Bodea, G.O.*, Ferreiro, M.E., Sanchez-Luque, F.J., Botto, J.M., Rasmussen, J., Rahman, M.A., Fenlon, L.R., Gubert, C., Gerdes, P., Bodea, L-G., Ajjikuttira, P., Kozulin, P., Billon, V., Morell, S., Kepmen, M-J.H.C., Love, C.J., Palmer, L.M., Ewing, A.D., Jhaveri, D.J., Richardson, S.R., Hannan, A.J., Faulkner, G.J.*

LINE-1 retrotransposon activation intrinsic to interneuron development. bioRxiv (2022) doi:


Gerdes, P., Lim, S.M., Ewing, A.D., Larcombe, M.R., Chan, D., Sanchez-Luque, F.J., Walker, L., James, C., Knaupp, A.S., Carreira, P.E., Nefzger, C.M., Lister, R., Richardson, S.R.*, Polo, J.M.*, Faulkner, G.J.*Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. bioRxiv (2022) doi:


Friedman, C.E., Cheetham, S.W., Mills, R.J., Ogawa, M., Redd, M.A., Chiu, H.S., Shen, S., Sun, Y., Mizikovsky, D., Bouveret, R., Chen, X., Voges, H., Paterson, S., de Angelis, J.E., Andersen, S.B., Yoon, S., Faulkner, G.J., Smith, K.A., Harvey, R.P., Hogan, B.M., Nguyen, Q., Kikuchi, K., Hudson, J.E., Palpant, N.J.

HOPX governs a molecular and physiological switch between cardiomyocyte progenitor and maturation gene programs. bioRxiv (2022)



Billon, V., Sanchez-Luque, F.J., Rasmussen, J., Bodea, G.O., Gerhardt, D.J., Gerdes, P., Cheetham, S.W., Schauer, S.N., Ajjikuttira, P., Meyer, T.J., Layman, C.E., Nevonen, K.A., Jansz, N., Gercia-Perez, J.L., Ricardson, S.R., Ewing. A.D.*, Carbone, L.*, Faulkner, G.J.* Somatic retrotransposition in the developing rhesus macaque brain. Genome Research (2022) doi: 10.1101/gr.276451.121



Faulkner, G.J.* HUSH, retrotransposon RNA, you’re NEXT to decay. Molecular Cell 82 1610-1612 (2022) doi:



Faulkner, G.J.* Retrotransposons: still mobile in humans. Nature Reviews Genetics (2022) doi:



Sanchez-Luque, F.J., Kempen, M.J., Faulkner, G.J.* Locus-specific DNA methylation profiling of human LINE-1 retrotransposons. Genomic Structural Variants in Nervous System Disorders Ed C. Proukakis (2022) doi:



Rasmussen, J., Ewing, A.D., Bodea, L.-G., Bodea, G.O., Gearing, M., Faulkner, G.J.*, An early proinflammatory transcriptional response to tau pathology is age-specific and foreshadows reduced tau burden. Brain Pathology 32 e13018 (2022) doi: 10.1111/bpa.13018  



Cheetham, S.W.*, Jafrani, Y.M.A., Andersen, S.B., Jansz., N., Ewing, A.D., Faulkner, G.J.*, Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID. bioRxiv (2021) doi:



Min, S., Li, Z., Shieh, A., Giase, G., Bao, R., Zhang, C., Kuney, L., Kopp, R., Asif, H., Alliey-Rodriguez, N., Qin, L., Craig, D.W., Faulkner, G.J., Gerson, E.S., Tang, B., Chen, C., Liu, C. 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 (2021) doi: 10.1016/j.neurobiolaging.2021.07.010.



Troskie, R-L., Jafrani, Y., Mercer, T.R., Ewing, A.D.*, Faulkner, G.J.*, Cheetham, S.W.* Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology 22 1-15 (2021) doi:



Drummond, K.D., Waring, M.L., Faulkner, G.J., Blewitt, M.E., Perry, C.J., Kim, J.H. Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence. Neurobiology of Stress 15 100367 (2021) doi: 10.1016/j.ynstr.2021.100367



Smits, N., Rasmussen, J, Bodea, G.O., Amarilla, A.A., Gerdes, P., Sanchez-Luque, F.J., Ajjikuttira, P., Modhiran, N., Liang, B., Faivre, J., Deveson, I.W., Khromykh, A.A., Watterson, D., Ewing, A.D., Faulkner, G.J.* No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports 36 109530 (2021) doi: 10.1016/j.celrep.2021.109530  



Sudhindar, P.D., Wainwright, D., Saha, S., Howarth, R., McCain, M., Bury, Y., Saha, S.S., McPherson, S., Reeves, H., Patel, A.H., Faulkner, G.J., Lunec, J., Shukla, R. HCV activates somatic L1 retrotransposition – a potential hepatocarcinogenesis pathway. Cancers 13 5079 (2021)




Troskie, R.L., Faulkner, G.J.*, Cheetham, S.W.*Processed pseudogenes: a substrate for evolutionary innovation. BioEssays 43 2100186-2100196 (2021)




Faulkner, G.J.* The evolving gene regulatory landscape – a tinkerer of complex creatures. Genome Biology 22 1-3 (2021)




Jansz, N., Faulkner, G.J.* Endogenous retroviruses in the origins and treatment of cancer. Genome Biology 22 1-22 (2021)




Ewing, A.D.*, Smits, N., Sanchez-Luque, F.J., Faivre, J., Brennan, P.M., Richardson, S.R., Cheetham, S.W.*, Faulkner, G.J.* Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell 80 915-928 (2020) doi: 10.1016/j.molcel.2020.10.024. Epub 2020 Nov 12.



Cheetham, S.W., Faulkner, G.J., Dinger, M. E. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics 21 191-201 (2020) doi:



Drummond, K., Waring, M., Blewitt, M., Faulkner, G.J., Perry, C., Kim, J.K. Sex-specific effect of early- life social isolation and exercise on the extinction of adolescent conditioned fear. Biological Psychiatry 87 S337 (2020) doi:



Sanchez-Luque, F.J.*, Kempen, M-J.H.C., Gerdes, P., Vargas-Landin, D.B., Richardson, S.R., Troskie, R-L., Jesuadian, J.S., Cheetham, S.W., Carreira, P.E., Salvador-Palomeque, C., Garcia-Canadas, M., Munoz-Lopez, M., Sanchez, L., Lundberg, M., Macia, A., Heras, S.R., Brennan, P.M., Lister, R., Garcia-Perez, J.L., Ewing, A.D., Faulkner, G.J.* LINE-1 evasion of epigenetic repression in humans. Molecular Cell 75 590-604 (2019) doi: 10.1016/j.molcel.2019.05.024



Nazarie, F.W., Shih, B., Angus, T., Barnett, M.W., Chen, S.-H., Summers, K.M., Klein, K., Faulkner, G.J., Saini, H.K., Watson, M., van Dongen, S., Enright, A.J., Freeman, T.C. Visualization and analysis of RNA-seq assembly graphs. Nucleic Acids Research 47 7262-7275 (2019) doi: 10.1093/nar/gkz599



Salvador-Palomeque, C., Sanchez-Luque, F.J., Fortuna, P.R.J., Ewing. A.D., Wolvetang, E.J., Richardson, S.R., Faulkner, G.J.*Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Molecular and Cellular Biology 39 e00499-18 (2019) doi: 10.1128/MCB.00499-18



Nguyen, T.H.M., Carreira, P.E., Sanchez-Luque, F.J., Schauer, S.N., Fagg, A.C., Richardson, S.R., Davies, C.M., Jesuadian, J.S., Kempen, M-J.H.C., Troskie, R-L., James, C., Beaven, E.A., Wallis, T.P., Coward, J.I.G., Chetty, N.P., Crandon, A.J., Venter, D.J., Armes, J.E., Perrin, L.C., Hooper, J.D., Ewing, A.D., Upton, K.R., Faulkner, G.J.* L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Reports 23 3730-3740 (2018). doi: 10.1016/j.celrep.2018.05.090



Schauer, S.N., Carreira, P.E., Shukla, R., Gerhardt, D.J., Gerdes, P., Sanchez-Luque, F.-J., Nicoli, P., Kindlova, M., Ghesletti, S., Santos, A.D., Faivre, J., Ewing, A.D.*, Richardson, S.R.*, Faulkner, G.J.* L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Research 28 639-653 (2018) doi: 10.1101/gr.226993.117



Baillie, J.K., Bretherick, A., Haley, C., Clohisey, S., Gray, A., Barrett, J.C., Stahl, E.A., Tenesa, A., Andersson, R., Brown, B., Faulkner, G.J., Lizio, M., Schaefer, U., Daub, C.O., Itoh, M., Kondo, N., Lassmann, T., Kawai, J., Bajic, V.B., Heutink, P., Rehli, M., Kawaji, H., Sandelin, A., Suzuki, H., Satsangi, J., Wells, C.A., Nir, H., Freeman, T., Hayashizaki, Y., Carninci, P., Forrest, A.R.R., Hume, D.A. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Computational Biology 14 e1005934 (2018) doi:



Abrams, J.M., Arkhipova, I.R., Belfort, M., Boeke, J.D., Curcio, M.J., Faulkner, G.J., Goodier, J.L., Lehmann, R., Levin, H.L. Meeting report: mobile genetic elements and genome plasticity 2018. doi: 


Mobile DNA 9 21 (2018) Faulkner, G.J.*, Billon, V. L1 retrotransposition in the soma: a field jumping ahead. Mobile DNA 9 22 (2018) doi:



Bodea, G.O., McKelvey, E.G.Z., Faulkner, G.J.* Retrotransposon-induced mosaicism in the neural genome. Open Biology 8 180074 (2018)


Richardson, S.R., Faulkner, G.J.* Heritable L1 retrotransposition events during development: understanding their origins. BioEssays 40 1700189-1700203 (2018) doi: 10.1002/bies.201700189



Baillie, J.K., Arner, E., Daub, C., De Hoon, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Forrest, A.R.R., Hayashizaki, Y., The FANTOM Consortium, Faulkner, G.J., Wells, C., Rehli, M., Pavli, P., Summers, K.M., Hume, D.A. 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 e1006641 (2017) doi:



Ravà, 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., Amati, B. Mutual epithelium‐macrophage dependency in liver carcinogenesis mediated by ST18. Hepatology 65 178-1719 (2017) doi: 10.1002/hep.28942



Wolf, G., Rebollo, R., Karimi, M.M., Ewing, A.D., Kamada, R., Wu, W., Wu, B., Bachu. M., Ozato, K., Faulkner, G.J., Mager, D.L., Lorincz, M.C., Macfarlan, T.S.

On the role of H3.3 in retroviral silencing. Nature 548 E1 (2017) doi: 10.1038/nature14345



Richardson, S.R.*, Gerdes, P., Gerhardt, D.J., Sanchez-Luque, F.J., Bodea, G.O., Munoz-Lopez, M., Jesuadian, J.S., Kempen, M.-J.H.C., Carreira, P.E., Jeddeloh, J.A., Garcia-Perez, J.L., Kazazian, H.H., Ewing, A.D., Faulkner, G.J.*, Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Research 27 1395-1405 (2017) doi: 10.1101/gr.219022.116



Noguchi S., Arakawa T., Fukuda S., Furuno M., Hasegawa A., Hori F., Ishikawa-Kato S., Kaida K., Kaiho A., Kanamori-Katayama M., Kawashima T., Kojima M., Kubosaki A., Manabe RI., Murata M., Nagao-Sato S., Nakazato K., Ninomiya N., Nishiyori-Sueki H., Noma S., Saijyo E., Saka A., Sakai M., Simon C., Suzuki N., Tagami M., Watanabe S., Yoshida S., Arner P., Axton R.A., Babina M., Baillie J.K., Barnett TC., Beckhouse A.G., Blumenthal A., Bodega B., Bonetti A., Briggs J., Brombacher F., Carlisle A.J., Clevers H.C., Davis C.A., Detmar M., Dohi T., Edge A.S.B., Edinger M., Ehrlund A., Ekwall K., Endoh M., Enomoto H., Eslami A., Fagiolini M., Fairbairn L., Farach-Carson M.C., Faulkner G.J., Ferrai C., Fisher M.E., Forrester L.M., Morimoto M., Moro K., Morris K.J., Motohashi H., Mummery C.L., Nakachi Y., Nakahara F., Nakamura T., Nakamura Y., Nozaki T., Ogishima S., Ohkura N., Ohno H., Ohshima M., Okada-Hatakeyama M., Okazaki Y., Orlando V., Ovchinnikov D.A., Passier R., Patrikakis M., Pombo A., Pradhan-Bhatt S., Qin X.Y., Rehli M., Rizzu P., Roy S., Sajantila A., Sakaguchi S., Sato H., Satoh H., Savvi S., Saxena A., Schmidl C., Schneider C., Schulze-Tanzil G.G., Schwegmann A., Sheng G., Shin J.W., Sugiyama D., Sugiyama T., Summers K.M., Takahashi N., Takai J., Tanaka H., Tatsukawa H., Tomoiu A., Toyoda H., van de Wetering M., van den Berg L.M., Verardo R., Vijayan D., Wells C.A., Winteringham L.N., Wolvetang E., Yamaguchi Y., Yamamoto M., Yanagi-Mizuochi C., Yoneda M., Yonekura Y., Zhang P.G., Zucchelli S., Abugessaisa I., Arner E., Harshbarger J., Kondo, N., Itoh M., Daub CO., Kasukawa T., Kawaji H., Carninci P., Forrest A.R.R., Hayashizaki Y. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data 4 (2017) doi: 10.1038/sdata.2017.112



Sanchez-Luque, F.J., Richardson, S.R., Faulkner, G.J.* Analysis of somatic L1 insertions in neurons. doi:



Ed J.M. Frade and F.H. Gage, Genomic Mosaicism in Neurons and Other Cell Types (2017) Link to Book



Faulkner, G.J.*, Garcia-Perez, J-L. L1 mosaicism in mammals: extent, effects, and evolution. Trends in Genetics 33 802-816 (2017)




Kempen, M.-J.C.H., Bodea, G.O., Faulkner, G.J.* Neuronal genome plasticity: retrotransposons, environment and disease. (2017) Link to Book


Ed. G. Cristofari, Human Retrotransposons in Health and Disease (2017) Link to Book



Gerdes, P., Richardson, S.R., Faulkner, G.J.* TET enzymes: double agents in the transposable element–host genome conflict. Genome Biology 17 259 (2016) doi: 10.1186/s13059-016-1124-8



Gerdes, P., Richardson, S.R., Mager, D.L., Faulkner, G.J.*, Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biology 17 100 (2016) doi: 10.1186/s13059-016-0965-5



Carreira, P.E., Ewing, A.D., Li, G., Schauer, S.N., Upton, K.R., Fagg, A.C., Morell, S., Kindlova, M., Gerdes, P., Richardson, S.R., Li, B., Gerhardt, D.J., Wang, J., Brennan, P.M., Faulkner, G.J.* Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mobile DNA 7 7-21 (2016) doi:



Li, J., Woods, S.L., Healey, S., Beesley, J., Chen, X., Lee, J.S., Sivakumaran, H., Wayte, N., Nones, K., Waterfall, J.J., Pearson, J., Patch, A.-M., Senz, J., Ferreira, M., Kaurah, P., Mackenzie, R., Heravi-Moussavi, A., Hansford, S., Lannagan, T.R.M., Spurdle, A.B., Simpson, P.T., da Silva, L., Lakhani, S.R., Clouston, A.D., Bettington, M., Grimpen, F., Busuttil, R.A., DiCostanzo, N., Boussioutas, A., Jeanjean, M., Chong, G., Fabre, A., Olschwang, S., Faulkner, G.J., Bellos, E., Coin, L., Rioux, K., Bathe, O.F., Wen, X., Martin, H.C., Neklason, D.W., Davis, S.R., Walker, R.L., Calzone, K.A., Avital, I., Heller, T., Koh, C., Pineda, M., Rudloff, U. Quezado, M. Pichurin, P.N., Hulick, P.J., Weissman, S.M., Newlin, A., Rubinstein, W.S., Sampson, J.E., Hamman, K., Goldgar, D., Poplawski, N., Phillips, K., Schofield, L., Armstrong, J., Kiraly-Borri, C., Suthers, G.K., Huntsman, D.G., Foulkes, W.D., Carneiro, F., Lindor, N.M., Edwards, S.L., French, J.D., Waddell, N., Meltzer, P.S., Worthley, D.L., Schrader, K.A., Chenevix-Trench, G. Point mutations in exon 1B of APC reveal gastric adenocarcinoma and proximal polyposis of the stomach as a familial adenomatous polyposis variant. The American Journal of Human Genetics 98 830-842 (2016) doi: 10.1016/j.ajhg.2016.03.001



Klawitter, S., Fuchs, N.V., Upton, K.R., Muñoz-Lopez, M., Shukla, R., Wang, J., Garcia-Canadas, M., Lopez-Ruiz, C., Gerhardt, D.J., Sebe, A., Grabundzija, I., Merkert, S., Bock, A., Held, U., Witthuhn, A., Haase, A., Sarkadi, B., Löwer, J., Wolvetang, E.J., Martin, U., Ivics, Z., Izsvák, Z., Garcia-Perez, J.L, Faulkner, G.J.*, Schumann, G.G. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nature Communications 7 10286 (2016) doi: 10.1038/ncomms10286



Upton, K.R., Gerhardt, D.J., Jesuadian, J.S., Richardson, S.R., Sanchez-Luque, F.J., Bodea, G.O., Salvador-Palomeque, C., van der Knaap, M.S., Brennan, P.M., Vanderver, A., Faulkner, G.J.* Ubiquitous L1 mosaicism in hippocampal neurons. Cell 161 228-239 (2015) doi: 10.1016/j.cell.2015.03.026



Arner, E., Daub, C.O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drablos, F., Lennartsson, A., Ronnerblad, M., Hrydziuszko, O., Vitezic, M., Freeman, T.C., Alhendi, A.M., Arner, P., Axton, R., Baillie, J.K., Beckhouse, A., Bodega, B., Briggs, J., Brombacher, F., Davis, M., Detmar, M., Ehrlund, A., Endoh, M., Eslami, A., Fagiolini, M., Fairbairn, L., Faulkner, G.J., Ferrai, C., Fisher, M.E., Forrester, L., Goldowitz, D., Guler, R., Ha, T., Hara, M., Herlyn, M., Ikawa, T., Kai, C., Kawamoto, H., Khachigian, L.M., Klinken, S.P., Kojima, S., Koseki, H., Klein, S., Mejhert, N., Miyaguchi, K., Mizuno, Y., Morimoto, M., Morris, K.J., Mummery, C., Nakachi, Y., Ogishima, S., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Passier, R., Patrikakis, M., Pombo, A., Qin, X.Y., Roy, S., Sato, H., Savvi, S., Saxena, A., Schwegmann, A., Sugiyama, D., Swoboda, R., Tanaka, H., Tomoiu, A., Winteringham, L.N., Wolvetang, E., Yanagi-Mizuochi, C., Yoneda, M., Zabierowski, S., Zhang, P., Abugessaisa, I., Bertin, N., Diehl, A.D., Fukuda, S., Furuno, M., Harshbarger, J., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Ishizu, Y., Itoh, M., Kawashima, T., Kojima, M., Kondo, N., Lizio, M., Meehan, T.F., Mungall, C.J., Murata, M., Nishiyori-Sueki, H., Sahin, S., Nagao-Sato, S., Severin, J., de Hoon, M.J., Kawai, J., Kasukawa, T., Lassmann, T., Suzuki, H., Kawaji, H., Summers, K.M., Wells, C., Fantom Consortium, Hume, D.A., Forrest, A.R., Sandelin, A., Carninci, P., Hayashizaki, Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 347 1010-14 (2015)

doi: 10.1126/science.1259418



Sanchez-Luque, F.J., Richardson, S.R., Faulkner, G.J.*, Retrotransposon capture sequencing (RC-seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans (2016). Link to Book



Ed J.L. Garcia-Perez Transposons and Retrotransposons: Methods and Protocols (2015) Link to Book



Richardson, S.R., Morell, S., Faulkner, G.J.*,L1 retrotransposons and somatic mosaicism in the brain. Annual Review of Genetics 48 1-27 (2014)

doi: 10.1146/annurev-genet-120213-092412



Upton, K.R., Faulkner, G.J.*, Blood from ‘junk’: the LTR chimeric transcript Pu.2 promotes erythropoiesis. Mobile DNA 5 15 (2014)




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



Carreira, P.E., Richardson, S.R., Faulkner, G.J.* L1 retrotransposons, cancer stem cells and oncogenesis. FEBS J. 281 63-73 (2014) doi: 10.1111/febs.12601



Forrest, A.R., Kawaji, H., Rehli, M., Baillie, J.K., de Hoon, M.J., Haberle, V., Lassmann, T., Kulakovskiy, I.V., Lizio, M., Itoh, M., Andersson, R., Mungall, C.J., Meehan, T.F., Schmeier, S., Bertin, N., Jorgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y.A., Plessy, C., Vitezic, M., Severin, J., Semple, C., Ishizu, Y., Young, R.S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G.M., Arakawa, T., Archer, J.A., Arner, P., Babina, M., Rennie, S., Balwierz, P.J., Beckhouse, A.G., Pradhan-Bhatt, S., Blake, J.A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A.M., Califano, A., Cannistraci, C.V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H.C., Dalla, E., Davis, C.A., Detmar, M., Diehl, A.D., Dohi, T., Drablos, F., Edge, A.S., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M.C., Faulkner, G.J., Favorov, A.V., Fisher, M.E., Frith, M.C., Fujita, R., Fukuda, S., Furlanello, C., Furino, M., Furusawa, J., Geijtenbeek, T.B., Gibson, A.P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T.J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K.J., Ho Sui, S.J., Hofmann, O.M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B.R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A.S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y.I., Kawashima, T., Kempfle, J.S., Kenna, T.J., Kere, J., Khachigian, L.M., Kitamura, T., Klinken, S.P., Knox, A.J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A.T., Laros, J.F., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-Sim, A., Manabe, R., Mar, J.C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., de Lima Morais, D.A., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C.L., Murata, M., Nagao-Sato, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Noma, S., Noazaki, T., Ogishima, S., Ohkura, N., Ohimiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D.A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J.G., Rackham, O.J., Ramilowski, J.A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M.B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E.A., Schulze-Tanzil, G.G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J.W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R.K., t Hoen, P.A., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyodo, H., Toyoda, T., Valen, E., van de Wetering, M., van den Berg, L.M., Verado, R., Vijayan, D., Vorontsov, I.E., Wasserman, W.W., Watanabe, S., Wells, C.A., Winteringham, L.N., Wolvetang, E., Wood, E.J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S.E., Zhang, P.G., Zhao, X., Zucchelli, S., Summers, K.M., Suzuki, H., Daub, C.O., Kawai, J., Heutink, P., Hide, W., Freeman, T.C., Lenhard, B., Bajic, V.B., Taylor, M.S., Makeev, V.J., Sandelin, A., Hume, D.A., Carninci, P., Hayashizaki, Y. A promoter level mammalian expression atlas. Nature 507 462-70 (2014) doi:



Pascarella, G., Lazarevic, D., Plessy, C., Bertin, N., Alkalin, A., Vlachouli, C., Simone, R., Faulkner, G.J., Zucchelli, S., Kawai, J., Daub, C.O., Hayashizaki, Y., Lenhard, B., Carninci, P., Gustincich, S. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience 8 41 (2014) doi: 10.3389/fncel.2014.00041



Li, J. L., Mazar, J., Zhong, C., Faulkner, G.J., Govindarajan, S.S., Zhang, Z., Dinger, M.E., Meredith, G., Adams, C., Zhang, S., Mattick, J.S., Ray, A., Perera, R.J. Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Scientific Reports 3 2962-2975 (2013)

doi: 10.1038/srep02962


Shukla, R., Upton, K.R., Muñoz-Lopez, M., Gerhardt, D.J., Fisher, M.E., Nguyen, T., Brennan P.M., Baillie, J.K., Collino, A., Ghisletti, S., Sinha, S., Iannelli, F., Radaelli, E., Dos Santos, A., Rapoud, D., Guettier, C., Samuel, D., Natoli, G., Carninci, P., Ciccarelli, F.D., Garcia-Perez, J.L., Faivre, J., Faulkner, G.J.* Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153 101-111 (2013) doi: 10.1016/j.cell.2013.02.032



Faulkner, G.J.* Retrotransposon silencing during embryogenesis: Dicer cuts in LINE. PLoS Genetics 9 e1003944 (2013) doi: 10.1371/journal.pgen.1003944



Reilly, M.T., Faulkner, G.J., Dubnau, J., Ponomarev, I., Gage, F.H. The role of transposable elements in health and diseases of the central nervous system. J. Neurosci. 33 17577-86 (2013) doi: 10.1523/JNEUROSCI.3369-13.2013



Groenen, M.A., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.L., Humphray, S.J., Hunt, T., Hornshoj, H., Jeon, J.T., Jern, P. Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.H., Kim, K.W., Kim, T.H., Larson, G., Lee, K., Lee, K.T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Nguyen, D.T., Ni, P., Oh, S.J., Onteru, S., Panitz, F., Park, E.W., Park, H.S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L.B. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491 393-8 (2012) doi:




Solyom, S., Ewing, A.D., Rahrmann, E.P., Doucet, T.T., Nelson, H.H., Burns, M.B., Harris, R.S., Sigmon, D.F., Casella, A., Erlanger, B., Wheelan, S., Upton, K.R., Shukla, R., Faulkner, G.J., Largaespada, D.A., Kazazian, H.H. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Research 22 2328-38 (2012)

doi: 10.1101/gr.145235.112


Plessy, C., Pascarella, G., Bertin, N., Akalin, A., Carrieri, C., Vassalli, A., Lazarevic, D., Severin, J., Vlachouli, C., Simone, R., Faulkner, G.J., Kawai, J., Daub, C.O., Zucchelli, S., Hayashizaki, Y., Mombaerts, P., Lenhard, B., Gustincich, S., Carninci, P. Promoter Architecture of Mouse Olfactory Receptor Genes. Genome Research 22 486-497 (2012) doi: 10.1101/gr.126201.111



Schroder, K., Irvine, K.M., Taylor, M.S., Bokil, N.J., Le Cao, K., Masterman, K., Labzin, L.I., Semple, C.A., Kapetanovic, R., Fairbairn, L., Akalin, A., Faulkner, G.J., Baillie, J.K., Gongora, M., Daub, C.O., McLachlan, G.J., Goldman, N., Grimmond, S.M., Carninci, P., Suzuki, H., Hayashizaki, Y., Lenhard, B., Hume, D.A., Sweet, M.J. Conservation and divergence in Toll-like Receptor 4-regulated gene expression in primary human versus mouse macrophages. PNAS 109 E944-E953 (2012) doi:



Baillie, J.K., Barnett, M.W., Upton, K.R., Gerhardt, D.J., Richmond, T., de Sapio, F., Brennan, P., Rizzu, P., Smith, S., Fell, M., Talbot, R.T., Gustincich, S., Freeman, T.C., Mattick., J.S., Hume, D.A., Heutink, P., Carninci, P., Jeddeloh, J.A., Faulkner, G.J.* Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479 534-537 (2011) doi:



Upton, K.R., Baillie, J.K., Faulkner, G.J.* Is somatic retrotransposition a parasitic or symbiotic phenomenon? Mobile Genetic Elements 1 279-328 (2011) doi: 10.4161/mge.18422



Faulkner, G.J.* Retrotransposons: mobile and mutagenic from conception to death. FEBS Letters 585 1589-1594 (2011) doi:


Mattick, J.S., Taft, R.J., Faulkner, G.J.*A global view of genomic information – moving beyond the gene and the master regulator. Trends in Genetics 26 21-8 (2010) doi:



de Hoon, M.J.L., Taft, R.J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., Kishima, M., Lassmann, T., Faulkner, G.J., Mattick, J.S., Daub, C.O., Carninci, P., Kawai, J., Suzuki, H., Hayashizaki, Y. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research 20 257-64 (2010) doi: 10.1101/gr.095273.109



Hashimoto, T., de Hoon, M.J.L., Grimmond, S.M., Daub, C.O., Hayashizaki, Y., Faulkner, G.J.* Probabilistic resolution of multi-mapping reads in next-generation sequence data using MuMRescueLite. Bioinformatics 25 2613-4 (2009) doi: 10.1093/bioinformatics/btp438



Cloonan, N., Xu, Q., Faulkner, G.J., Taylor, D.F., Tang, D.T.P., Grimmond, S.M. RNA-MATE: A recursive mapping strategy for high throughput RNA-sequencing data. Bioinformatics 25 2615-6 (2009) doi: 10.1093/bioinformatics/btp459



Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A.R.R., Suzuki, H., Hayashizaki, Y., Hume, D.A., Orlando, V., Grimmond, S.M., Carninci, P. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41 563-71 (2009) doi:



Taft, R.J., Glazov, E.A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G.,J., Lassmann, T., Forrest, A.R.R., Grimmond, S.M., Schroder, K., Irvine, K., Arakawa, T., Nakamura, M., Kubosaki, A., Hayashida, K., Kawazu, C., Murata, M., Nishiyori, H., Fukuda, S., Kawai, J., Daub, C.O., Hume, D.A., Suzuki, H., Orlando, V., Carninci, P., Hayashizaki, Y., Mattick, J.S. Tiny RNAs associated with transcription start sites in animals. Nature Genetics 41 572-8 (2009) doi: 10.1038/ng.312



Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., 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, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M.C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., Hayashizaki, Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics 41 553-62 (2009)




Faulkner, G.J.*, Carninci, P. Altruistic functions for selfish DNA. Cell Cycle 8 2895-900 (2009) doi: 10.4161/cc.8.18.9536



Faulkner, G.J.*, Grimmond, S.M., Setting CAGE tags in a genomic context. CAGE Analysis Ed P. Carninci (2008) Link to Book



Cloonan, N., Forrest, A.R.R., Kolle, G., Gardiner, B.B.A., Faulkner, G.J., Brown, M.K., Taylor, D.F., Steptoe, A.L., Wani, S., Bethel, G., Robertson, A.J., Perkins, A.C., Bruce, S.J., Lee, C.C., Ranade, S.S., Peckham, H.E., Manning, J.M., McKernan, K.J., Grimmond, S.M. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 5 613-9 (2008) doi:



Faulkner, G.J.*, Forrest, A.R., Chalk, A.M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D.A., Grimmond, S.M.

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91 281-8 (2008)

doi: 10.1016/j.ygeno.2007.11.003



Meadows, N.A., Sharma, S.M., Faulkner, G.J., Ostrowski, M.C., Hume, D.A., Cassady, A.I. The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor. Journal Biological Chemistry 282 1891-904 (2007) doi: 10.1074/jbc.M608572200



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., Grimmond, S.M. Alternate transcription of the Toll-like receptor signaling cascade. Genome Biology 7 R10 (2006)



Forrest, A.R., Taylor, D.F., Crowe, M.L., Chalk, A.M., Waddell, N.J., Kolle, G., Faulkner, G.J., Kodzius, R., Katayama, S., Wells, C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Grimmond, S.M. Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biology 7 R5 (2006) doi: 10.1186/gb-2006-7-1-r5



Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V.B., Brenner, S.E., Batalov, S., Forrest, A.R., Zavolan, M., Davis, M.J., Wilming, L.G., Aidinis, V., Allen, J.E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R.N., Bailey, T.L., Bansal, M., Baxter, L., Beisel, K.W., Bersano, T., Bono, H., Chalk, A.M., Chiu, K.P., Choudhary, V., Christoffels, A., Clutterbuck, D.R., Crowe, M.L., Dalla, E., Dalrymple, B.P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G.J., Fletcher, C.F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T.R., Gojobori, T., Green, R.E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T.K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S.P., Kruger, A., Kummerfeld, S.K., Kurochkin, I.V., Lareau, L.F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K.C., Pavan, W.J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J.F., Ring, B.Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S.L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C.A., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S.L., Tang, S., Taylor, M.S., Tegner, J., Teichmann, S.A., Ueda, H.R., van Nimwegen, E., Verardo, R., Wei, C.L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S.M., Teasdale, R.D., Liu, E.T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J.S., Hume, D.A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y. The transcriptional landscape of the mammalian genome. Science 309 1559-63 (2005) doi: 10.1126/science.1112014



Meadows, N.A., Faulkner, G., Wells, C., Ravasi, T., Hume, D., Sankar, U., Hu, R., Ostrowski, M., Cassady, A. Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts. Journal of Bone and Mineral Research 19 S413 (2004) doi:



Huber, T., Faulkner, G., Hugenholtz, P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 2317-9 (2004) doi: 10.1093/bioinformatics/bth226



Wells, C.A., Ravasi, T., Sultana, R., Yagi, K., Carninci, P., Bono, H., Faulkner, G., Okazaki, Y., Quackenbush, J., Hume, D.A., Lyons, P.A.

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Research 13 1360-5 (2003)

doi: 10.1101/gr.1056103



Wells, C.A., Ravasi, T., Faulkner, G.J., Carninci, P., Okazaki, Y., Hayashizaki, Y., Sweet, M., Wainwright, B.J., Hume, D.A.

Genetic control of the innate immune response. BMC Immunology 4 5 (2003) doi: