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Sam Griffiths-Jones

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Publications

TOP 3
Jerome H L Hui; Suzanne Hunt; Antonio Marco; Janet Melling; Sam Griffiths-Jones; Matthew Ronshaugen
Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods.
Antonio Marco; Katarzyna Hooks; Sam Griffiths-Jones
Evolution and function of the extended miR-2 microRNA family.
Antonio Marco; Sam Griffiths-Jones
Detection of microRNAs in color space.

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All Publications

2013: Jerome H L Hui; Suzanne Hunt; Antonio Marco; Janet Melling; Sam Griffiths-Jones; Matthew Ronshaugen
Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods.
Nucleic acids research 2013;41(5):3352-61.
2012: Antonio Marco; Katarzyna Hooks; Sam Griffiths-Jones
Evolution and function of the extended miR-2 microRNA family.
RNA biology 2012;9(3):242-8.
2012: Antonio Marco; Sam Griffiths-Jones
Detection of microRNAs in color space.
Bioinformatics (Oxford, England) 2012;28(3):318-23.
2012: Antonio Marco; Matthew Ronshaugen; Jamie I Macpherson; Sam Griffiths-Jones
MicroRNAs from the same precursor have different targeting properties.
Silence 2012;3(1):8.
2012: Karim Sorefan; Sam Griffiths-Jones; Adam E Hall; Ana Kozomara; Vincent Moulton; Helio Pais; Tamas Dalmay
Reducing ligation bias of small RNAs in libraries for next generation sequencing.
Silence 2012;3(1):4.
2012: Hubert H Rogers; Sam Griffiths-Jones
Mitochondrial pseudogenes in the nuclear genomes of Drosophila.
PloS one 2012;7(3):e32593.
2011: Alex Bateman; Ewan Birney; Elspeth A Bruford; Janusz M Bujnicki; Guy Cochrane; James R Cole; Marcel E Dinger; Anton J Enright; Paul P Gardner; Daniel Gautheret; Sam Griffiths-Jones; Jen Harrow; Javier Herrero; Ian H Holmes; Hsien-Da Huang; Krystyna A Kelly; Paul Kersey; Ana Kozomara; Todd M Lowe; Manja Marz; Simon Moxon; Kim D Pruitt; Tore Samuelsson; Peter F Stadler; Albert J Vilella; Jan-Hinnerk Vogel; Kelly P Williams; Mathew W Wright; Shipra Agrawal; Christian Zwieb
RNAcentral: A vision for an international database of RNA sequences.
RNA (New York, N.Y.) 2011;17(11):1941-6.
2011: Katarzyna B Hooks; Sam Griffiths-Jones
Conserved RNA structures in the non-canonical Hac1/Xbp1 intron.
RNA biology 2011;8(4):552-6.
2011: Sam Griffiths-Jones; Jerome H L Hui; Antonio Marco; Matthew Ronshaugen
MicroRNA evolution by arm switching.
EMBO reports 2011;12(2):172-7.
2011: Preethi H Gunaratne; Jong H Kim; Ya-Chi Lin; Aleksandar Milosavljevic; Jayantha B Tennakoon; Michael Watson; Cristian Coarfa; Chad J Creighton; Jenny Drnevich; Sam Griffiths-Jones; Ashley L Benham; David F Clayton
Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain.
BMC genomics 2011;12(1):277.
2011: Paul P Gardner; Jennifer Daub; J Tate; Benjamin L Moore; Isabelle H Osuch; Sam Griffiths-Jones; Robert D Finn; Eric P Nawrocki; Diana L Kolbe; Sean R Eddy; Alex Bateman
Rfam: Wikipedia, clans and the "decimal" release.
Nucleic acids research 2011;39(Database issue):D141-5.
2011: Ana Kozomara; Sam Griffiths-Jones
miRBase: integrating microRNA annotation and deep-sequencing data.
Nucleic acids research 2011;39(Database issue):D152-7.
2010: Sam Griffiths-Jones
miRBase: microRNA sequences and annotation.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2010;Chapter 12():Unit 12.9.1-10.
2010: Antonio Marco; Jerome H L Hui; Matthew Ronshaugen; Sam Griffiths-Jones
Functional shifts in insect microRNA evolution.
Genome biology and evolution 2010;2():686-96.
2010: Hubert H Rogers; Casey M Bergman; Sam Griffiths-Jones
The evolution of tRNA genes in Drosophila.
Genome biology and evolution 2010;2():467-77.
2009: Sam Griffiths-Jones
The role of RNA molecules in cellular biology. Editorial.
Briefings in functional genomics & proteomics 2009;8(6):405-6.
2008: Blake C Meyers; Michael J Axtell; Bonnie Bartel; David P Bartel; David Baulcombe; John L Bowman; Xiaofeng Cao; James C Carrington; Xuemei Chen; Pamela J Green; Sam Griffiths-Jones; Steven E Jacobsen; Allison C Mallory; Robert A Martienssen; R Scott Poethig; Yijun Qi; Herve Vaucheret; Olivier Voinnet; Yuichiro Watanabe; Detlef Weigel; Jian-Kang Zhu
Criteria for annotation of plant MicroRNAs.
The Plant cell 2008;20(12):3186-90.
2008: Jennifer Daub; Paul P Gardner; John Tate; Daniel Ramsköld; Magnus Manske; William G Scott; Zasha Weinberg; Sam Griffiths-Jones; Alex Bateman
The RNA WikiProject: community annotation of RNA families.
RNA (New York, N.Y.) 2008;14(12):2462-4.
2008: Guillaume Smits; Andrew Mungall; Sam Griffiths-Jones; Paul Smith; Delphine Beury; Lucy Matthews; Jane Rogers; Andrew J Pask; geoffrey shaw; John VandeBerg; John R McCarrey; Marilyn Renfree; Wolf Reik; Ian Dunham
Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.
Nature genetics 2008;40(8):971-6.
2008: Tobias Mourier; Celine Carret; Sue Kyes; Zoe Christodoulou; Paul P Gardner; Daniel C Jeffares; Robert Pinches; Bart Barrell; Matt Berriman; Sam Griffiths-Jones; Alasdair Ivens; Chris Newbold; Arnab Pain
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.
Genome research 2008;18(2):281-92.
2008: Harpreet Kaur Saini; Anton J Enright; Sam Griffiths-Jones
Annotation of mammalian primary microRNAs.
BMC genomics 2008;9():564.
2008: Sam Griffiths-Jones; Harpreet Kaur Saini; Stijn van Dongen; Anton J Enright
miRBase: tools for microRNA genomics.
Nucleic acids research 2008;36(Database issue):D154-8.
2007: Harpreet Kaur Saini; Sam Griffiths-Jones; Anton J Enright
Genomic analysis of human microRNA transcripts.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(45):17719-24.
2007: Sam Griffiths-Jones
Annotating noncoding RNA genes.
Annual review of genomics and human genetics 2007;8():279-98.
2006: Sam Griffiths-Jones
miRBase: the microRNA sequence database.
Methods in molecular biology (Clifton, N.J.) 2006;342():129-38.
2006: Robert D Finn; Jaina Mistry; Benjamin Schuster-Böckler; Sam Griffiths-Jones; Volker Hollich; Timo Lassmann; Simon Moxon; Mhairi Marshall; Ajay Khanna; Richard Durbin; Sean R Eddy; Erik L L Sonnhammer; Alex Bateman
Pfam: clans, web tools and services.
Nucleic acids research 2006;34(Database issue):D247-51.
2006: Sam Griffiths-Jones; Russell J Grocock; Stijn van Dongen; Alex Bateman; Anton J Enright
miRBase: microRNA sequences, targets and gene nomenclature.
Nucleic acids research 2006;34(Database issue):D140-4.
2005: Sam Griffiths-Jones
Annotating non-coding RNAs with Rfam.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2005;Chapter 12():Unit 12.5.
2005: Tobias Mourier; Arnab Pain; Bart Barrell; Sam Griffiths-Jones
A selenocysteine tRNA and SECIS element in Plasmodium falciparum.
RNA (New York, N.Y.) 2005;11(2):119-22.
2005: Sam Griffiths-Jones
RALEE--RNA ALignment editor in Emacs.
Bioinformatics (Oxford, England) 2005;21(2):257-9.
2005: Shawn L Stricklin; Sam Griffiths-Jones; Sean R Eddy
C. elegans noncoding RNA genes.
WormBook : the online review of C. elegans biology 2005;():1-7.
2005: John A Jenkins; Sam Griffiths-Jones; Peter R Shewry; Heimo Breiteneder; E N Clare Mills
Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: an in silico analysis.
The Journal of allergy and clinical immunology 2005;115(1):163-70.
2005: Sam Griffiths-Jones; Simon Moxon; Mhairi Marshall; Ajay Khanna; Sean R Eddy; Alex Bateman
Rfam: annotating non-coding RNAs in complete genomes.
Nucleic acids research 2005;33(Database issue):D121-4.
2005: Simon Hubbard; Darren V Grafham; Kevin J Beattie; Ian M Overton; Stuart R McLaren; Michael D R Croning; Paul E Boardman; James K Bonfield; Joan Burnside; Robert M Davies; Elizabeth R Farrell; Matthew D Francis; Sam Griffiths-Jones; Sean Humphray; Christopher Hyland; Carol E Scott; Haizhou Tang; Ruth G Taylor; Cheryll Tickle; William R A Brown; Ewan Birney; Jane Rogers; Stuart A Wilson
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Genome research 2005;15(1):174-83.
2004: Antony Rodriguez; Sam Griffiths-Jones; Jennifer L Ashurst; Allan Bradley
Identification of mammalian microRNA host genes and transcription units.
Genome research 2004;14(10A):1902-10.
2004: Alex Bateman; Lachlan Coin; Richard Durbin; Robert D Finn; Volker Hollich; Sam Griffiths-Jones; Ajay Khanna; Mhairi Marshall; Simon Moxon; Erik L L Sonnhammer; David J Studholme; Corin Yeats; Sean R Eddy
The Pfam protein families database.
Nucleic acids research 2004;32(Database issue):D138-41.
2004: Sam Griffiths-Jones
The microRNA Registry.
Nucleic acids research 2004;32(Database issue):D109-11.
2003: Robert Finn; Sam Griffiths-Jones; Alex Bateman
Identifying protein domains with the Pfam database.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2003;Chapter 2():Unit 2.5.
2003: Victor Ambros; Bonnie Bartel; David P Bartel; Christopher B Burge; James C Carrington; Xuemei Chen; Gideon Dreyfuss; Sean R Eddy; Sam Griffiths-Jones; Mhairi Marshall; Marjori Matzke; Gary Ruvkun; Thomas Tuschl
A uniform system for microRNA annotation.
RNA (New York, N.Y.) 2003;9(3):277-9.
2003: Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Rfam: an RNA family database.
Nucleic acids research 2003;31(1):439-41.
2002: Peter R Shewry; Frédéric Beaudoin; J Jenkins; Sam Griffiths-Jones; E N Clare Mills
Plant protein families and their relationships to food allergy.
Biochemical Society transactions 2002;30(Pt 6):906-10.
2002: Sam Griffiths-Jones; Alex Bateman
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
Bioinformatics (Oxford, England) 2002;18(9):1243-9.
2002: Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
The Pfam protein families database.
Nucleic acids research 2002;30(1):276-80.