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EBIGroupsEnright GroupPublications

Enright Group : Publications


Researcher ID: F-3094-2011.


Google Scholar Citations

Publications from our Lab

Enright lab publications from 1999 to present. All publications are peer-reviewed unless marked otherwise. Enright lab members underlined.



A Wordle word cloud for the abstracts of all published papers below

Words are stemmed and filtered with a stoplist of common english words.


Publications By Year


[2011] [2010] [2009] [2008] [2007] [2006] [2005] [2004] [2003] [2002] [2001] [2000] [1999] 

2011

Tripathi R., Saini HK., Rad R., Abreu-Goodger C., van Dongen S., Enright AJ. (2011)
Messenger RNA and microRNA profiling during early mouse EB formation.
Gene Expr Patterns 11(5-6): 334-44
pubmed full-text PDF

Manakov SA., Morton A., Enright AJ., Grant SGN. (2011)
A neuronal transcriptome response involving stress pathways is buffered by neuronal microRNAs.
Submitted


Guerra-Assuncao JA., Enright AJ. (2011)
Large-scale analysis of microRNA evolution.
Submitted


Puri V., Goyal A., Sankaranarayanan R., Enright AJ., Vaidya T. (2011)
Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.
BMC Evolutionary Biology (In Press)


Mayoral RJ., Deho L., Rusca N., Bartonicek N., Saini HK., Enright AJ., Monticelli S. (2011)
MiR-221 Influences Effector Functions and Actin Cytoskeleton in Mast Cells.
PLoS One 6(10): e26133
pubmed full-text PDF

Hu M., Ayub Q., Guerra-Assuncao 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. (2011)
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Hum Genet :
pubmed full-text PDF

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

Gurha P., Abreu-Goodger C., Ramirez MO., Drumond AL., van Dongen S., Chen Y., Bartonicek N., Chen C., Kelm RJ., Enright AJ., Lee B., Taffet GE., Bradley A., Entman ML., Rodriguez A. (2011)
microRNA-22 is required for adaptive cardiac remodeling and compensation to hemodynamic stress in mice.
Submitted


Keane TM., Goodstadt L., Danecek P., White MA., Wong K., Yalcin B., Heger A., Agam A., Slater G., Goodson M., Furlotte NA., Eskin E., Nellaker C., Whitley H., Cleak J., Janowitz D., Hernandez-Pliego P., Edwards A., Belgard TG., Oliver PL., McIntyre RE., Bhomra A., Nicod J., Gan X., Yuan W., van der Weyden L., Steward CA., Bala S., Stalker J., Mott R., Durbin R., Jackson IJ., Czechanski A., Guerra-Assuncao JA., Donahue LR., Reinholdt LG., Payseur BA., Ponting CP., Birney E., Flint J., Adams DJ. (2011)
Mouse genomic variation and its effect on phenotypes and gene regulation.
Nature 477(7364): 289-94
pubmed full-text PDF

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. (2011)
RNAcentral: A vision for an international database of RNA sequences.
RNA 17(11): 1941-6
pubmed full-text PDF

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2010

Sudbery I., Enright AJ., Fraser AG., Dunham I. (2010)
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
BMC Genomics 11: 175
pubmed full-text PDF

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

Bartonicek N., Enright AJ. (2010)
SylArray: a web server for automated detection of miRNA effects from expression data.
Bioinformatics 26(22): 2900-1
pubmed full-text PDF

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. (2010)
The miR-144/451 locus is required for erythroid homeostasis.
J Exp Med 207(7): 1351-8
pubmed full-text PDF

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. (2010)
Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.
Proc Natl Acad Sci U S A 107(31): 13830-5
pubmed full-text PDF

Guerra-Assuncao JA., Enright AJ. (2010)
MapMi: automated mapping of microRNA loci.
BMC Bioinformatics 11: 133
pubmed full-text PDF

Piipari M., Down TA., Saini H., Enright A., Hubbard TJ. (2010)
iMotifs: an integrated sequence motif visualization and analysis environment.
Bioinformatics 26(6): 843-4
pubmed full-text PDF

Palmer RD., Murray MJ., Saini HK., van Dongen S., Abreu-Goodger C., Muralidhar B., Pett MR., Thornton CM., Nicholson JC., Enright AJ., Coleman N. (2010)
Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.
Cancer Res 70(7): 2911-23
pubmed full-text PDF

Fabani MM., Abreu-Goodger C., Williams D., Lyons PA., Torres AG., Smith KG., Enright AJ., Gait MJ., Vigorito E. (2010)
Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.
Nucleic Acids Res 38(13): 4466-75
pubmed full-text PDF

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2009

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. (2009)
An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.
Nat Genet 41(5): 614-8
pubmed full-text PDF

Theocharidis A., van Dongen S., Enright AJ., Freeman TC. (2009)
Network visualization and analysis of gene expression data using BioLayout Express(3D).
Nat Protoc 4(10): 1535-50
pubmed full-text PDF

Mishima Y., Abreu-Goodger C., Staton AA., Stahlhut C., Shou C., Cheng C., Gerstein M., Enright AJ., Giraldez AJ. (2009)
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Genes Dev 23(5): 619-32
pubmed full-text PDF

Manakov SA., Grant SG., Enright AJ. (2009)
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
BMC Genomics 10: 419
pubmed full-text PDF

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2008

Skrabanek L., Saini HK., Bader GD., Enright AJ. (2008)
Computational prediction of protein-protein interactions.
Mol Biotechnol 38(1): 1-17
pubmed full-text PDF

Saini HK., Enright AJ., Griffiths-Jones S. (2008)
Annotation of mammalian primary microRNAs.
BMC Genomics 9: 564
pubmed full-text PDF

Griffiths-Jones S., Saini HK., van Dongen S., Enright AJ. (2008)
miRBase: tools for microRNA genomics.
Nucleic Acids Res 36(Database issue): D154-8
pubmed full-text PDF

van Dongen S. (2008)
Graph Clustering Via a Discrete Uncoupling Process.
SIAM Journal on Matrix Analysis and Applications 30(1):121-141
full-text PDF

Raza S., Robertson KA., Lacaze PA., Page D., Enright AJ., Ghazal P., Freeman TC. (2008)
A logic-based diagram of signalling pathways central to macrophage activation.
BMC Syst Biol 2: 36
pubmed full-text PDF

van Dongen S., Abreu-Goodger C., Enright AJ. (2008)
Detecting microRNA binding and siRNA off-target effects from expression data.
Nat Methods 5(12): 1023-5
pubmed full-text PDF

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2007

Freeman TC., Goldovsky L., Brosch M., van Dongen S., Maziere P., Grocock RJ., Freilich S., Thornton J., Enright AJ. (2007)
Construction, visualisation, and clustering of transcription networks from microarray expression data.
PLoS Comput Biol 3(10): 2032-42
pubmed full-text PDF

Rodriguez A., Vigorito E., Clare S., Warren MV., Couttet P., Soond DR., van Dongen S., Grocock RJ., Das PP., Miska EA., Vetrie D., Okkenhaug K., Enright AJ., Dougan G., Turner M., Bradley A. (2007)
Requirement of bic/microRNA-155 for normal immune function.
Science 316(5824): 608-11
pubmed full-text PDF

O'Carroll D., Mecklenbrauker I., Das PP., Santana A., Koenig U., Enright AJ., Miska EA., Tarakhovsky A. (2007)
A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway.
Genes Dev 21(16): 1999-2004
pubmed full-text PDF

Kamburov A., Goldovsky L., Freilich S., Kapazoglou A., Kunin V., Enright AJ., Tsaftaris A., Ouzounis CA. (2007)
Denoising inferred functional association networks obtained by gene fusion analysis.
BMC Genomics 8: 460
pubmed full-text PDF

Saini HK., Griffiths-Jones S., Enright AJ. (2007)
Genomic analysis of human microRNA transcripts.
Proc Natl Acad Sci U S A 104(45): 17719-24
pubmed full-text PDF

Maziere P., Enright AJ. (2007)
Prediction of microRNA targets.
Drug Discov Today 12(11-12): 452-8
pubmed full-text PDF

Vigorito E., Perks KL., Abreu-Goodger C., Bunting S., Xiang Z., Kohlhaas S., Das PP., Miska EA., Rodriguez A., Bradley A., Smith KG., Rada C., Enright AJ., Toellner KM., Maclennan IC., Turner M. (2007)
microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells.
Immunity 27(6): 847-59
pubmed full-text PDF

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2006

Enright AJ., Griffiths-Jones S. (2006)
miRBase: A database of miRNA Sequences, Targets and Nomenclature
microRNAs: From Basic Science to Disease Biology (Cambridge University Press) pp 323-335
ISBN:9780521865982

Giraldez AJ., Mishima Y., Rihel J., Grocock RJ., Van Dongen S., Inoue K., Enright AJ., Schier AF. (2006)
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.
Science 312(5770): 75-9
pubmed full-text PDF

Enright AJ. (2006)
Computational Prediction of miRNA Targets
MicroRNA: Biology, Function & Expression (DNA Press)
ISBN:1933255196

Griffiths-Jones S., Grocock RJ., van Dongen S., Bateman A., Enright AJ. (2006)
miRBase: microRNA sequences, targets and gene nomenclature.
Nucleic Acids Res 34(Database issue): D140-4
pubmed full-text PDF

Blow MJ., Grocock RJ., van Dongen S., Enright AJ., Dicks E., Futreal PA., Wooster R., Stratton MR. (2006)
RNA editing of human microRNAs.
Genome Biol 7(4): R27
pubmed full-text PDF

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2005

Enright AJ., Ouzounis CA. (2005)
Computational Detection of Genome-wide Protein Interaction
Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition (CSHL Press)
ISBN:0879697237

Goldovsky L., Janssen P., Ahren D., Audit B., Cases I., Darzentas N., Enright AJ., Lopez-Bigas N., Peregrin-Alvarez JM., Smith M., Tsoka S., Kunin V., Ouzounis CA. (2005)
CoGenT++: an extensive and extensible data environment for computational genomics.
Bioinformatics 21(19): 3806-10
pubmed full-text PDF

Smith M., Kunin V., Goldovsky L., Enright AJ., Ouzounis CA. (2005)
MagicMatch - cross-referencing sequence identifiers across databases.
Bioinformatics 21(16): 3429-30
pubmed full-text PDF

Giraldez AJ., Cinalli RM., Glasner ME., Enright AJ., Thomson JM., Baskerville S., Hammond SM., Bartel DP., Schier AF. (2005)
MicroRNAs regulate brain morphogenesis in zebrafish.
Science 308(5723): 833-8
pubmed full-text PDF

Goldovsky L., Cases I., Enright AJ., Ouzounis CA. (2005)
BioLayout(Java): versatile network visualisation of structural and functional relationships.
Appl Bioinformatics 4(1): 71-4
pubmed full-text PDF

Enright AJ., Skrabanek L., Bader GD. (2005)
Computational Prediction of Protein-Protein Interactions
The Proteomics Protocols Handbook (Humana Press)
ISBN:9781588295934

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2004

Pereira-Leal JB., Enright AJ., Ouzounis CA. (2004)
Detection of functional modules from protein interaction networks.
Proteins 54(1): 49-57
pubmed full-text PDF

John B., Enright AJ., Aravin A., Tuschl T., Sander C., Marks DS. (2004)
Human MicroRNA targets.
PLoS Biol 2(11): e363
pubmed full-text PDF

Bader GD., Enright AJ. (2004)
Biomolecular Interactions and Biological Pathways
Bioinformatics: A Practical Guide to the analysis of Genes and Proteins , 3rd Edition (Wiley Press) pp 253-295
ISBN: 0471478784

Pfeffer S., Zavolan M., Grasser FA., Chien M., Russo JJ., Ju J., John B., Enright AJ., Marks D., Sander C., Tuschl T. (2004)
Identification of virus-encoded microRNAs.
Science 304(5671): 734-6
pubmed full-text PDF

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2003

Iliopoulos I., Tsoka S., Andrade MA., Enright AJ., Carroll M., Poullet P., Promponas V., Liakopoulos T., Palaios G., Pasquier C., Hamodrakas S., Tamames J., Yagnik AT., Tramontano A., Devos D., Blaschke C., Valencia A., Brett D., Martin D., Leroy C., Rigoutsos I., Sander C., Ouzounis CA. (2003)
Evaluation of annotation strategies using an entire genome sequence.
Bioinformatics 19(6): 717-26
pubmed full-text PDF

Ouzounis CA., Coulson RM., Enright AJ., Kunin V., Pereira-Leal JB. (2003)
Classification schemes for protein structure and function.
Nat Rev Genet 4(7): 508-19
pubmed full-text PDF

Kunin V., Cases I., Enright AJ., de Lorenzo V., Ouzounis CA. (2003)
Myriads of protein families, and still counting.
Genome Biol 4(2): 401
pubmed full-text PDF

Enright AJ., John B., Gaul U., Tuschl T., Sander C., Marks DS. (2003)
MicroRNA targets in Drosophila.
Genome Biol 5(1): R1
pubmed full-text PDF

Janssen P., Enright AJ., Audit B., Cases I., Goldovsky L., Harte N., Kunin V., Ouzounis CA. (2003)
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics.
Bioinformatics 19(11): 1451-2
pubmed full-text PDF

Iliopoulos I., Enright AJ., Poullet P., Ouzounis CA. (2003)
Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis.
Comp Funct Genomics 4(3): 337-41
pubmed full-text PDF

Enright AJ., Kunin V., Ouzounis CA. (2003)
Protein families and TRIBES in genome sequence space.
Nucleic Acids Res 31(15): 4632-8
pubmed full-text PDF

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2002

Enright AJ., Van Dongen S., Ouzounis CA. (2002)
An efficient algorithm for large-scale detection of protein families.
Nucleic Acids Res 30(7): 1575-84
pubmed full-text PDF

Enright AJ., Ouzounis CA. (2002)
Computational Detection of Genome-wide Protein Interaction
Protein-Protein Interactions: A Molecular Cloning Manual (CSHL Press)
ISBN:0879696281

Enright AJ. (2002)
Computational Analysis of Protein Function in Complete Genomes
Ph.D. Thesis (University of Cambridge)
full-text PDF

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2001

Boucher L., Ouzounis CA., Enright AJ., Blencowe BJ. (2001)
A genome-wide survey of RS domain proteins.
RNA 7(12): 1693-701
pubmed full-text PDF

Enright AJ., Ouzounis CA. (2001)
Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions.
Genome Biol 2(9): RESEARCH0034
pubmed full-text PDF

Coulson RM., Enright AJ., Ouzounis CA. (2001)
Transcription-associated protein families are primarily taxon-specific.
Bioinformatics 17(1): 95-7
pubmed full-text PDF

Enright AJ., Ouzounis CA. (2001)
BioLayout - an automatic graph layout algorithm for similarity visualization.
Bioinformatics 17(9): 853-4
pubmed full-text PDF

Iliopoulos I., Enright AJ., Ouzounis CA. (2001)
Textquest: document clustering of Medline abstracts for concept discovery in molecular biology.
Pac Symp Biocomput : 384-95
pubmed full-text PDF

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2000

Enright AJ., Ouzounis CA. (2000)
GeneRAGE: a robust algorithm for sequence clustering and domain detection.
Bioinformatics 16(5): 451-7
pubmed full-text PDF

McLysaght A., Enright AJ., Skrabanek L., Wolfe KH. (2000)
Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.
Yeast 17(1): 22-36
pubmed full-text PDF

Promponas VJ., Enright AJ., Tsoka S., Kreil DP., Leroy C., Hamodrakas S., Sander C., Ouzounis CA. (2000)
CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts.
Bioinformatics 16(10): 915-22
pubmed full-text PDF

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1999

Enright AJ., Iliopoulos I., Kyrpides NC., Ouzounis CA. (1999)
Protein interaction maps for complete genomes based on gene fusion events.
Nature 402(6757): 86-90
pubmed full-text PDF

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