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Items: 1 to 50 of 55

1.

Visualization and analysis of RNA-Seq assembly graphs.

Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC.

Nucleic Acids Res. 2019 Jul 15. pii: gkz599. doi: 10.1093/nar/gkz599. [Epub ahead of print]

PMID:
31305886
2.

LINE-1 Evasion of Epigenetic Repression in Humans.

Sanchez-Luque FJ, Kempen MHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie RL, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas M, Muñoz-Lopez M, Sanchez L, Lundberg M, Macia A, Heras SR, Brennan PM, Lister R, Garcia-Perez JL, Ewing AD, Faulkner GJ.

Mol Cell. 2019 Jun 20. pii: S1097-2765(19)30396-X. doi: 10.1016/j.molcel.2019.05.024. [Epub ahead of print]

PMID:
31230816
3.

Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation.

Salvador-Palomeque C, Sanchez-Luque FJ, Fortuna PRJ, Ewing AD, Wolvetang EJ, Richardson SR, Faulkner GJ.

Mol Cell Biol. 2019 Mar 19;39(7). pii: e00499-18. doi: 10.1128/MCB.00499-18. Print 2019 Apr 1.

4.

Author Correction: Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG.

Nat Commun. 2018 Dec 19;9(1):5398. doi: 10.1038/s41467-018-07917-0.

5.

Meeting report: mobile genetic elements and genome plasticity 2018.

Abrams JM, Arkhipova IR, Belfort M, Boeke JD, Joan Curcio M, Faulkner GJ, Goodier JL, Lehmann R, Levin HL.

Mob DNA. 2018 Jun 22;9:21. doi: 10.1186/s13100-018-0126-3. eCollection 2018.

6.

Retrotransposon-induced mosaicism in the neural genome.

Bodea GO, McKelvey EGZ, Faulkner GJ.

Open Biol. 2018 Jul;8(7). pii: 180074. doi: 10.1098/rsob.180074. Review.

7.

L1 retrotransposition in the soma: a field jumping ahead.

Faulkner GJ, Billon V.

Mob DNA. 2018 Jul 7;9:22. doi: 10.1186/s13100-018-0128-1. eCollection 2018. Review.

8.

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution.

Nguyen THM, Carreira PE, Sanchez-Luque FJ, Schauer SN, Fagg AC, Richardson SR, Davies CM, Jesuadian JS, Kempen MHC, Troskie RL, James C, Beaven EA, Wallis TP, Coward JIG, Chetty NP, Crandon AJ, Venter DJ, Armes JE, Perrin LC, Hooper JD, Ewing AD, Upton KR, Faulkner GJ.

Cell Rep. 2018 Jun 26;23(13):3730-3740. doi: 10.1016/j.celrep.2018.05.090.

10.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis.

Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ.

Genome Res. 2018 May;28(5):639-653. doi: 10.1101/gr.226993.117. Epub 2018 Apr 11.

11.

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

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.

12.

FANTOM5 CAGE profiles of human and mouse samples.

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 RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T, Edge ASB, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Ferrai C, Fisher ME, Forrester LM, Fujita R, Furusawa JI, Geijtenbeek TB, Gingeras T, Goldowitz D, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Heutink P, Hitchens KJ, Hume DA, Ikawa T, Ishizu Y, Kai C, Kawamoto H, Kawamura YI, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klein S, Klinken SP, Knox AJ, Kojima S, Koseki H, Koyasu S, Lee W, Lennartsson A, Mackay-Sim A, Mejhert N, Mizuno Y, Morikawa H, Morimoto M, Moro K, Morris KJ, Motohashi H, Mummery CL, 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 DA, Passier R, Patrikakis M, Pombo A, Pradhan-Bhatt S, Qin XY, Rehli M, Rizzu P, Roy S, Sajantila A, Sakaguchi S, Sato H, Satoh H, Savvi S, Saxena A, Schmidl C, Schneider C, Schulze-Tanzil GG, Schwegmann A, Sheng G, Shin JW, Sugiyama D, Sugiyama T, Summers KM, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tomoiu A, Toyoda H, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Wells CA, Winteringham LN, Wolvetang E, Yamaguchi Y, Yamamoto M, Yanagi-Mizuochi C, Yoneda M, Yonekura Y, Zhang PG, Zucchelli S, Abugessaisa I, Arner E, Harshbarger J, Kondo A, Lassmann T, Lizio M, Sahin S, Sengstag T, Severin J, Shimoji H, Suzuki M, Suzuki H, Kawai J, Kondo N, Itoh M, Daub CO, Kasukawa T, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y.

Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.

13.

L1 Mosaicism in Mammals: Extent, Effects, and Evolution.

Faulkner GJ, Garcia-Perez JL.

Trends Genet. 2017 Nov;33(11):802-816. doi: 10.1016/j.tig.2017.07.004. Epub 2017 Aug 7. Review.

14.

On the role of H3.3 in retroviral silencing.

Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner GJ, Mager DL, Lorincz MC, Macfarlan TS.

Nature. 2017 Aug 2;548(7665):E1-E3. doi: 10.1038/nature23277. No abstract available.

15.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo.

Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH Jr, Ewing AD, Faulkner GJ.

Genome Res. 2017 Aug;27(8):1395-1405. doi: 10.1101/gr.219022.116. Epub 2017 May 8.

16.

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

Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Faulkner GJ, Wells CA, Rehli M, Pavli P, Summers KM, Hume DA.

PLoS Genet. 2017 Mar 6;13(3):e1006641. doi: 10.1371/journal.pgen.1006641. eCollection 2017 Mar.

17.

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

Gerdes P, Richardson SR, Faulkner GJ.

Genome Biol. 2016 Dec 20;17(1):259.

18.

Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18.

Ravà M, D'Andrea A, Doni M, Kress TR, Ostuni R, Bianchi V, Morelli MJ, Collino A, Ghisletti S, Nicoli P, Recordati C, Iascone M, Sonzogni A, D'Antiga L, Shukla R, Faulkner GJ, Natoli G, Campaner S, Amati B.

Hepatology. 2017 May;65(5):1708-1719. doi: 10.1002/hep.28942. Epub 2016 Dec 30.

19.

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

Carreira PE, Ewing AD, Li G, Schauer SN, Upton KR, Fagg AC, Morell S, Kindlova M, Gerdes P, Richardson SR, Li B, Gerhardt DJ, Wang J, Brennan PM, Faulkner GJ.

Mob DNA. 2016 Nov 11;7:21. doi: 10.1186/s13100-016-0076-6. eCollection 2016.

20.

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

Gerdes P, Richardson SR, Mager DL, Faulkner GJ.

Genome Biol. 2016 May 9;17:100. doi: 10.1186/s13059-016-0965-5. Review.

21.

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

Li J, Woods SL, Healey S, Beesley J, Chen X, Lee JS, Sivakumaran H, Wayte N, Nones K, Waterfall JJ, Pearson J, Patch AM, Senz J, Ferreira MA, Kaurah P, Mackenzie R, Heravi-Moussavi A, Hansford S, Lannagan TRM, Spurdle AB, Simpson PT, da Silva L, Lakhani SR, Clouston AD, Bettington M, Grimpen F, Busuttil RA, Di Costanzo N, Boussioutas A, Jeanjean M, Chong G, Fabre A, Olschwang S, Faulkner GJ, Bellos E, Coin L, Rioux K, Bathe OF, Wen X, Martin HC, Neklason DW, Davis SR, Walker RL, Calzone KA, Avital I, Heller T, Koh C, Pineda M, Rudloff U, Quezado M, Pichurin PN, Hulick PJ, Weissman SM, Newlin A, Rubinstein WS, Sampson JE, Hamman K, Goldgar D, Poplawski N, Phillips K, Schofield L, Armstrong J, Kiraly-Borri C, Suthers GK, Huntsman DG, Foulkes WD, Carneiro F, Lindor NM, Edwards SL, French JD, Waddell N, Meltzer PS, Worthley DL, Schrader KA, Chenevix-Trench G.

Am J Hum Genet. 2016 May 5;98(5):830-842. doi: 10.1016/j.ajhg.2016.03.001. Epub 2016 Apr 14.

22.

Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans.

Sanchez-Luque FJ, Richardson SR, Faulkner GJ.

Methods Mol Biol. 2016;1400:47-77. doi: 10.1007/978-1-4939-3372-3_4.

PMID:
26895046
23.

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

Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG.

Nat Commun. 2016 Jan 8;7:10286. doi: 10.1038/ncomms10286. Erratum in: Nat Commun. 2018 Dec 19;9(1):5398.

24.

Ubiquitous L1 mosaicism in hippocampal neurons.

Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, van der Knaap MS, Brennan PM, Vanderver A, Faulkner GJ.

Cell. 2015 Apr 9;161(2):228-39. doi: 10.1016/j.cell.2015.03.026.

25.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, 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 TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.

Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.

26.

L1 retrotransposons and somatic mosaicism in the brain.

Richardson SR, Morell S, Faulkner GJ.

Annu Rev Genet. 2014;48:1-27. doi: 10.1146/annurev-genet-120213-092412. Epub 2014 Jul 14. Review.

PMID:
25036377
27.

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

Upton KR, Faulkner GJ.

Mob DNA. 2014 May 9;5:15. doi: 10.1186/1759-8753-5-15. eCollection 2014.

28.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, 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 DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, 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 LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

29.

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

Richardson SR, Salvador-Palomeque C, Faulkner GJ.

Bioessays. 2014 May;36(5):475-81. doi: 10.1002/bies.201300181. Epub 2014 Feb 25. Erratum in: Bioessays. 2014 May;36(5):538-9.

30.

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

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S.

Front Cell Neurosci. 2014 Feb 18;8:41. doi: 10.3389/fncel.2014.00041. eCollection 2014.

31.

L1 retrotransposons, cancer stem cells and oncogenesis.

Carreira PE, Richardson SR, Faulkner GJ.

FEBS J. 2014 Jan;281(1):63-73. doi: 10.1111/febs.12601. Epub 2013 Nov 28. Review.

32.

Retrotransposon silencing during embryogenesis: dicer cuts in LINE.

Faulkner GJ.

PLoS Genet. 2013 Nov;9(11):e1003944. doi: 10.1371/journal.pgen.1003944. Epub 2013 Nov 7. No abstract available.

33.

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

Reilly MT, Faulkner GJ, Dubnau J, Ponomarev I, Gage FH.

J Neurosci. 2013 Nov 6;33(45):17577-86. doi: 10.1523/JNEUROSCI.3369-13.2013. Review.

34.

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

Li JL, Mazar J, Zhong C, Faulkner GJ, Govindarajan SS, Zhang Z, Dinger ME, Meredith G, Adams C, Zhang S, Mattick JS, Ray A, Perera RJ.

Sci Rep. 2013 Oct 16;3:2962. doi: 10.1038/srep02962.

35.

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.

Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, Samuel D, Natoli G, Carninci P, Ciccarelli FD, Garcia-Perez JL, Faivre J, Faulkner GJ.

Cell. 2013 Mar 28;153(1):101-11. doi: 10.1016/j.cell.2013.02.032.

36.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, 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 SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, 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 LB.

Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.

37.

Extensive somatic L1 retrotransposition in colorectal tumors.

Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B, Wheelan S, Upton KR, Shukla R, Faulkner GJ, Largaespada DA, Kazazian HH Jr.

Genome Res. 2012 Dec;22(12):2328-38. doi: 10.1101/gr.145235.112. Epub 2012 Sep 11.

38.

Is somatic retrotransposition a parasitic or symbiotic phenomenon?

Upton KR, Baillie JK, Faulkner GJ.

Mob Genet Elements. 2011 Nov 1;1(4):279-282.

39.

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

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. doi: 10.1073/pnas.1110156109. Epub 2012 Mar 26.

40.

Promoter architecture of mouse olfactory receptor genes.

Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P.

Genome Res. 2012 Mar;22(3):486-97. doi: 10.1101/gr.126201.111. Epub 2011 Dec 22.

41.

Somatic retrotransposition alters the genetic landscape of the human brain.

Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ.

Nature. 2011 Oct 30;479(7374):534-7. doi: 10.1038/nature10531.

42.

Retrotransposons: mobile and mutagenic from conception to death.

Faulkner GJ.

FEBS Lett. 2011 Jun 6;585(11):1589-94. doi: 10.1016/j.febslet.2011.03.061. Epub 2011 Apr 6.

43.

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Genome Res. 2010 Feb;20(2):257-64. doi: 10.1101/gr.095273.109. Epub 2010 Jan 5.

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Trends Genet. 2010 Jan;26(1):21-8. doi: 10.1016/j.tig.2009.11.002. Epub 2009 Nov 26. Review.

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Bioinformatics. 2009 Oct 1;25(19):2615-6. doi: 10.1093/bioinformatics/btp459. Epub 2009 Jul 30.

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Bioinformatics. 2009 Oct 1;25(19):2613-4. doi: 10.1093/bioinformatics/btp438. Epub 2009 Jul 15.

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Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.

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