Andrew E Firth

Summary

Affiliation: University College Cork
Country: Ireland

Publications

  1. ncbi Detecting overlapping coding sequences with pairwise alignments
    Andrew E Firth
    Department of Biochemistry, University of Otago, P O Box 56, Dunedin, New Zealand
    Bioinformatics 21:282-92. 2005
  2. pmc Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virology 399:153-66. 2010
  3. pmc HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences
    Nattanan Panjaworayan
    Department of Biochemistry, University of Otago, Dunedin, New Zealand
    Virol J 4:136. 2007
  4. pmc Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 5:108. 2008
  5. pmc A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:14. 2009
  6. pmc Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:32. 2009
  7. pmc A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:136. 2009
  8. pmc Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:193. 2009
  9. pmc Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:222. 2009
  10. pmc Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 7:17. 2010

Collaborators

Detail Information

Publications29

  1. ncbi Detecting overlapping coding sequences with pairwise alignments
    Andrew E Firth
    Department of Biochemistry, University of Otago, P O Box 56, Dunedin, New Zealand
    Bioinformatics 21:282-92. 2005
    ..Furthermore, the constraints imposed by double-coding can result in atypical codon biases. However, these same constraints lead to particular mutation patterns that may be detectable in sequence alignments...
  2. pmc Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virology 399:153-66. 2010
    ....
  3. pmc HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences
    Nattanan Panjaworayan
    Department of Biochemistry, University of Otago, Dunedin, New Zealand
    Virol J 4:136. 2007
    ..2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses...
  4. pmc Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 5:108. 2008
    ..In protein gels, 6K migrates as a doublet--a result that, to date, has been attributed to differing degrees of acylation. Nonetheless, despite many years of research, its role is still relatively poorly understood...
  5. pmc A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:14. 2009
    ..We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'...
  6. pmc Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:32. 2009
    ..Possible translation mechanisms for this unusually positioned ORF are discussed...
  7. pmc A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:136. 2009
    ..We propose that the new ORF utilizes a non-AUG initiation codon--namely a conserved CUG codon in a strong Kozak context--upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'...
  8. pmc Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:193. 2009
    ..We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop...
  9. pmc Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:222. 2009
    ..We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein...
  10. pmc Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 7:17. 2010
    ..In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community...
  11. doi Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Arch Virol 153:1379-83. 2008
    ..The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis...
  12. pmc Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 5:62. 2008
    ..The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5-10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels...
  13. pmc Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene
    Andrew E Firth
    Department of Biochemistry, Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 5:48. 2008
    ..These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic...
  14. pmc Observation of dually decoded regions of the human genome using ribosome profiling data
    Audrey M Michel
    Biochemistry Department, University College Cork, Ireland
    Genome Res 22:2219-29. 2012
    ....
  15. pmc Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome
    Gary Loughran
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 108:E1111-9. 2011
    ..Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses...
  16. pmc Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)
    Pavel V Baranov
    Biochemistry Department, University College Cork, Cork, Ireland
    RNA Biol 8:637-47. 2011
    ..Three other proposed PRF candidates (Xbp1, CG32736, CG14047) with switches in conservation of reading frames are likely explained by mechanisms other than PRF...
  17. pmc A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment
    Virag Sharma
    Department of Biochemistry, University College Cork, Cork, Ireland
    Mol Biol Evol 28:3195-211. 2011
    ..In addition to the identification of a large number of recoded genes, a surprising observation is that nearly half of them are expressed via PTR-a mechanism that, in contrast to PRF, has not yet received substantial attention...
  18. pmc Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences
    Ivaylo P Ivanov
    Biosciences Institute, University College Cork, Cork, Ireland
    Nucleic Acids Res 39:4220-34. 2011
    ..In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data...
  19. pmc Recode-2: new design, new search tools, and many more genes
    Michael Bekaert
    School of Biology and Environmental Science, University College Dublin, Biosciences Institute, University College Cork, Ireland
    Nucleic Acids Res 38:D69-74. 2010
    ..Recode-2 is available at http://recode.ucc.ie...
  20. pmc An overlapping essential gene in the Potyviridae
    Betty Y W Chung
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 105:5897-902. 2008
    ....
  21. doi Frameshifting in alphaviruses: a diversity of 3' stimulatory structures
    Betty Y W Chung
    Biosciences Institute, University College Cork, Cork, Ireland
    J Mol Biol 397:448-56. 2010
    ..The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems...
  22. pmc Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
    Virag Sharma
    School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
    Nucleic Acids Res 42:7210-25. 2014
    ..The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting. ..
  23. pmc Effect of 5'UTR introns on gene expression in Arabidopsis thaliana
    Betty Y W Chung
    Biochemistry Department, University of Otago, Dunedin, New Zealand
    BMC Genomics 7:120. 2006
    ..Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome...
  24. pmc Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
    John F Atkins
    School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
    Nucleic Acids Res 44:7007-78. 2016
    ..This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression. ..
  25. doi Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function
    Ivaylo P Ivanov
    Biosciences Institute, University College Cork, Ireland
    J Mol Evol 70:289-302. 2010
    ....
  26. pmc GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Nucleic Acids Res 36:W281-5. 2008
    ..Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html...
  27. pmc Detecting overlapping coding sequences in virus genomes
    Andrew E Firth
    Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
    BMC Bioinformatics 7:75. 2006
    ..g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites--which can conceal potentially coding open reading frames (ORFs)...
  28. ncbi Strategies and computational tools for improving randomized protein libraries
    Wayne M Patrick
    Center for Fundamental and Applied Molecular Evolution, Emory University, 1510 Clifton Road, Atlanta GA 30322, USA
    Biomol Eng 22:105-12. 2005
    ..In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants...
  29. ncbi Statistics of protein library construction
    Andrew E Firth
    Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
    Bioinformatics 21:3314-5. 2005
    ....