Publications

2016

Improved definition of the mouse transcriptome via targeted RNA sequencing.
Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ.
Genome research Volume 26 (2016) p.705-716

Focus on Extracellular Vesicles: Physiological Role and Signalling Properties of Extracellular Membrane Vesicles.
Iraci N, Leonardi T, Gessler F, Vega B, Pluchino S.
International journal of molecular sciences Volume 17 (2016) p.171

2015

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.
GigaScience Volume 4 (2015) p.38

Solid tumors of childhood display specific serum microRNA profiles.
Murray MJ, Raby KL, Saini HK, Bailey S, Wool SV, Tunnacliffe JM, Enright AJ, Nicholson JC, Coleman N.
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Volume 24 (2015) p.350-360

Acellular approaches for regenerative medicine: on the verge of clinical trials with extracellular membrane vesicles?
Fuster-Matanzo A, Gessler F, Leonardi T, Iraci N, Pluchino S.
Stem cell research & therapy Volume 6 (2015) p.227

Applying extracellular vesicles based therapeutics in clinical trials - an ISEV position paper.
Lener T, Gimona M, Aigner L, Börger V, Buzas E, Camussi G, Chaput N, Chatterjee D, Court FA, Del Portillo HA, O'Driscoll L, Fais S, Falcon-Perez JM, Felderhoff-Mueser U, Fraile L, Gho YS, Görgens A, Gupta RC, Hendrix A, Hermann DM, Hill AF, Hochberg F, Horn PA, de Kleijn D, Kordelas L, Kramer BW, Krämer-Albers EM, Laner-Plamberger S, Laitinen S, Leonardi T, Lorenowicz MJ, Lim SK, Lötvall J, Maguire CA, Marcilla A, Nazarenko I, Ochiya T, Patel T, Pedersen S, Pocsfalvi G, Pluchino S, Quesenberry P, Reischl IG, Rivera FJ, Sanzenbacher R, Schallmoser K, Slaper-Cortenbach I, Strunk D, Tonn T, Vader P, van Balkom BW, Wauben M, Andaloussi SE, Théry C, Rohde E, Giebel B.
Journal of extracellular vesicles Volume 4 (2015) p.30087

Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases.
Smith JA, Leonardi T, Huang B, Iraci N, Vega B, Pluchino S.
Biogerontology Volume 16 (2015) p.147-185

Chimira: analysis of small RNA sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics (Oxford, England) Volume 31 (2015) p.3365-3367

High-density P300 enhancers control cell state transitions.
Witte S, Bradley A, Enright AJ, Muljo SA.
BMC genomics Volume 16 (2015) p.903

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME.
Nature methods Volume 12 (2015) p.339-342

2014

Serum levels of mature microRNAs in DICER1-mutated pleuropulmonary blastoma.
Murray MJ, Bailey S, Raby KL, Saini HK, de Kock L, Burke GA, Foulkes WD, Enright AJ, Coleman N, Tischkowitz M.
Oncogenesis Volume 3 (2014) p.e87

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.
Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J.
Molecular cancer Volume 13 (2014) p.28

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.
Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S.
Molecular cell Volume 56 (2014) p.193-204

Visualisation of BioPAX Networks using BioLayout Express (3D).
Wright DW, Angus T, Enright AJ, Freeman TC.
F1000Research Volume 3 (2014) p.246

2013

Detecting and comparing non-coding RNAs in the high-throughput era.
Bussotti G, Notredame C, Enright AJ.
International journal of molecular sciences Volume 14 (2013) p.15423-15458

Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state.
Hanning JE, Saini HK, Murray MJ, Caffarel MM, van Dongen S, Ward D, Barker EM, Scarpini CG, Groves IJ, Stanley MA, Enright AJ, Pett MR, Coleman N.
The Journal of pathology Volume 231 (2013) p.354-366

Enhanced susceptibility to Citrobacter rodentium infection in microRNA-155-deficient mice.
Clare S, John V, Walker AW, Hill JL, Abreu-Goodger C, Hale C, Goulding D, Lawley TD, Mastroeni P, Frankel G, Enright AJ, Vigorito E, Dougan G.
Infection and immunity Volume 81 (2013) p.723-732

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ.
Methods (San Diego, Calif.) Volume 63 (2013) p.41-49

LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.
Murray MJ, Saini HK, Siegler CA, Hanning JE, Barker EM, van Dongen S, Ward DM, Raby KL, Groves IJ, Scarpini CG, Pett MR, Thornton CM, Enright AJ, Nicholson JC, Coleman N, CCLG.
Cancer research Volume 73 (2013) p.4872-4884

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics.
Hill AF, Pegtel DM, Lambertz U, Leonardi T, O'Driscoll L, Pluchino S, Ter-Ovanesyan D, Nolte-'t Hoen EN.
Journal of extracellular vesicles Volume 2 (2013) p.

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D.
Molecular cell Volume 50 (2013) p.601-608

The zebrafish reference genome sequence and its relationship to the human genome.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett JC, Koch R, Rauch GJ, White S, Chow W, Kilian B, Quintais LT, Guerra-Assunção JA, Zhou Y, Gu Y, Yen J, Vogel JH, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire SF, Laird GK, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliot D, Eliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Mortimer B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley CM, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster SC, Carter NP, Harrow J, Ning Z, Herrero J, Searle SM, Enright A, Geisler R, Plasterk RH, Lee C, Westerfield M, de Jong PJ, Zon LI, Postlethwait JH, Nüsslein-Volhard C, Hubbard TJ, Roest Crollius H, Rogers J, Stemple DL.
Nature Volume 496 (2013) p.498-503

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene.
Hanning JE, Saini HK, Murray MJ, van Dongen S, Davis MP, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, Coleman N.
British journal of cancer Volume 108 (2013) p.450-460

miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs.
Lupini L, Bassi C, Ferracin M, Bartonicek N, D'Abundo L, Zagatti B, Callegari E, Musa G, Moshiri F, Gramantieri L, Corrales FJ, Enright AJ, Sabbioni S, Negrini M.
Frontiers in genetics Volume 4 (2013) p.64

2012

Large-scale analysis of microRNA evolution.
Guerra-Assunção JA, Enright AJ.
BMC genomics Volume 13 (2012) p.218

A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs.
Manakov SA, Morton A, Enright AJ, Grant SG.
Frontiers in neuroscience Volume 6 (2012) p.156

Targeted deletion of microRNA-22 promotes stress-induced cardiac dilation and contractile dysfunction.
Gurha P, Abreu-Goodger C, Wang T, Ramirez MO, Drumond AL, van Dongen S, Chen Y, Bartonicek N, Enright AJ, Lee B, Kelm RJ, Reddy AK, Taffet GE, Bradley A, Wehrens XH, Entman ML, Rodriguez A.
Circulation Volume 125 (2012) p.2751-2761

MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs.
Lu D, Davis MP, Abreu-Goodger C, Wang W, Campos LS, Siede J, Vigorito E, Skarnes WC, Dunham I, Enright AJ, Liu P.
PloS one Volume 7 (2012) p.e40938

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Davis MP, Abreu-Goodger C, van Dongen S, Lu D, Tate PH, Bartonicek N, Kutter C, Liu P, Skarnes WC, Enright AJ, Dunham I.
PloS one Volume 7 (2012) p.e41762

Extracellular membrane vesicles and immune regulation in the brain.
Cossetti C, Smith JA, Iraci N, Leonardi T, Alfaro-Cervello C, Pluchino S.
Frontiers in physiology Volume 3 (2012) p.117

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y.
Human genetics Volume 131 (2012) p.665-674

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.
Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C.
The Journal of biological chemistry Volume 287 (2012) p.29516-29528

Extent, causes, and consequences of small RNA expression variation in human adipose tissue.
Parts L, Hedman ÅK, Keildson S, Knights AJ, Abreu-Goodger C, van de Bunt M, Guerra-Assunção JA, Bartonicek N, van Dongen S, Mägi R, Nisbet J, Barrett A, Rantalainen M, Nica AC, Quail MA, Small KS, Glass D, Enright AJ, Winn J, MuTHER Consortium, Deloukas P, Dermitzakis ET, McCarthy MI, Spector TD, Durbin R, Lindgren CM.
PLoS genetics Volume 8 (2012) p.e1002704

2011

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.
De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D.
Nature Volume 480 (2011) p.259-263

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.
Puri V, Goyal A, Sankaranarayanan R, Enright AJ, Vaidya T.
BMC evolutionary biology Volume 11 (2011) p.334

MiR-221 influences effector functions and actin cytoskeleton in mast cells.
Mayoral RJ, Deho L, Rusca N, Bartonicek N, Saini HK, Enright AJ, Monticelli S.
PloS one Volume 6 (2011) p.e26133

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA (New York, N.Y.) Volume 17 (2011) p.1941-1946

Messenger RNA and microRNA profiling during early mouse EB formation.
Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S, Enright AJ.
Gene expression patterns : GEP Volume 11 (2011) p.334-344

2010

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression.
Murray MJ, Saini HK, van Dongen S, Palmer RD, Muralidhar B, Pett MR, Piipari M, Thornton CM, Nicholson JC, Enright AJ, Coleman N.
Molecular cancer Volume 9 (2010) p.290

iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M, Down TA, Saini H, Enright A, Hubbard TJ.
Bioinformatics (Oxford, England) Volume 26 (2010) p.843-844

SylArray: a web server for automated detection of miRNA effects from expression data.
Bartonicek N, Enright AJ.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2900-2901

The miR-144/451 locus is required for erythroid homeostasis.
Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D.
The Journal of experimental medicine Volume 207 (2010) p.1351-1358

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.
Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KG, Enright AJ, Gait MJ, Vigorito E.
Nucleic acids research Volume 38 (2010) p.4466-4475

MapMi: automated mapping of microRNA loci.
Guerra-Assunção JA, Enright AJ.
BMC bioinformatics Volume 11 (2010) p.133

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
Sudbery I, Enright AJ, Fraser AG, Dunham I.
BMC genomics Volume 11 (2010) p.175

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.
Santhakumar D, Forster T, Laqtom NN, Fragkoudis R, Dickinson P, Abreu-Goodger C, Manakov SA, Choudhury NR, Griffiths SJ, Vermeulen A, Enright AJ, Dutia B, Kohl A, Ghazal P, Buck AH.
Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.13830-13835

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.
Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C, Muralidhar B, Pett MR, Thornton CM, Nicholson JC, Enright AJ, Coleman N, Children's Cancer and Leukaemia Group.
Cancer research Volume 70 (2010) p.2911-2923

2009

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ.
Genes & development Volume 23 (2009) p.619-632

Network visualization and analysis of gene expression data using BioLayout Express(3D).
Theocharidis A, van Dongen S, Enright AJ, Freeman TC.
Nature protocols Volume 4 (2009) p.1535-1550

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
Manakov SA, Grant SG, Enright AJ.
BMC genomics Volume 10 (2009) p.419

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.
Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP.
Nature genetics Volume 41 (2009) p.614-618

2008

A logic-based diagram of signalling pathways central to macrophage activation.
Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC.
BMC systems biology Volume 2 (2008) p.36

Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S.
BMC genomics Volume 9 (2008) p.564

Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ.
Molecular biotechnology Volume 38 (2008) p.1-17

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic acids research Volume 36 (2008) p.D154-8

Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ.
Nature methods Volume 5 (2008) p.1023-1025

Fusion and fission of genes define a metric between fungal genomes.
Durrens P, Nikolski M, Sherman D.
PLoS computational biology Volume 4 (2008) p.e1000200

0

Metric distances derived from cosine similarity and Pearson and Spearman correlations
van Dongen S, Enright AJ.
Volume (0) p.