Publications of the Faulknerlab

Major Publications

2019

Sanchez-Luque, Francisco J; Kempen, Marie-Jeanne H C; Gerdes, Patricia; Vargas-Landin, Dulce B; Richardson, Sandra R; Troskie, Robin-Lee; Jesuadian, Samuel J; 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; Faulkner, Geoffrey J

LINE-1 Evasion of Epigenetic Repression in Humans (Journal Article)

Molecular Cell, 0 (0), 2019, ISSN: 1097-2765.

(Abstract | Links | BibTeX | Altmetric)

2018

Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, Samuel J; 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; Faulkner, Geoffrey J

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution (Journal Article)

Cell Reports, 23 (13), pp. 3730–3740, 2018, ISSN: 2211-1247.

(Abstract | Links | BibTeX | Altmetric)

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; Faulkner, Geoffrey J

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis (Journal Article)

Genome Research, 2018, ISSN: 1088-9051, 1549-5469.

(Abstract | Links | BibTeX | Altmetric)

2017

Richardson, Sandra R; Gerdes, Patricia; Gerhardt, Daniel J; Sanchez-Luque, Francisco J; Bodea, Gabriela-Oana; ~n, Martin Mu; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Carreira, Patricia E; Jeddeloh, Jeffrey A; Garcia-Perez, Jose L; Jr, Haig Kazazian H; Ewing, Adam D; Faulkner, Geoffrey J

Heritable L1 retrotransposition in the mouse primordial germline and early embryo (Journal Article)

Genome Res., 27 (8), pp. 1395–1405, 2017.

(Abstract | Links | BibTeX)

Faulkner, Geoffrey J; Garcia-Perez, Jose L

L1 Mosaicism in Mammals: Extent, Effects, and Evolution (Journal Article)

Trends Genet., 33 (11), pp. 802–816, 2017.

(Abstract | Links | BibTeX)

2016

Klawitter, Sabine; Fuchs, Nina V; Upton, Kyle R; ~n, Martin Mu; Shukla, Ruchi; Wang, Jichang; ~n, Marta Garcia-Ca; Lopez-Ruiz, Cesar; Gerhardt, Daniel J; Sebe, Attila; Grabundzija, Ivana; Merkert, Sylvia; Gerdes, Patricia; Pulgarin, Andres J; 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; Schumann, Gerald G

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Journal Article)

Nat. Commun., 7 , pp. 10286, 2016.

(Abstract | Links | BibTeX)

2015

Upton, Kyle R; Gerhardt, Daniel J; Jesuadian, Samuel J; Richardson, Sandra R; Sánchez-Luque, Francisco J; Bodea, Gabriela O; Ewing, Adam D; Salvador-Palomeque, Carmen; van der Knaap, Marjo S; Brennan, Paul M; Vanderver, Adeline; Faulkner, Geoffrey J

Ubiquitous L1 mosaicism in hippocampal neurons (Journal Article)

Cell, 161 (2), pp. 228–239, 2015.

(Abstract | Links | BibTeX)

2013

Shukla, Ruchi; Upton, Kyle R; ~n, Martin Mu; Gerhardt, Daniel J; Fisher, Malcolm E; Nguyen, Thu; Brennan, Paul M; Baillie, Kenneth J; Collino, Agnese; Ghisletti, Serena; Sinha, Shruti; Iannelli, Fabio; Radaelli, Enrico; Santos, Alexandre Dos; Rapoud, Delphine; Guettier, Catherine; Samuel, Didier; Natoli, Gioacchino; Carninci, Piero; Ciccarelli, Francesca D; Garcia-Perez, Jose Luis; Faivre, Jamila; Faulkner, Geoffrey J

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma (Journal Article)

Cell, 153 (1), pp. 101–111, 2013.

(Abstract | Links | BibTeX)

2011

Baillie, Kenneth J; Barnett, Mark W; Upton, Kyle R; Gerhardt, Daniel J; Richmond, Todd A; Sapio, Fioravante De; 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; Faulkner, Geoffrey J

Somatic retrotransposition alters the genetic landscape of the human brain (Journal Article)

Nature, 479 (7374), pp. 534–537, 2011.

(Abstract | Links | BibTeX)

2009

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; Carninci, Piero

The regulated retrotransposon transcriptome of mammalian cells (Journal Article)

Nat. Genet., 41 (5), pp. 563–571, 2009.

(Abstract | Links | BibTeX)


All other publicationssee all publications

62 entries « 1 of 2 »

2019

Salvador-Palomeque, Carmen; Sanchez-Luque, Francisco J; Fortuna, Patrick R J; Ewing, Adam D; Wolvetang, Ernst J; Richardson, Sandra R; Faulkner, Geoffrey J

Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation (Journal Article)

Mol Cell Biol, 39 (7), 2019, ISSN: 0270-7306.

(Abstract | Links | BibTeX | Altmetric)

Sanchez-Luque, Francisco J; Kempen, Marie-Jeanne H C; Gerdes, Patricia; Vargas-Landin, Dulce B; Richardson, Sandra R; Troskie, Robin-Lee; Jesuadian, Samuel J; 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; Faulkner, Geoffrey J

LINE-1 Evasion of Epigenetic Repression in Humans (Journal Article)

Molecular Cell, 0 (0), 2019, ISSN: 1097-2765.

(Abstract | Links | BibTeX | Altmetric)

2018

Bodea, Gabriela O; McKelvey, Eleanor G Z; Faulkner, Geoffrey J

Retrotransposon-induced mosaicism in the neural genome (Journal Article)

Open Biology, 8 (7), pp. 180074, 2018, ISSN: 2046-2441.

(Abstract | Links | BibTeX | Altmetric)

Richardson, Sandra R; Faulkner, Geoffrey J

Heritable L1 Retrotransposition Events During Development: Understanding Their Origins (Journal Article)

BioEssays, 40 (6), pp. 1700189, 2018, ISSN: 1521-1878.

(Abstract | Links | BibTeX | Altmetric)

Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, Samuel J; 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; Faulkner, Geoffrey J

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution (Journal Article)

Cell Reports, 23 (13), pp. 3730–3740, 2018, ISSN: 2211-1247.

(Abstract | Links | BibTeX | Altmetric)

Faulkner, Geoffrey J; Billon, Victor

L1 retrotransposition in the soma: a field jumping ahead (Journal Article)

Mobile DNA, 9 (1), pp. 22, 2018, ISSN: 1759-8753.

(Abstract | Links | BibTeX | Altmetric)

Abrams, John M; Arkhipova, Irina R; Belfort, Marlene; Boeke, Jef D; Curcio, Joan M; Faulkner, Geoffrey J; Goodier, John L; Lehmann, Ruth; Levin, Henry L

Meeting report: mobile genetic elements and genome plasticity 2018 (Journal Article)

Mobile DNA, 9 (1), pp. 21, 2018, ISSN: 1759-8753.

(Abstract | Links | BibTeX | Altmetric)

Baillie, Kenneth J; Bretherick, Andrew; Haley, Christopher S; Clohisey, Sara; Gray, Alan; Neyton, Lucile P A; Barrett, Jeffrey; Stahl, Eli A; Tenesa, Albert; Andersson, Robin; Brown, Ben J; Faulkner, Geoffrey J; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Itoh, Masayoshi; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Consortium, Iibdgc; Mole, Damian; Bajic, Vladimir B; Heutink, Peter; Rehli, Michael; Kawaji, Hideya; Sandelin, Albin; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A; Hacohen, Nir; Freeman, Thomas C; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Hume, David A

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

PLOS Computational Biology, 14 (3), pp. e1005934, 2018, ISSN: 1553-7358.

(Abstract | Links | BibTeX | Altmetric)

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; Faulkner, Geoffrey J

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis (Journal Article)

Genome Research, 2018, ISSN: 1088-9051, 1549-5469.

(Abstract | Links | BibTeX | Altmetric)

2017

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 ; Axton, Richard A; Babina, Magda ; Baillie, Kenneth J; Barnett, Timothy C; Beckhouse, Anthony G; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessandro ; Briggs, James ; Brombacher, Frank ; Carlisle, Ailsa J; Clevers, Hans C; Davis, Carrie A; Detmar, Michael ; Dohi, Taeko ; Edge, Albert S B; Edinger, Matthias ; Ehrlund, Anna ; Ekwall, Karl ; Endoh, Mitsuhiro ; Enomoto, Hideki ; Eslami, Afsaneh ; Fagiolini, Michela ; Fairbairn, Lynsey ; Farach-Carson, Mary C; Faulkner, Geoffrey J

FANTOM5 CAGE profiles of human and mouse samples (Journal Article)

Scientific Data, 4 , pp. 170112, 2017, ISSN: 2052-4463.

(Abstract | Links | BibTeX | Altmetric)

Richardson, Sandra R; Gerdes, Patricia; Gerhardt, Daniel J; Sanchez-Luque, Francisco J; Bodea, Gabriela-Oana; ~n, Martin Mu; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Carreira, Patricia E; Jeddeloh, Jeffrey A; Garcia-Perez, Jose L; Jr, Haig Kazazian H; Ewing, Adam D; Faulkner, Geoffrey J

Heritable L1 retrotransposition in the mouse primordial germline and early embryo (Journal Article)

Genome Res., 27 (8), pp. 1395–1405, 2017.

(Abstract | Links | BibTeX)

Ravà, Micol; D'Andrea, Aleco; Doni, Mirko; Kress, Theresia R; Ostuni, Renato; Bianchi, Valerio; Morelli, Marco J; Collino, Agnese; Ghisletti, Serena; Nicoli, Paola; Recordati, Camilla; Iascone, Maria; Sonzogni, Aurelio; D'Antiga, Lorenzo; Shukla, Ruchi; Faulkner, Geoffrey J; Natoli, Gioacchino; Campaner, Stefano; Amati, Bruno

Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18 (Journal Article)

Hepatology, 65 (5), pp. 1708–1719, 2017.

(Abstract | Links | BibTeX)

Baillie, Kenneth J; Arner, Erik; Daub, Carsten; Hoon, Michiel De; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Carninci, Piero; Forrest, Alistair R R; Hayashizaki, Yoshihide; Consortium, FANTOM; Faulkner, Geoffrey J; Wells, Christine A; Rehli, Michael; Pavli, Paul; Summers, Kim M; Hume, David A

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

PLoS Genet., 13 (3), pp. e1006641, 2017.

(Abstract | Links | BibTeX)

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; Macfarlan, Todd S

On the role of H3.3 in retroviral silencing (Journal Article)

Nature, 548 (7665), pp. E1–E3, 2017.

(Links | BibTeX)

Kempen, Marie-Jeanne H C; Bodea, Gabriela O; Faulkner, Geoffrey J

Neuronal Genome Plasticity: Retrotransposons, Environment and Disease (Incollection)

Human Retrotransposons in Health and Disease, pp. 107–125, Springer, Cham, 2017.

(Abstract | Links | BibTeX)

Faulkner, Geoffrey J; Garcia-Perez, Jose L

L1 Mosaicism in Mammals: Extent, Effects, and Evolution (Journal Article)

Trends Genet., 33 (11), pp. 802–816, 2017.

(Abstract | Links | BibTeX)

Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J

Analysis of Somatic LINE-1 Insertions in Neurons (Incollection)

Genomic Mosaicism in Neurons and Other Cell Types, pp. 219–251, Humana Press, New York, NY, 2017, ISBN: 978-1-4939-7279-1 978-1-4939-7280-7, (DOI: 10.1007/978-1-4939-7280-7_12).

(Abstract | Links | BibTeX)

2016

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; Costanzo, Natasha Di; Boussioutas, Alex; Jeanjean, Marie; Chong, George; Fabre, Aurélie; Olschwang, Sylviane; Faulkner, Geoffrey J; Bellos, Evangelos; Coin, Lachlan; Rioux, Kevin; Bathe, Oliver F; Wen, Xiaogang; Martin, Hilary C; Neklason, Deborah W; Davis, Sean R; Walker, Robert L; Calzone, Kathleen A; Avital, Itzhak; Heller, Theo; Koh, Christopher; Pineda, Marbin; Rudloff, Udo; Quezado, Martha; Pichurin, Pavel N; Hulick, Peter J; Weissman, Scott M; Newlin, Anna; Rubinstein, Wendy S; Sampson, Jone E; Hamman, Kelly; Goldgar, David; Poplawski, Nicola; Phillips, Kerry; Schofield, Lyn; Armstrong, Jacqueline; Kiraly-Borri, Cathy; Suthers, Graeme K; Huntsman, David G; Foulkes, William D; Carneiro, Fatima; Lindor, Noralane M; Edwards, Stacey L; French, Juliet D; Waddell, Nicola; Meltzer, Paul S; Worthley, Daniel L; Schrader, Kasmintan A; Chenevix-Trench, Georgia

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

Am. J. Hum. Genet., 98 (5), pp. 830–842, 2016.

(Abstract | Links | BibTeX)

Gerdes, Patricia; Richardson, Sandra R; Mager, Dixie L; Faulkner, Geoffrey J

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service (Journal Article)

Genome Biol., 17 , pp. 100, 2016.

(Abstract | Links | BibTeX)

Gerdes, Patricia; Richardson, Sandra R; Faulkner, Geoffrey J

TET enzymes: double agents in the transposable element-host genome conflict (Journal Article)

Genome Biol., 17 (1), pp. 259, 2016.

(Abstract | Links | BibTeX)

Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J

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

Methods Mol. Biol., 1400 , pp. 47–77, 2016.

(Abstract | Links | BibTeX)

Klawitter, Sabine; Fuchs, Nina V; Upton, Kyle R; ~n, Martin Mu; Shukla, Ruchi; Wang, Jichang; ~n, Marta Garcia-Ca; Lopez-Ruiz, Cesar; Gerhardt, Daniel J; Sebe, Attila; Grabundzija, Ivana; Merkert, Sylvia; Gerdes, Patricia; Pulgarin, Andres J; 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; Schumann, Gerald G

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Journal Article)

Nat. Commun., 7 , pp. 10286, 2016.

(Abstract | Links | BibTeX)

Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J

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

Methods in Molecular Biology (Clifton, N.J.), 1400 , pp. 47–77, 2016, ISSN: 1940-6029.

(Abstract | Links | BibTeX | Altmetric)

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; Faulkner, Geoffrey J

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme (Journal Article)

Mob. DNA, 7 (1), pp. 21, 2016.

(Abstract | Links | BibTeX)

2015

Upton, Kyle R; Gerhardt, Daniel J; Jesuadian, Samuel J; Richardson, Sandra R; Sánchez-Luque, Francisco J; Bodea, Gabriela O; Ewing, Adam D; Salvador-Palomeque, Carmen; van der Knaap, Marjo S; Brennan, Paul M; Vanderver, Adeline; Faulkner, Geoffrey J

Ubiquitous L1 mosaicism in hippocampal neurons (Journal Article)

Cell, 161 (2), pp. 228–239, 2015.

(Abstract | Links | BibTeX)

Arner, Erik; Daub, Carsten O; Vitting-Seerup, Kristoffer; Andersson, Robin; Lilje, Berit; ø, Finn Drabl; Lennartsson, Andreas; Rönnerblad, Michelle; Hrydziuszko, Olga; Vitezic, Morana; Freeman, Tom C; Alhendi, Ahmad M N; Arner, Peter; Axton, Richard; Baillie, Kenneth J; 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; Forrester, Lesley; Goldowitz, Daniel; Guler, Reto; Ha, Thomas; Hara, Mitsuko; Herlyn, Meenhard; Ikawa, Tomokatsu; Kai, Chieko; Kawamoto, Hiroshi; Khachigian, Levon M; Klinken, Peter S; Kojima, Soichi; Koseki, Haruhiko; Klein, Sarah; Mejhert, Niklas; Miyaguchi, Ken; Mizuno, Yosuke; Morimoto, Mitsuru; Morris, Kelly J; Mummery, Christine; Nakachi, Yutaka; Ogishima, Soichi; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Qin, Xian-Yang; Roy, Sugata; Sato, Hiroki; Savvi, Suzana; Saxena, Alka; Schwegmann, Anita; Sugiyama, Daisuke; Swoboda, Rolf; Tanaka, Hiroshi; Tomoiu, Andru; Winteringham, Louise N; Wolvetang, Ernst; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Zabierowski, Susan; Zhang, Peter; Abugessaisa, Imad; Bertin, Nicolas; Diehl, Alexander D; Fukuda, Shiro; Furuno, Masaaki; Harshbarger, Jayson; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Ishizu, Yuri; Itoh, Masayoshi; Kawashima, Tsugumi; Kojima, Miki; Kondo, Naoto; Lizio, Marina; Meehan, Terrence F; Mungall, Christopher J; Murata, Mitsuyoshi; Nishiyori-Sueki, Hiromi; Sahin, Serkan; Nagao-Sato, Sayaka; Severin, Jessica; de Hoon, Michiel J L; Kawai, Jun; Kasukawa, Takeya; Lassmann, Timo; Suzuki, Harukazu; Kawaji, Hideya; Summers, Kim M; Wells, Christine; Consortium, FANTOM; Hume, David A; Forrest, Alistair R R; Sandelin, Albin; Carninci, Piero; Hayashizaki, Yoshihide

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells (Journal Article)

Science, 347 (6225), pp. 1010–1014, 2015.

(Abstract | Links | BibTeX)

2014

Upton, Kyle R; Faulkner, Geoffrey J

Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis (Journal Article)

Mob. DNA, 5 , pp. 15, 2014.

(Abstract | Links | BibTeX)

Richardson, Sandra R; Salvador-Palomeque, Carmen; Faulkner, Geoffrey J

Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population (Journal Article)

Bioessays, 36 (5), pp. 475–481, 2014.

(Abstract | Links | BibTeX)

Consortium, {FANTOM; the PMI, RIKEN; (DGT)}, CLST; Forrest, Alistair R R; Kawaji, Hideya; ..., ; Faulkner, Geoffrey J; ..., ; Hume, David A; Carninci, Piero; Hayashizaki, Yoshihide

A promoter-level mammalian expression atlas (Journal Article)

Nature, 507 (7493), pp. 462-470, 2014.

(Abstract | Links | BibTeX | Altmetric)

Pascarella, Giovanni; Lazarevic, Dejan; Plessy, Charles; Bertin, Nicolas; Akalin, Altuna; Vlachouli, Christina; Simone, Roberto; Faulkner, Geoffrey J; Zucchelli, Silvia; Kawai, Jun; Daub, Carsten O; Hayashizaki, Yoshihide; Lenhard, Boris; Carninci, Piero; Gustincich, Stefano

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements (Journal Article)

Front. Cell. Neurosci., 8 , pp. 41, 2014.

(Abstract | Links | BibTeX)

Richardson, Sandra R; Morell, Santiago; Faulkner, Geoffrey J

L1 retrotransposons and somatic mosaicism in the brain (Journal Article)

Annu. Rev. Genet., 48 , pp. 1–27, 2014.

(Abstract | Links | BibTeX)

Carreira, Patricia E; Richardson, Sandra R; Faulkner, Geoffrey J

L1 retrotransposons, cancer stem cells and oncogenesis (Journal Article)

FEBS J., 281 (1), pp. 63–73, 2014.

(Abstract | Links | BibTeX)

2013

Faulkner, Geoffrey J

Retrotransposon silencing during embryogenesis: dicer cuts in LINE (Journal Article)

PLoS Genet., 9 (11), pp. e1003944, 2013.

(Links | BibTeX)

Reilly, Matthew T; Faulkner, Geoffrey J; Dubnau, Joshua; Ponomarev, Igor; Gage, Fred H

The role of transposable elements in health and diseases of the central nervous system (Journal Article)

J. Neurosci., 33 (45), pp. 17577–17586, 2013.

(Abstract | Links | BibTeX)

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; Perera, Ranjan J

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network (Journal Article)

Sci. Rep., 3 , pp. 2962, 2013.

(Abstract | Links | BibTeX)

Shukla, Ruchi; Upton, Kyle R; ~n, Martin Mu; Gerhardt, Daniel J; Fisher, Malcolm E; Nguyen, Thu; Brennan, Paul M; Baillie, Kenneth J; Collino, Agnese; Ghisletti, Serena; Sinha, Shruti; Iannelli, Fabio; Radaelli, Enrico; Santos, Alexandre Dos; Rapoud, Delphine; Guettier, Catherine; Samuel, Didier; Natoli, Gioacchino; Carninci, Piero; Ciccarelli, Francesca D; Garcia-Perez, Jose Luis; Faivre, Jamila; Faulkner, Geoffrey J

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma (Journal Article)

Cell, 153 (1), pp. 101–111, 2013.

(Abstract | Links | BibTeX)

2012

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; Jr, Haig Kazazian H

Extensive somatic L1 retrotransposition in colorectal tumors (Journal Article)

Genome Res., 22 (12), pp. 2328–2338, 2012.

(Abstract | Links | BibTeX)

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; Bujie, Zhan; Bystrom, Megan; Capitanu, Boris; Carvalho-Silva, Denise; Chardon, Patrick; Chen, Celine; Cheng, Ryan; Choi, Sang-Haeng; Chow, William; Clark, Richard C; Clee, Christopher; Crooijmans, Richard P M A; Dawson, Harry D; Dehais, Patrice; Sapio, Fioravante De; Dibbits, Bert; Drou, Nizar; Du, Zhi-Qiang; Eversole, Kellye; ~a, Jo; Fairley, Susan; Faraut, Thomas; Faulkner, Geoffrey J; Fowler, Katie E; Fredholm, Merete; Fritz, Eric; Gilbert, James G R; Giuffra, Elisabetta; Gorodkin, Jan; Griffin, Darren K; Harrow, Jennifer L; Hayward, Alexander; Howe, Kerstin; Hu, Zhi-Liang; Humphray, Sean J; Hunt, Toby; ø, Henrik Hornsh; Jeon, Jin-Tae; Jern, Patric; Jones, Matthew; Jurka, Jerzy; Kanamori, Hiroyuki; Kapetanovic, Ronan; Kim, Jaebum; Kim, Jae-Hwan; Kim, Kyu-Won; Kim, Tae-Hun; Larson, Greger; Lee, Kyooyeol; Lee, Kyung-Tai; Leggett, Richard; Lewin, Harris A; Li, Yingrui; Liu, Wansheng; Loveland, Jane E; Lu, Yao; Lunney, Joan K; Ma, Jian; Madsen, Ole; Mann, Katherine; Matthews, Lucy; McLaren, Stuart; Morozumi, Takeya; Murtaugh, Michael P; Narayan, Jitendra; Nguyen, Dinh Truong; Ni, Peixiang; Oh, Song-Jung; Onteru, Suneel; Panitz, Frank; Park, Eung-Woo; Park, Hong-Seog; Pascal, Geraldine; Paudel, Yogesh; Perez-Enciso, Miguel; Ramirez-Gonzalez, Ricardo; Reecy, James M; Rodriguez-Zas, Sandra; Rohrer, Gary A; Rund, Lauretta; Sang, Yongming; Schachtschneider, Kyle; Schraiber, Joshua G; Schwartz, John; Scobie, Linda; Scott, Carol; Searle, Stephen; Servin, Bertrand; Southey, Bruce R; Sperber, Goran; Stadler, Peter; Sweedler, Jonathan V; Tafer, Hakim; Thomsen, Bo; Wali, Rashmi; Wang, Jian; Wang, Jun; White, Simon; Xu, Xun; Yerle, Martine; Zhang, Guojie; Zhang, Jianguo; Zhang, Jie; Zhao, Shuhong; Rogers, Jane; Churcher, Carol; Schook, Lawrence B

Analyses of pig genomes provide insight into porcine demography and evolution (Journal Article)

Nature, 491 (7424), pp. 393–398, 2012.

(Abstract | Links | BibTeX)

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; Carninci, Piero

Promoter architecture of mouse olfactory receptor genes (Journal Article)

Genome Res., 22 (3), pp. 486–497, 2012.

(Abstract | Links | BibTeX)

Schroder, Kate; Irvine, Katharine M; Taylor, Martin S; Bokil, Nilesh J; Cao, Kim-Anh Le; 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; Sweet, Matthew J

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

Proc. Natl. Acad. Sci. U. S. A., 109 (16), pp. E944–53, 2012.

(Abstract | Links | BibTeX)

2011

Upton, Kyle R; Baillie, Kenneth J; Faulkner, Geoffrey J

Is somatic retrotransposition a parasitic or symbiotic phenomenon? (Journal Article)

Mob. Genet. Elements, 1 (4), pp. 279–282, 2011.

(Abstract | Links | BibTeX)

Baillie, Kenneth J; Barnett, Mark W; Upton, Kyle R; Gerhardt, Daniel J; Richmond, Todd A; Sapio, Fioravante De; 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; Faulkner, Geoffrey J

Somatic retrotransposition alters the genetic landscape of the human brain (Journal Article)

Nature, 479 (7374), pp. 534–537, 2011.

(Abstract | Links | BibTeX)

Faulkner, Geoffrey J

Retrotransposons: mobile and mutagenic from conception to death (Journal Article)

FEBS Lett., 585 (11), pp. 1589–1594, 2011.

(Abstract | Links | BibTeX)

2010

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; Hayashizaki, Yoshihide

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

Genome Res., 20 (2), pp. 257–264, 2010.

(Abstract | Links | BibTeX)

Mattick, John S; Taft, Ryan J; Faulkner, Geoffrey J

A global view of genomic information--moving beyond the gene and the master regulator (Journal Article)

Trends Genet., 26 (1), pp. 21–28, 2010.

(Abstract | Links | BibTeX)

2009

Faulkner, Geoffrey J; Grimmond, Sean M

Setting CAGE tags in a genomic context (Book Chapter)

Carninci, Piero (Ed.): Cap-Analysis Gene Expression (CAGE) - the Science of Decoding Genes Transcription, Chapter 8, pp. 93-100, 2009, ISBN: 9789814241342, (Accessed: 2017-11-24).

(Abstract | Links | BibTeX | Altmetric)

Cloonan, Nicole; Xu, Qinying; Faulkner, Geoffrey J; Taylor, Darrin F; Tang, Dave T P; Kolle, Gabriel; Grimmond, Sean M

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data (Journal Article)

Bioinformatics, 25 (19), pp. 2615–2616, 2009.

(Abstract | Links | BibTeX)

Hashimoto, Takehiro; de Hoon, Michiel J L; Grimmond, Sean M; Daub, Carsten O; Hayashizaki, Yoshihide; Faulkner, Geoffrey J

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite (Journal Article)

Bioinformatics, 25 (19), pp. 2613–2614, 2009.

(Abstract | Links | BibTeX)

Taft, Ryan J; Glazov, Evgeny A; Cloonan, Nicole; Simons, Cas; Stephen, Stuart; Faulkner, Geoffrey J; Lassmann, Timo; Forrest, Alistair R R; Grimmond, Sean M; Schroder, Kate; Irvine, Katharine; Arakawa, Takahiro; Nakamura, Mari; Kubosaki, Atsutaka; Hayashida, Kengo; Kawazu, Chika; Murata, Mitsuyoshi; Nishiyori, Hiromi; Fukuda, Shiro; Kawai, Jun; Daub, Carsten O; Hume, David A; Suzuki, Harukazu; Orlando, Valerio; Carninci, Piero; Hayashizaki, Yoshihide; Mattick, John S

Tiny RNAs associated with transcription start sites in animals (Journal Article)

Nat. Genet., 41 (5), pp. 572–578, 2009.

(Abstract | Links | BibTeX)

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; Carninci, Piero

The regulated retrotransposon transcriptome of mammalian cells (Journal Article)

Nat. Genet., 41 (5), pp. 563–571, 2009.

(Abstract | Links | BibTeX)

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