2013

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 MPA, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, et al.
British journal of cancer. Volume 108, (2013), p.450–460 doi:
The zebrafish reference genome sequence and its relationship to the human genome
Howe, K., Clark M. D., Torroja C. F., Torrance J., Berthelot C., Muffato M., Collins J. E., Humphray S., McLaren K., Matthews L., et al.
Nature. Apr, Volume 496, (2013), p.498–503 doi:
Enhanced susceptibility to Citrobacter rodentium infection in miR-155-deficient mice
Clare, S., John V., Walker A. W., Hill J. L., ABREU-GOODGER C., Hale C., Goulding D., Lawley T. D., Mastroeni P., Frankel G., et al.
Infection and Immunity. (2013), doi:
Kraken: A set of tools for quality control and analysis of high-throughput sequence data
Davis, Matthew, van Dongen Stijn, Abreu-Goodger Cei, Bartonicek Nenad, and Enright Anton J.
Methods. (2013), doi:
LIN28 expression in malignant germ cell tumors down-regulates let-7 and increases oncogene levels.
Murray, Matthew J., Saini Harpreet K., Siegler Charlotte A., Hanning Jennifer E., Barker Emily M., van Dongen Stijn, Ward Dawn M., Raby Katie L., Groves Ian J., Scarpini Cinzia G., et al.
Cancer research. Volume 73, Issue 14, (2013), doi: 10.1158/0008-5472.CAN-12-2085
Multiple Epigenetic Mechanisms and the piRNA Pathway Enforce LINE1 Silencing during Adult Spermatogenesis
Di Giacomo, Monica, Comazzetto Stefano, Saini Harpreet, De Fazio Serena, Carrieri Claudia, Morgan Marcos, Vasiliauskaite Lina, Benes Vladimir, Enright Anton J., and O’Carroll Dónal
Molecular cell. Volume 50, (2013), p.601–608 doi:
miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs
Lupini, Laura, Bassi Cristian, Ferracin Manuela, Bartonicek Nenad, D'Abundo Lucilla, Zagatti Barbara, Callegari Elisa, Musa Gentian, Moshiri Farzaneh, Gramantieri Laura, et al.
Frontiers in genetics. Volume 4, Issue 64, (2013), doi:

2012

A neuronal transcriptome response involving stress pathways is buffered by neuronal microRNAs
MANAKOV, S. A., Morton A., Enright A. J., and Grant S. G. N.
Frontiers in Neuroscience. Volume 6, (2012),
Metric distances derived from cosine similarity and Pearson and Spearman correlations
Van Dongen, S., and Enright A. J.
arXiv preprint arXiv:1208.3145. (2012),
Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines
Davis, M. P. A., ABREU-GOODGER C., Van Dongen S., Lu D., Tate P. H., BARTONICEK N., Kutter C., Liu P., Skarnes W. C., Enright A. J., et al.
PloS one. Volume 7, Number 8, (2012), p.e41762
MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs
Lu, D., Davis M. P. A., ABREU-GOODGER C., Wang W., Campos L. S., Siede J., Vigorito E., Skarnes W. C., Dunham I., Enright A. J., et al.
PloS one. Volume 7, Number 8, (2012), p.e40938
MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells
Selcuklu, S. D., Donoghue M. T. A., Rehmet K., de Souza Gomes M., Fort A., Kovvuru P., Muniyappa M. K., Kerin M. J., Enright A. J., and Spillane C.
Journal of Biological Chemistry. Volume 287, Number 35, (2012), p.29516–29528
Large-scale analysis of microRNA evolution
GUERRA-ASSUNÇÃO, J. A., and Enright A. J.
BMC genomics. Volume 13, Number 1, (2012), p.218
Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Parts, L., Hedman K., Keildson S., Knights A. J., ABREU-GOODGER C., van de Bunt M., GUERRA-ASSUNÇÃO J. A., BARTONICEK N., Van Dongen S., Mägi R., et al.
PLoS Genetics. Volume 8, Number 5, (2012), p.e1002704 doi:
Targeted Deletion of MicroRNA-22 Promotes Stress-Induced Cardiac Dilation and Contractile DysfunctionClinical Perspective
Gurha, P., ABREU-GOODGER C., Wang T., Ramirez M. O., Drumond A. L., Van Dongen S., Chen Y., BARTONICEK N., Enright A. J., Lee B., et al.
Circulation. Volume 125, Number 22, (2012), p.2751–2761

2011

MiR-221 Influences Effector Functions and Actin Cytoskeleton in Mast Cells
Mayoral, R. J., Deho L., Rusca N., BARTONICEK N., Saini H. K., Enright A. J., and Monticelli S.
PloS one. Volume 6, Number 10, (2011), p.e26133
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data
Hu, M., Ayub Q., GUERRA-ASSUNÇÃO J. A., Long Q., Ning Z., Huang N., Romero I. G., Mamanova L., Akan P., Liu X., et al.
Human Genetics. (2011), p.1–10
RNAcentral: A vision for an international database of RNA sequences
Bateman, A., Agrawal S., Birney E., Bruford E. A., Bujnicki J. M., Cochrane G., Cole J. R., Dinger M. E., Enright A. J., Gardner P. P., et al.
RNA. Volume 17, Number 11, (2011), p.1941–1946 doi:
Messenger RNA and microRNA profiling during early mouse EB formation
Tripathi, R., Saini H. K., Rad R., ABREU-GOODGER C., Van Dongen S., and Enright A. J.
Gene Expression Patterns. (2011),
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 A. J., and Vaidya T.
BMC evolutionary biology. Volume 11, Number 1, (2011), p.334
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 P. N., Enright A. J., and O’Carroll D.
Nature. (2011),

2010

SylArray: a web server for automated detection of miRNA effects from expression data
BARTONICEK, N., and Enright A. J.
Bioinformatics. Volume 26, Number 22, (2010), p.2900
iMotifs: an integrated sequence motif visualization and analysis environment
Piipari, M., Down T. A., Saini H., Enright A., and Hubbard T. J. P.
Bioinformatics. Volume 26, Number 6, (2010), p.843–844
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis
Sudbery, I., Enright A., Fraser A., and Dunham I.
BMC genomics. Volume 11, Number 1, (2010), p.175
Combined agonist–antagonist genome-wide functional screening identifies broadly active antiviral microRNAs
Santhakumar, D., Forster T., Laqtom N. N., Fragkoudis R., Dickinson P., ABREU-GOODGER C., MANAKOV S. A., Choudhury N. R., Griffiths S. J., Vermeulen A., et al.
Proceedings of the National Academy of Sciences. Volume 107, Number 31, (2010), p.13830–13835
Efficient inhibition of miR-155 function in vivo by peptide nucleic acids
Fabani, M. M., ABREU-GOODGER C., Williams D., Lyons P. A., Torres A. G., Smith K. G. C., Enright A. J., Gait M. J., and Vigorito E.
Nucleic acids research. Volume 38, Number 13, (2010), p.4466–4475
The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression
Murray, M. J., Saini H. K., Van Dongen S., Palmer R. D., Muralidhar B., Pett M. R., Piipari M., Thornton C. M., Nicholson J. C., Enright A. J., et al.
Molecular cancer. Volume 9, Number 1, (2010), p.290
Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets
Palmer, R. D., Murray M. J., Saini H. K., Van Dongen S., ABREU-GOODGER C., Muralidhar B., Pett M. R., Thornton C. M., Nicholson J. C., Enright A. J., et al.
Cancer research. Volume 70, Number 7, (2010), p.2911
The miR-144/451 locus is required for erythroid homeostasis
Rasmussen, K. D., Simmini S., ABREU-GOODGER C., BARTONICEK N., Di Giacomo M., Bilbao-Cortes D., Horos R., Von Lindern M., Enright A. J., and O’Carroll D.
The Journal of experimental medicine. Volume 207, Number 7, (2010), p.1351
MapMi: automated mapping of microRNA loci
Guerra-Assunção, J., and Enright A.
BMC bioinformatics. Volume 11, Number 1, (2010), p.133

2009

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice
Lewis, M. A., Quint E., Glazier A. M., Fuchs H., de Angelis M. H., Langford C., Van Dongen S., ABREU-GOODGER C., Piipari M., Redshaw N., et al.
Nature genetics. Volume 41, Number 5, (2009), p.614–618
Network visualization and analysis of gene expression data using BioLayout Express3D
Theocharidis, A., Van Dongen S., Enright A. J., and Freeman T. C.
Nature protocols. Volume 4, Number 10, (2009), p.1535–1550
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization
Mishima, Y., ABREU-GOODGER C., Staton A. A., Stahlhut C., Shou C., Cheng C., Gerstein M., Enright A. J., and Giraldez A. J.
Genes & development. Volume 23, Number 5, (2009), p.619
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Manakov, S., Grant S., and Enright A.
BMC genomics. Volume 10, Number 1, (2009), p.419

2008

miRBase: a database of microRNA sequences, targets and nomenclature
Enright, A. J., and Griffiths-Jones S.
MicroRNAs: from basic science to disease biology. (2008), p.157
A logic-based diagram of signalling pathways central to macrophage activation
Raza, S., Robertson K., Lacaze P., Page D., Enright A., Ghazal P., and Freeman T.
BMC systems biology. Volume 2, Number 1, (2008), p.36
Annotation of mammalian primary microRNAs
Saini, H., Enright A., and Griffiths-Jones S.
BMC genomics. Volume 9, Number 1, (2008), p.564
miRBase: tools for microRNA genomics
Griffiths-Jones, S., Saini H. K., Van Dongen S., and Enright A. J.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D154–D158
Computational prediction of protein–protein interactions
Skrabanek, L., Saini H. K., Bader G. D., and Enright A. J.
Molecular biotechnology. Volume 38, Number 1, (2008), p.1–17
Detecting microRNA binding and siRNA off-target effects from expression data
Van Dongen, S., ABREU-GOODGER C., and Enright A. J.
Nature methods. Volume 5, Number 12, (2008), p.1023–1025

2007

Construction, visualisation, and clustering of transcription networks from microarray expression data
Freeman, T. C., Goldovsky L., Brosch M., Van Dongen S., Mazière P., Grocock R. J., Freilich S., Thornton J., and Enright A. J.
PLoS computational biology. Volume 3, Number 10, (2007), p.e206
Denoising inferred functional association networks obtained by gene fusion analysis
Kamburov, A., Goldovsky L., Freilich S., Kapazoglou A., Kunin V., Enright A., Tsaftaris A., and Ouzounis C.
BMC genomics. Volume 8, Number 1, (2007), p.460
A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway
O’Carroll, D., Mecklenbrauker I., Das P. P., Santana A., Koenig U., Enright A. J., Miska E. A., and Tarakhovsky A.
Genes & development. Volume 21, Number 16, (2007), p.1999
Prediction of microRNA targets
Maziere, P., and Enright A. J.
Drug discovery today. Volume 12, Number 11-12, (2007), p.452–458
Genomic analysis of human microRNA transcripts
Saini, H. K., Griffiths-Jones S., and Enright A. J.
Proceedings of the National Academy of Sciences. Volume 104, Number 45, (2007), p.17719
microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells
Vigorito, E., Perks K. L., ABREU-GOODGER C., Bunting S., Xiang Z., Kohlhaas S., Das P. P., Miska E. A., Rodriguez A., Bradley A., et al.
Immunity. Volume 27, Number 6, (2007), p.847–859
Requirement of bic/microRNA-155 for normal immune function
Rodriguez, A., Vigorito E., Clare S., Warren M. V., Couttet P., Soond D. R., Van Dongen S., Grocock R. J., Das P. P., Miska E. A., et al.
Science. Volume 316, Number 5824, (2007), p.608

2006

miRBase: microRNA sequences, targets and gene nomenclature
Griffiths-Jones, S., Grocock R. J., Van Dongen S., Bateman A., and Enright A. J.
Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D140–D144 doi:
RNA editing of human microRNAs
Blow, M. J., Grocock R. J., Van Dongen S., Enright A. J., and others
Genome biology. Volume 7, Number 4, (2006), p.R27
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs
Giraldez, A. J., Mishima Y., Rihel J., Grocock R. J., Van Dongen S., Inoue K., Enright A. J., and Schier A. F.
Science. Volume 312, Number 5770, (2006), p.75

2005

MagicMatch—cross-referencing sequence identifiers across databases
Smith, M., Kunin V., Goldovsky L., Enright A. J., and Ouzounis C. A.
Bioinformatics. Volume 21, Number 16, (2005), p.3429–3430
CoGenT++: an extensive and extensible data environment for computational genomics
Goldovsky, L., Janssen P., Ahrén D., Audit B., Cases I., Darzentas N., Enright A. J., López-Bigas N., Peregrin-Alvarez J. M., Smith M., et al.
Bioinformatics. Volume 21, Number 19, (2005), p.3806
Intermolecular interactions and biological pathways
Bader, G. D., and Enright A. J.
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Third ed. Hoboken, New Jersey: John Wiley & Sons, Inc. Volume 254, (2005),
Computational Prediction of Protein-Protein Interactions
Enright, A. J., Skrabanek L., and Bader G. D.
The Proteomics Protocols Handbook. (2005), p.629–652 doi:
BioLayoutJava: versatile network visualisation of structural and functional relationships
Goldovsky, L., Cases I., Enright A. J., and Ouzounis C. A.
Applied bioinformatics. Volume 4, Number 1, (2005), p.71–74
MicroRNAs regulate brain morphogenesis in zebrafish
Giraldez, A. J., Cinalli R. M., Glasner M. E., Enright A. J., Thomson J. M., Baskerville S., Hammond S. M., Bartel D. P., and Schier A. F.
Science. Volume 308, Number 5723, (2005), p.833

2004

Identification of virus-encoded microRNAs
Pfeffer, S., Zavolan M., Grässer F. A., Chien M., Russo J. J., Ju J., John B., Enright A. J., Marks D., Sander C., et al.
Science. Volume 304, Number 5671, (2004), p.734
Human microRNA targets
John, B., Enright A. J., Aravin A., Tuschl T., Sander C., and Marks D. S.
PLoS biology. Volume 2, Number 11, (2004), p.e363
Detection of functional modules from protein interaction networks
Pereira-Leal, J. B., Enright A. J., and Ouzounis C. A.
PROTEINS: Structure, Function, and Bioinformatics. Volume 54, Number 1, (2004), p.49–57

2003

MicroRNA targets in Drosophila
Enright, A. J., John B., Gaul U., Tuschl T., Sander C., and Marks D. S.
Genome biology. Volume 5, Number 1, (2003), p.1–1
Classification schemes for protein structure and function
Ouzounis, C. A., COULSON R. M. R., Enright A. J., Kunin V., Pereira-Leal J. B., and others
Nature Reviews Genetics. Volume 4, Number 7, (2003), p.508–519
Evaluation of annotation strategies using an entire genome sequence
Iliopoulos, I., Tsoka S., Andrade M. A., Enright A. J., Carroll M., Poullet P., Promponas V., Liakopoulos T., Palaios G., Pasquier C., et al.
Bioinformatics. Volume 19, Number 6, (2003), p.717
Protein families and TRIBES in genome sequence space
Enright, A. J., Kunin V., and Ouzounis C. A.
Nucleic acids research. Volume 31, Number 15, (2003), p.4632
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
Janssen, P., Enright A. J., Audit B., Cases I., Goldovsky L., Harte N., Kunin V., and Ouzounis C. A.
Bioinformatics. Volume 19, Number 11, (2003), p.1451
Myriads of protein families, and still counting
Kunin, V., Cases I., Enright A. J., de Lorenzo V., and Ouzounis C. A.
Genome Biol. Volume 4, Number 2, (2003), p.401
Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis
Iliopoulos, I., Enright A. J., Poullet P., and Ouzounis C. A.
Comparative and functional genomics. Volume 4, Number 3, (2003), p.337–341

2002

Computational analysis of protein function within complete genomes
Enright, A. J.
(2002),
An efficient algorithm for large-scale detection of protein families
Enright, A. J., Van Dongen S., and Ouzounis C. A.
Nucleic acids research. Volume 30, Number 7, (2002), p.1575

2001

Transcription-associated protein families are primarily taxon-specific
COULSON, R. M. R., Enright A. J., and Ouzounis C. A.
Bioinformatics. Volume 17, Number 1, (2001), p.95–97
Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
Enright, A. J., Ouzounis C. A., and others
Genome Biol. Volume 2, Number 9, (2001), p.R34
Textquest: document clustering of Medline abstracts for concept discovery in molecular biology
Iliopoulos, I., Enright A. J., and Ouzounis C. A.
Pacific Symposium on Biocomputing. Volume 6, (2001), p.384–395
BioLayout—an automatic graph layout algorithm for similarity visualization
Enright, A. J., and Ouzounis C. A.
Bioinformatics. Volume 17, Number 9, (2001), p.853–854
A genome-wide survey of RS domain proteins.
Boucher, L., Ouzounis C. A., Enright A. J., and Blencowe B. J.
Rna. Volume 7, Number 12, (2001), p.1693–1701

2000

Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human
McLysaght, A., Enright A. J., Skrabanek L., and Wolfe K. H.
Yeast. Volume 17, Number 1, (2000), p.22–36
CAST: an iterative algorithm for the complexity analysis of sequence tracts
Promponas, V. J., Enright A. J., Tsoka S., Kreil D. P., Leroy C., Hamodrakas S., Sander C., and Ouzounis C. A.
Bioinformatics. Volume 16, Number 10, (2000), p.915
GeneRAGE: a robust algorithm for sequence clustering and domain detection
Enright, A. J., and Ouzounis C. A.
Bioinformatics. Volume 16, Number 5, (2000), p.451

1999

Protein interaction maps for complete genomes based on gene fusion events
Enright, A. J., Iliopoulos I., Kyrpides N. C., and Ouzounis C. A.
Nature. Volume 402, Number 6757, (1999), p.86–90