hayashizaki, Yoshihide (2014). A promoter-level mammalian expression atlas. Nature, 507 (7493), 462-470. doi: 10.1038/nature13182

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

Richardson, Sandra R., Salvador-Palomeque, Carmen and Faulkner, Geoffrey J. (2014). Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population. BioEssays, 36 (5), 475-481. doi: 10.1002/bies.201300181

L1 retrotransposons, cancer stem cells and oncogenesis

Carreira, Patricia E., Richardson, Sandra R. and Faulkner, Geoffrey J. (2014). L1 retrotransposons, cancer stem cells and oncogenesis. FEBS Journal, 281 (1), 63-73. doi: 10.1111/febs.12601

Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE

Faulkner, Geoffrey J. (2013). Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE. PLoS Genetics, 9 (11) e1003944, e1003944. doi: 10.1371/journal.pgen.1003944

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

Li, Jian-Liang, Mazar, Joseph, Zhong, Cuncong, Faulkner, Geoffrey J., Govindarajan, Subramaniam S., Zhang, Zhan, Dinger, Marcel E., Meredith, Gavin, Adams, Christopher, Zhang, Shaojie, Mattick, John S., Ray, Animesh and Perera, Ranjan J. (2013). Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Scientific Reports, 3 (1) 2962, 02962.1-02962.12. doi: 10.1038/srep02962

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

The role of transposable elements in health and diseases of the central nervous system

Reilly, Matthew T., Faulkner, Geoffrey J., Dubnau, Joshua, Ponomarev, Igor and Gage, Fred H. (2013). The role of transposable elements in health and diseases of the central nervous system. Journal of Neuroscience, 33 (45), 17577-17586. doi: 10.1523/JNEUROSCI.3369-13.2013

Extensive somatic L1 retrotransposition in colorectal tumors

Solyom, Szilvia, Ewing, Adam D., Rahrmann, Eric P., Doucet, Tara, Nelson, Heather H., Burns, Michael B., Harris, Reuben S., Sigmon, David F., Casella, Alex, Erlanger, Bracha, Wheelan, Sarah, Upton, Kyle R., Shukla, Ruchi, Faulkner, Geoffrey J., Largaespada, David A. and Kazazian, Haig H. (2012). Extensive somatic L1 retrotransposition in colorectal tumors. Genome Research, 22 (12), 2328-2338. doi: 10.1101/gr.145235.112

Analyses of pig genomes provide insight into porcine demography and evolution

Groenen, Martien A. M., Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Denis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara ... Schook, Lawrence B. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424), 393-398. doi: 10.1038/nature11622

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

Schroder, Kate, Irvine, Katharine M., Taylor, Martin S., Bokil, Nilesh J., Le Cao, Kim-Anh, Masterman, Kelly-Anne, Labzin, Larisa I., Semple, Colin A., Kapetanovic, Ronan, Fairbairn, Lynsey, Akalin, Altuna, Faulkner, Geoffrey J., Baillie, John Kenneth, Gongora, Milena, Daub, Carsten O., Kawaji, Hideya, McLachlan, Geoffrey J., Goldman, Nick, Grimmond, Sean M., Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Lenhard, Boris, Hume, David A. and Sweet, Matthew J. (2012). Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of the National Academy of Sciences of the USA, 109 (16), E944-E953. doi: 10.1073/pnas.1110156109

Promoter architecture of mouse olfactory receptor genes

Plessy, Charles, Pascarella, Giovanni, Bertin, Nicolas, Akalin, Altuna, Carrieri, Claudia, Vassalli, Anne, Lazarevic, Dejan, Severin, Jessica, Vlachouli, Christina, Simone, Roberto, Faulkner, Geoffrey J., Kawai, Jun, Daub, Carsten O., Zucchelli, Silvia, Hayashizaki, Yoshihide, Mombaerts, Peter, Lenhard, Boris, Gustincich, Stefano and Carninci, Piero (2012). Promoter architecture of mouse olfactory receptor genes. Genome Research, 22 (3), 486-497. doi: 10.1101/gr.126201.111

Is somatic retrotransposition a parasitic or symbiotic phenomenon?

Upton, Kyle R., Baillie, J. Kenneth and Faulkner, Geoffrey J. (2011). Is somatic retrotransposition a parasitic or symbiotic phenomenon?. Mobile Genetic Elements, 1 (4), 279-282. doi: 10.4161/mge.18422

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

Retrotransposons: mobile and mutagenic from conception to death

Faulkner, Geoffrey J. (2011). Retrotransposons: mobile and mutagenic from conception to death. FEBS Letters, 585 (11), 1589-1594. doi: 10.1016/j.febslet.2011.03.061

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

de Hoon, Michiel J. L., Taft, Ryan J., Hashimoto, Takehiro, Kanamori-Katayama, Mutsumi, Kawaji, Hideya, Kawano, Mitsuoki, Kishima, Mami, Lassmann, Timo, Faulkner, Geoffrey J., Mattick, John S., Daub, Carsten O., Carninci, Piero, Kawai, Jun, Suzuki, Harukazu and Hayashizaki, Yoshihide (2010). Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research, 20 (2), 257-264. doi: 10.1101/gr.095273.109

A global view of genomic information - moving beyond the gene and the master regulator

Mattick, John S., Taft, Ryan J. and Faulkner, Geoffrey J. (2010). A global view of genomic information - moving beyond the gene and the master regulator. Trends in Genetics, 26 (1), 21-28. doi: 10.1016/j.tig.2009.11.002

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Hashimoto, T, de Hoon, M. J. L., Grimmond, S. M., Daub, C. O., Hayashizaki, Y and Faulkner, G. J. (2009). Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. Bioinformatics, 25 (19), 2613-2614. doi: 10.1093/bioinformatics/btp438

Altruistic functions for selfish DNA

Faulkner, Geoffrey J. and Carninci, Piero (2009). Altruistic functions for selfish DNA. Cell Cycle, 8 (18), 2895-2900. doi: 10.4161/cc.8.18.9536

RNA-MATE: a recursive mapping strategy for high throughput RNA-sequencing data

Cloonan, Nicole, Xu, Qinying, Faulkner, Geoffrey J., Taylor, Darrin F., Tang, Dave T. P., Kolle, Gabriel and Grimmond, Sean M. (2009). RNA-MATE: a recursive mapping strategy for high throughput RNA-sequencing data. Bioinformatics, 25 (19), 2615-2616. doi: 10.1093/bioinformatics/btp459

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

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E ... Riken Omics Science Center (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 (5), 553-562. doi: 10.1038/ng.375

Tiny RNAs associated with transcription start sites in animals

Taft, RJ, Glazov, EA, Cloonan, N, Simons, C, Stephen, S, Faulkner, GJ, Lassmann, T, Forrest, ARR, Grimmond, SM, Schroder, K, Irvine, K, Arakawa, T, Nakamura, M, Kubosaki, A, Hayashida, K, Kawazu, C, Murata, M, Nishiyori, H, Fukuda, S, Kawai, J, Daub, CO, Hume, DA, Suzuki, H, Orlando, V, Carninci, P, Hayashizaki, Y and Mattick, JS (2009). Tiny RNAs associated with transcription start sites in animals. Nature Genetics, 41 (5), 572-578. doi: 10.1038/ng.312

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

Faulkner, G. J., Forrest, A. R. R., Chalk, A. M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D. A. and Grimmond, S. M. (2008). A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics, 91 (3), 281-288. doi: 10.1016/j.ygeno.2007.11.003

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Cloonan, Nicole, Forrest, Alistair R. R., Kolle, Gabriel, Gardiner, Brooke B. A., Faulkner, Geoffrey J., Brown, Mellissa K., Taylor, Darrin F ., Steptoe, Anita L., Wani, Shivangi, Bethel, Graeme, Robertson, Alan J., Perkins, Andrew C., Bruce, Stephen J., Clarence, C. Lee, Ranade, Swati S., Peckham, Heather E, Manning, Jonathan M, McKernan, Kevin J and Grimmond, Sean M (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5 (7), 613-619. doi: 10.1038/nmeth.1223

The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor

Meadows, Nicholas A., Sharma, Sudarshana M., Faulkner, Geoffrey J., Ostrowski, Michael C., Hume, David A. and Cassady, Alan I. (2007). The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor. Journal of Biological Chemistry, 282 (3), 1891-1904. doi: 10.1074/jbc.M608572200

Alternate transcription of the Toll-like receptor signaling cascade

Wells, C. A., Chalk, A. M., Forrest, A., Taylor, D., Waddell, N., Schroder, K., Himes, S. R., Faulkner, G., Lo, S., Kasukawa, T., Kawaji, H., Kai, C., Kawai, J., Katayama, S., Carninci, P., Hayashizaki, Y., Hume, D. A. and Grimmond, S. M. (2006). Alternate transcription of the Toll-like receptor signaling cascade. Genome Biology, 7 (2) R10, R10.1-R10.17. doi: 10.1186/gb-2006-7-2-r10

Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases

Forrest, Alistair R. R., Taylor, Darrin F., Crowe, Mark L., Chalk, Alistair M., Waddell, Nic J., Kolle, Gabriel, Faulkner, Geoffrey J., Kodzius, Rimantas, Katayama, Shintaro, Wells, Christine, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Grimmond, Sean M. (2006). Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biology, 7 (1) R5, R5.1-R5.15. doi: 10.1186/gb-2006-7-1-r5

The transcriptional landscape of the mammalian genome

The FANTOM Consortium, Gough, J., Frith, M. C., Ravasi, T., Wells, C., Forrest, A. R. R., Davis, M. J., Aturaliya, R. N., Bailey, T. L., Crowe, M. L., Faulkner, G., Pang, K. C., Teasdale, R. D., Grimmond, S. M., Mattick, J. S., Hume, D. A. and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Core Team) (2005). The transcriptional landscape of the mammalian genome. Science, 309 (5740), 1559-1563. doi: 10.1126/science.1112014

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Huber, T, Faulkner, G and Hugenholtz, P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20 (14), 2317-2319. doi: 10.1093/bioinformatics/bth226

Genetic control of the innate immune response

Wells, C. A., Ravasi, T., Faulkner, G. J., Carninci, P., Okazaki, Y., Hayashizaki, Y., Sweet, M.J., Wainwright, B. J. and Hume, D. A. (2003). Genetic control of the innate immune response. BMC Immunology, 4 (Article 5) 5, 1-18. doi: 10.1186/1471-2172-4-5

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

Wells, C. A., Ravasi, T., Sultana, R., Yagi, K., Carninci, P., Bono, H., Faulkner, G. J., Okazaki, Y., Quackenbush, J., Hume, D. A., RIKEN GER Group,, GSL Members, and Lyons, P. A. (2003). Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Research, 13 (6B), 1360-1365. doi: 10.1101/gr.1056103

Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fear

Drummond, 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

YY1: an enduring repressor of L1 retrotransposition during human neurodevelopment

Faulkner, G. J. (2019). YY1: an enduring repressor of L1 retrotransposition during human neurodevelopment. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, Sweden, 15-18 June 2019. LONDON: NATURE PUBLISHING GROUP.

Meeting report: mobile genetic elements and genome plasticity 2018

Abrams, John M., Arkhipova, Irina R., Belfort, Marlene, Boeke, Jef D., Curcio, M. Joan, Faulkner, Geoffrey J., Goodier, John L., Lehmann, Ruth and Levin, Henry L. (2018). Meeting report: mobile genetic elements and genome plasticity 2018. London, United Kingdom: BioMed Central. doi: 10.1186/s13100-018-0126-3

Reprogramming triggers mobilisation of endogenous retrotransposons in human induced pluripotent stem cells with genotoxic effects on host gene expression

Jung-Klawitter, S., Fuchs, N. V., Upton, K. R., Froemmrich, A., Miskey, C., Munoz-Lopez, M., Shukla, R., Wang, J., Sebe, A., Merkert, S., Bock, A., Held, U., Menzel, M., Gogol-Doering, A., Haase, A., Izsvak, Z., Ivics, Z., Martin, U., Garcia-Perez, J., Faulkner, G. J. and Schumann, G. G. (2017). Reprogramming triggers mobilisation of endogenous retrotransposons in human induced pluripotent stem cells with genotoxic effects on host gene expression. European-Society-of-Gene-and-Cell-Therapy (ESCGT) Congress, Berlin, Germany, 2017. New Rochelle, NY, United States: Mary Ann Liebert.

Line-1, a novel biomarker for high-grade serous ovarian carcinoma

Nguyen, T. H. M., Upton, K. R. and Faulkner, G. J. (2014). Line-1, a novel biomarker for high-grade serous ovarian carcinoma. 15th Biennial Meeting of the International Gynecologic Cancer Society, Melbourne, Australia, 8 -11 November 2014. New York, United States: Lippincott Williams & Wilkins. doi: 10.1097/01.IGC.0000457075.08973.89

Retrotransposition and the genetic identity of human neurons

Faulkner, G. J. (2011). Retrotransposition and the genetic identity of human neurons. 36th FEBS Congress of the Biochemistry for Tomorrows Medicine, Torino Italy, Jun 25-30, 2011. MALDEN: WILEY-BLACKWELL.

Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts

Meadows, N. A., Faulkner, G., Wells, C., Ravasi, T., Hume, D., Sankar, U., Hu, R., Ostrowski, M. and Cassady, A. (2004). Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts. 26th Annual Meeting of the American-Society-for-Bone-and-Mineral-Research, Seattle, WA, United States, 1-5 October 2004. Malden, MA, United States: Wiley-Blackwell. doi: 10.1002/jbmr.5650191306

Short sequence tags reveal global transcription of repetitive elements in mammalian genomes

Faulkner, Geoffrey (2008). Short sequence tags reveal global transcription of repetitive elements in mammalian genomes. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland. doi: 10.14264/167578