PResident's RePORt 2009/2010 - University College Cork

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President’s Report
College of Science, Engineering and Food Science
Biochemistry
Book Chapters
· Atkins, JF; Fayet, O; Baranov, PV (2010) ‘Bacterial and phage recoding: programmed frameshifting, bypassing, and
redefinition including readthrough’ In: Escherichia coli and Salmonella: Cellular and Molecular Biology. : ASM Press.
· Baranov, PV; Gurvich, OL (2010) ‘Sequences promoting recoding are singular genomic elements’ In: Recoding: Expansion
of Decoding Rules Enriches Gene Expression. Heidelberg and New York: Springer Publishers.
· Firth, AE; Bekaert, M; Baranov, PV (2010) ‘Computational resources for studying recoding’ In: Recoding: Expansion of
Decoding Rules Enriches Gene Expression. Heidelberg and New York: Springer Publishers.
· Madadlou, A; O’Sullivan SM; Sheehan D (2010) ‘Fast protein liquid chromatography’ In: Walls D and Loughran S (Eds.).
Protein Chromatography: Methods and Protocols. Totowa, New Jersey, USA: Humana.
· Papkovksy, Dmitri B (2010) ‘Live Cell Imaging: Methods and Protocols’ In: Methods in Molecular Biology. USA: Humana
Press.
· Sheehan, D; O’Sullivan, S (2009) ‘A computer-assisted learning exercise for teaching of structural biology: A case of
simulated discovery to promote active learning’ In: Proceedings of EduLearn 2009, Barcelona, Spain. Madrid: IATED.
Peer Reviewed Journals
· Atkins, JF; Baranov, PV (2010) ‘The distinction between recoding and codon reassignment’. Genetics, 185:1535-1536.
· Bekaert, M; Firth, AE; Zhang, Y; Gladyshev, VN; Atkins, JF; Baranov, PV (2010) ‘Recode-2: new design, new search tools,
and many more genes’. Nucleic acids research.
· Bhatt, L; Groeger, G; McDermott, K; Cotter, TG (2010) ‘Rod and cone photoreceptor cells produce ROS in response to
stress in a live retinal explant system’. Molecular vision, 16:283-293.
· Cao, W; McMahon, M; Wang, B; O’Connor, R; Clarkson, M (2010) ‘A case report of spontaneous mutation (C33U) in the
iron-responsive element of L-ferritin causing hyperferritinemia-cataract syndrome’. Blood Cells Mol Dis, 44:22-27.
· Chung, BY; Firth, AE; Atkins, JF (2010) ‘Frameshifting in alphaviruses: a diversity of 3’ stimulatory structures’. Journal of
Molecular Biology, 397 (2):448-456.
· Dmitriev, RI; Zhdanov, AV; Ponomarev, GV; Yashunski, DV; Papkovsky, DB (2010) ‘Intracellular oxygen-sensitive
phosphorescent probes based on cell-penetrating peptides’. Analytical Biochemistry, 398 (1):24-33.
· Favre C, Zhdanov A, Leahy M, Papkovsky D, O’Connor R (2010) ‘Mitochondrial pyrimidine nucleotide carrier (PNC1)
regulates mitochondrial biogenesis and the invasive phenotype of cancer cells’. Oncogene, 29 (27):3964-3976.
· Fercher, A; O’Riordan, TC; Zhdanov, AV; Dmitriev, RI; Papkovsky, DB (2010) ‘Imaging of cellular oxygen and analysis of
metabolic responses of mammalian cells’. Methods (San Diego, Calif.), 591:257-273.
· Firth, AE; Atkins, JF (2009) ‘Evidence for a novel coding sequence overlapping the 5’-terminal approximately 90 codons of
the gill-associated and yellow head okavirus envelope glycoprotein gene’. Virology Journal, 6.
· Firth, AE; Atkins, JF (2010) ‘Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1
frame overlapping genes accessed by leaky scanning’. Virology Journal, 7.
· Firth, AE; Blitvich, BJ; Wills, NM; Miller, CL; Atkins, JF (2010) ‘Evidence for ribosomal frameshifting and a novel overlapping
gene in the genomes of insect-specific flaviviruses’. Virology, 399 (1):153-166.
· Firth, AE; Wang, QS; Jan, E; Atkins, JF (2009) ‘Bioinformatic evidence for a stem-loop structure 5’-adjacent to the IGR-IRES
and for an overlapping gene in the bee paralysis dicistroviruses’. Virology Journal, 6 (6).
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