Biography

Geoff FaulknerI am a computational and molecular biologist with research interests in transposable elements, single-cell genomics and neuroscience. In 2009, I published a first-author Nature Genetics paper describing the transcriptional activity and domestication of mammalian repetitive elements (>500 citations). In the same year, I finished a PhD at the University of Queensland, and was awarded an NHMRC C.J. Martin Fellowship to undertake postdoctoral work at the University of Edinburgh. Whilst in Edinburgh I published Baillie et al. (Nature, 2011). Fulfilling the terms of the C.J. Martin Fellowship, I established my group to the Mater Research Institute – University of Queensland (MRI-UQ) in 2012. I subsequently obtained grant funding from the NIH and NHMRC, including an NHMRC Career Development Fellowship, and published Shukla et al. (Cell, 2013) and Upton et al. (Cell, 2015). I was awarded an NHMRC Research Fellowship (SRFB) in 2016 and a prestigious CSL Centenary Fellowship in 2017. I was promoted to full Professor (Level E) by the University of Queensland in 2016.

To date, I have published 52 peer-reviewed articles, book chapters and reviews (>11,000 citations, h-index 32). 24 of these are as first or last author, including Faulkner et al. (Nature Genetics, 2009), as well as other work published in Nature, Science, Cell, AJHG, NAR, Nature Communications, PNAS, Nature Genetics, Nature Methods, Genome Biology and Genome Research. I have published 3 landmark papers in Nature and Cell as last and sole corresponding author. These papers significantly advanced the somatic L1 mosaicism field. I have written 11 invited reviews, including works in Genome Biology, The Journal of Neuroscience, Annual Reviews GeneticsPLoS Genetics, Trends in Genetics and BioEssays.

I have enjoyed continuous NHMRC fellowship support since 2009 (C.J. Martin 2009-2013; CDF1 2013-2015; SRFB 2016-2020). Baillie et al. (Nature, 2011) was named by the US National Institute of Mental Health as the “No. 1 research advance of 2011”. Baillie et al. (Nature, 2011), Shukla et al. (Cell, 2013) and Upton et al. (Cell, 2015) were highlighted by Faculty of 1000. I am the recipient of the ASMR Queensland Premier’s Award (2009), the FEBS Anniversary Prize (2011) awarded to “the top molecular geneticist in Europe aged <40yrs”, the Lorne Genome Millennium Science Award (2014) for “outstanding contributions to Australian scientific research”, the Centenary Institute Lawrence Creative Prize (2014) “awarded for creative biomedical research excellence”, the Ruth Stephens Gani Medal by the Australian Academy of Science (2016), the Scopus Eureka Prize for Excellence in International Scientific Collaboration (2016) and a CSL Centenary Fellowship (2017).

 


Qualifications:

PhD, University of Queensland, 2009

BSc (First Class Honours), University of Queensland, 2004

 


Research Links:


Publications:

64 entries « 1 of 2 »

2020

Ewing, Adam D; Smits, Nathan; Sanchez-Luque, Francisco J; Faivre, Jamila; Brennan, Paul M; Richardson, Sandra R; Cheetham, Seth W; Faulkner, Geoffrey J

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling (Journal Article)

Molecular Cell, 2020, ISSN: 1097-2765.

(Abstract | Links | BibTeX | Altmetric)

Cheetham, Seth W; Faulkner, Geoffrey J; Dinger, Marcel E

Overcoming challenges and dogmas to understand the functions of pseudogenes (Journal Article)

Nature Reviews Genetics, 21 (3), pp. 191–201, 2020, ISSN: 1471-0064, (Number: 3 Publisher: Nature Publishing Group).

(Abstract | Links | BibTeX | Altmetric)

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.

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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.

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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)

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