Sam Griffiths-Jones

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. pmc Reducing ligation bias of small RNAs in libraries for next generation sequencing
    Karim Sorefan
    School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
    Silence 3:4. 2012
  2. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
  3. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
  4. ncbi request reprint Annotating noncoding RNA genes
    Sam Griffiths-Jones
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    Annu Rev Genomics Hum Genet 8:279-98. 2007
  5. pmc MicroRNA evolution by arm switching
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    EMBO Rep 12:172-7. 2011
  6. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
  7. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
  8. pmc Functional shifts in insect microRNA evolution
    Antonio Marco
    Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
    Genome Biol Evol 2:686-96. 2010
  9. pmc Rfam: annotating non-coding RNAs in complete genomes
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 33:D121-4. 2005
  10. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003

Detail Information

Publications46

  1. pmc Reducing ligation bias of small RNAs in libraries for next generation sequencing
    Karim Sorefan
    School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
    Silence 3:4. 2012
    ..abstract:..
  2. pmc Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
    Preethi H Gunaratne
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
    BMC Genomics 12:277. 2011
    ..To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence...
  3. pmc miRBase: tools for microRNA genomics
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Nucleic Acids Res 36:D154-8. 2008
    ..miRBase is available at http://microrna.sanger.ac.uk/...
  4. ncbi request reprint Annotating noncoding RNA genes
    Sam Griffiths-Jones
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    Annu Rev Genomics Hum Genet 8:279-98. 2007
    ..Meanwhile, various experimental studies have suggested that the vast majority of the human genome is transcribed, although the proportion of the detected RNAs that is functional remains unknown...
  5. pmc MicroRNA evolution by arm switching
    Sam Griffiths-Jones
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    EMBO Rep 12:172-7. 2011
    ..Arm switching is likely to be general, and provides a fundamental mechanism to evolve the function of a miRNA locus and target gene network...
  6. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  7. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/)...
  8. pmc Functional shifts in insect microRNA evolution
    Antonio Marco
    Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
    Genome Biol Evol 2:686-96. 2010
    ..In general, Tribolium miRNAs are more representative of the insect ancestor than Drosophila miRNAs and are more conserved in vertebrates...
  9. pmc Rfam: annotating non-coding RNAs in complete genomes
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 33:D121-4. 2005
    ..Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/...
  10. pmc Rfam: an RNA family database
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:439-41. 2003
    ..wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database...
  11. pmc Rfam: Wikipedia, clans and the "decimal" release
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
    Nucleic Acids Res 39:D141-5. 2011
    ..We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk...
  12. ncbi request reprint RALEE--RNA ALignment editor in Emacs
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK
    Bioinformatics 21:257-9. 2005
    ..This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS...
  13. pmc miRBase: microRNA sequences, targets and gene nomenclature
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 34:D140-4. 2006
    ..miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/...
  14. pmc Genomic analysis of human microRNA transcripts
    Harpreet Kaur Saini
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 104:17719-24. 2007
    ..We provide strong evidence for the complete transcript structure of a small number of human miRNAs...
  15. pmc Clusters of microRNAs emerge by new hairpins in existing transcripts
    Antonio Marco
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    Nucleic Acids Res 41:7745-52. 2013
    ..Our analysis suggests that the study of microRNAs and small RNAs must consider linkage associations. ..
  16. pmc Evolution and function of the extended miR-2 microRNA family
    Antonio Marco
    Faculty of Life Sciences, University of Manchester, Manchester, UK
    RNA Biol 9:242-8. 2012
    ..Therefore, redundancy in microRNA families may facilitate the acquisition of novel functional features...
  17. doi request reprint miRBase: microRNA sequences and annotation
    Sam Griffiths-Jones
    University of Manchester, Manchester, United Kingdom
    Curr Protoc Bioinformatics . 2010
    ..The database provides a variety of methods to query the data, by specific searches of sequences and associated text and literature. All miRBase data are also available for download from the miRBase FTP site...
  18. ncbi request reprint The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 18:1243-9. 2002
    ..The performance of profile HMMs derived from the structural and sequence-based alignments has been assessed for homologue detection...
  19. ncbi request reprint miRBase: the microRNA sequence database
    Sam Griffiths-Jones
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Methods Mol Biol 342:129-38. 2006
    ..The methods outlined in this chapter describe these functions. miRBase is freely available to all at http://microrna.sanger.ac.uk/...
  20. pmc Pfam: clans, web tools and services
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nucleic Acids Res 34:D247-51. 2006
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)...
  21. pmc The evolution of tRNA genes in Drosophila
    Hubert H Rogers
    Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
    Genome Biol Evol 2:467-77. 2010
    ..We also demonstrate that tRNA isoacceptor and alloacceptor changes by anticodon shifts have occurred several times in Drosophila, annotating 16 such events in functional tRNAs during the evolution of the genus...
  22. pmc The microRNA Registry
    Sam Griffiths-Jones
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 9SA, UK
    Nucleic Acids Res 32:D109-11. 2004
    ..sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for download. Release 2.0 of the database contains 506 miRNA entries from six organisms...
  23. pmc Annotation of mammalian primary microRNAs
    Harpreet K Saini
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 9:564. 2008
    ..The 3' end of the pri-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data. The predicted pri-miRNAs are also analyzed for promoter and insulator-associated regulatory regions...
  24. pmc Rfam: updates to the RNA families database
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nucleic Acids Res 37:D136-40. 2009
    ..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
  25. pmc Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
    Simon J Hubbard
    Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom
    Genome Res 15:174-83. 2005
    ....
  26. pmc The InterPro Database, 2003 brings increased coverage and new features
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 31:315-8. 2003
    ..The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  27. pmc Sex-biased expression of microRNAs in Schistosoma mansoni
    Antonio Marco
    Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom School of Biological Sciences, University of Essex, Colchester, United Kingdom
    PLoS Negl Trop Dis 7:e2402. 2013
    ..We propose that the recent emergence of separate sexes in Schistosoma had an effect on the chromosomal distribution and evolution of microRNAs, and that microRNAs are likely to participate in the sex differentiation/maintenance process. ..
  28. pmc Detection of microRNAs in color space
    Antonio Marco
    University of Manchester, M13 9PT Manchester, UK
    Bioinformatics 28:318-23. 2012
    ..Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs...
  29. pmc Mitochondrial pseudogenes in the nuclear genomes of Drosophila
    Hubert H Rogers
    Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
    PLoS ONE 7:e32593. 2012
    ..We estimate genus average rates of insertion of 0.75 per million years, and a duplication rate of 0.010 duplications per numt per million years...
  30. pmc Conserved RNA structures in the non-canonical Hac1/Xbp1 intron
    Katarzyna B Hooks
    Faculty of Life Sciences, University of Manchester, Manchester UK
    RNA Biol 8:552-6. 2011
    ..We identified six species with unambiguous Hac1/Xbp1 homologs that have lost the non-canonical intron structure. We propose that these species use a different mechanism to regulate the UPR...
  31. doi request reprint Multiple products from microRNA transcripts
    Antonio Marco
    Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester M13 9PT, UK
    Biochem Soc Trans 41:850-4. 2013
    ....
  32. pmc Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods
    Jerome H L Hui
    School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong, China
    Nucleic Acids Res 41:3352-61. 2013
    ..Our evolutionary and functional characterization of a bi-directionally transcribed microRNA establishes the iab-4/iab-8 system as a model for understanding how multiple products from sense and antisense microRNAs target common sites...
  33. doi request reprint Annotating non-coding RNAs with Rfam
    Sam Griffiths-Jones
    Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
    Curr Protoc Bioinformatics . 2005
    ..Rfam is a database of families of ncRNAs, represented by structure-annotated multiple sequence alignments and covariance models...
  34. pmc MicroRNAs from the same precursor have different targeting properties
    Antonio Marco
    Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester M13 9PT, UK
    Silence 3:8. 2012
    ..abstract:..
  35. pmc Identification of mammalian microRNA host genes and transcription units
    Antony Rodriguez
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 14:1902-10. 2004
    ....
  36. doi request reprint miRBase: annotating high confidence microRNAs using deep sequencing data
    Ana Kozomara
    Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
    Nucleic Acids Res 42:D68-73. 2014
    ..mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information. ..
  37. pmc miRBase: integrating microRNA annotation and deep-sequencing data
    Ana Kozomara
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    Nucleic Acids Res 39:D152-7. 2011
    ..miRBase is available online at: http://www.mirbase.org/...
  38. ncbi request reprint Genome of the host-cell transforming parasite Theileria annulata compared with T. parva
    Arnab Pain
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Science 309:131-3. 2005
    ....
  39. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  40. pmc A uniform system for microRNA annotation
    Victor Ambros
    Dartmouth Medical School Department of Genetics, Hanover, New Hampshire 03755, USA
    RNA 9:277-9. 2003
    ..Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families...
  41. pmc A selenocysteine tRNA and SECIS element in Plasmodium falciparum
    Tobias Mourier
    RNA 11:119-22. 2005
    ..To our knowledge, this is the first report of an identification of protozoan selenocysteine insertion machinery at the sequence level...
  42. pmc Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
    Tobias Mourier
    Ancient DNA and Evolution Group, Department of Biology, University of Copenhagen, Copenhagen DK 2100, Denmark
    Genome Res 18:281-92. 2008
    ..reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism's life cycle...
  43. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  44. doi request reprint Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians
    Guillaume Smits
    The Babraham Institute, Laboratory of Developmental Genetics and Imprinting, Cambridge CB22 3AT, UK
    Nat Genet 40:971-6. 2008
    ..The conservation in all therians of the mechanism controlling imprinting of the IGF2-H19 locus suggests a sequential model of imprinting evolution...
  45. ncbi request reprint Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...