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Authored Book - Research

Brumby, A. M., Lamont, I. L., Dodd, I. B., Egan, J. B., Walling, G. A., McEwan, J. C., … Montgomery, G. (1996). Defining the SOS operon of coliphage 186. N/A, 114p.

Edited Book - Research

Eaton-Rye, J. J., Tripathy, B. C., & Sharkey, T. D. (Eds.). (2012). Photosynthesis: Plastid biology, energy conversion and carbon assimilation. New York: Springer, 856p. doi: 10.1007/978-94-007-1579-0

Chapter in Book - Research

Brownfield, L., & Twell, D. (2016). Plant Reproduction. In eLS. Chichester, UK: John Wiley & Sons. doi: 10.1002/9780470015902.a0002046.pub2

Reid, S., Chan, L. C. L., Matindoost, L., Pushparajan, C., & Visnovsky, G. (2016). Cell culture for production of insecticidal viruses. In T. R. Glare & M. E. Moran-Diez (Eds.), Microbial-based biopesticides: Methods and protocols: Methods in molecular biology (Vol. 1477). (pp. 95-117). New York: Springer. doi: 10.1007/978-1-4939-6367-6_9

Biswas, A., Fineran, P. C., & Brown, C. M. (2015). Computational detection of CRISPR/crRNA targets. In M. Lundgren, E. Charpentier & P. C. Fineran (Eds.), CRISPR: Methods in molecular biology (Vol. 1311). (pp. 77-89). New York, NY: Humana Press. doi: 10.1007/978-1-4939-2687-9_5

Empson, R. M., Tantirigama, M. L. S., Oswald, M. J., Hughes, S. M., & Knöpfel, T. (2015). Combined immunochemistry and live imaging of fluorescent protein expressing neurons in mouse brain. In A. Merighi & L. Lossi (Eds.), Immunocytochemistry and related techniques. (pp. 357-373). New York: Springer. doi: 10.1007/978-1-4939-2313-7_19

Poulter, R. T. M., & Butler, M. I. (2015). Tyrosine recombinase retrotransposons and transposons. In N. L. Craig, M. Chandler, M. Gellert, A. M. Lambowitz, P. A. Rice & S. B. Sandmeyer (Eds.), Mobile DNA III. (pp. 1271-1291). Washington, DC: ASM Press.

Copp, J. N., Hanson-Manful, P., Ackerley, D. F., & Patrick, W. M. (2014). Error-prone PCR and effective generation of gene variant libraries for directed evolution. In E. M. J. Gillam, J. N. Copp & D. F. Ackerley (Eds.), Directed evolution library creation: Methods and protocols. (2nd ed.) (pp. 3-22). New York: Springer. doi: 10.1007/978-1-4939-1053-3_16

Day, R., & Macknight, R. (2014). Screening for imprinted genes using high-resolution melting analysis of PCR amplicons. In C. Spillane & P. C. McKeown (Eds.), Plant epigentics and epigenomics: Methods and protocols. (pp. 71-83). Humana Press. doi: 10.1007/978-1-62703-773-0_5

Hill, R. E., & Eaton-Rye, J. J. (2014). Plasmid Construction by SLIC or Sequence and Ligation-Independent Cloning. In S. Valla & R. Lale (Eds.), DNA cloning and assembly methods: Methods in molecular biology (Vol. 1116). (pp. 25-36). New York: Humana. doi: 10.1007/978-1-62703-764-8_2

Mace, P. D., Riedl, S. J., & Salvesen, G. S. (2014). Caspase enzymology and activation mechanisms. In A. Ashkenasi, J. Yuan & J. A. Wells (Eds.), Methods in enzymology: Regulated cell death Part A: Apoptotic mechanisms (Vol.544). (pp. 161-178). San Diego, CA: Academic Press. doi: 10.1016/b978-0-12-417158-9.00007-8

Middleton, A. J., Budhidarmo, R., & Day, C. L. (2014). Use of E2~ubiquitin conjugates for the characterization of ubiquitin transfer by RING E3 ligases such as the inhibitor of apoptosis proteins. In A. Ashkenazi, J. A. Wells & J. Yuan (Eds.), Methods in enzymology (Vol. 545). (pp. 243-263). San Diego, CA: Elsevier. doi: 10.1016/B978-0-12-801430-1.00010-X

Middleton, A. J., Vanderbeld, B., Bredow, M., Tomalty, H., Davies, P. L., & Walker, V. K. (2014). Isolation and characterization of ice-binding proteins from higher plants. In D. K. Hincha & E. Zuther (Eds.), Plant cold acclimation: Methods and Protocols (Methods in Molecular Biology: Vol. 1166). (pp. 255-277). New York: Springer. doi: 10.1007/978-1-4939-0844-8_19

Najafpour, M. M., Sedigh, D. J., Eaton-Rye, J. J., & Allakhverdiev, S. I. (2014). The water-oxidizing complex in Photosystem II. In S. I. Allakhverdiev, A. B. Rubin & V. A. Shuvalov (Eds.), Contemporary problems of photosynthesis (Vol. 1). (pp. 325-341). Moscow, Russia: Izhevsk Institute of Computer Science.

Osborne, A. J., Duncan, E. J., Cridge, A. G., & Dearden, P. K. (2014). Epigenetics and the maternal germline. In T. Tollefsbol (Ed.), Transgenerational epigenetics: Evidence and debate. (pp. 27-41). London, UK: Academic Press. doi: 10.1016/B978-0-12-405944-3.00004-0

Patrick, W. M., & Gerth, M. L. (2014). ITCHY: Incremental Truncation for the Creation of Hybrid Enzymes. In E. M. J. Gillam, J. N. Copp & D. F. Ackerley (Eds.), Directed evolution library creation: Methods and protocols. (2nd ed.) (pp. 225-244). New York: Springer. doi: 10.1007/978-1-4939-1053-3_16

Sharpe, M. L., Hastings, J. W., & Krause, K. L. (2014). Luciferases and light-emitting accessory proteins: Structural biology. In eLS. Chichester, UK: John Wiley & Sons. doi: 10.1002/9780470015902.a0003064.pub2

Stevens, S. G., & Brown, C. M. (2014). Bioinformatic methods to discover Cis-regulatory elements in mRNAs. In N. K. Kasabov (Ed.), Springer handbook of bio-/neuro-informatics. (pp. 151-169). Dordrecht, The Netherlands: Springer. doi: 10.1007/978-3-642-30574-0_10

Bekhit, A. E., Hopkins, D. L., Farouk, M. M., & Carne, A. (2013). Interventions to improve the tenderness of fresh meat: A future prospect for camel meat research. In I. T. Kadim, O. Mahgoub, B. Faye & M. Farouk (Eds.), Camel meat and meat products. (pp. 153-185). Oxford, UK: CABI.

Hanson-Manful, P., & Patrick, W. M. (2013). Construction and analysis of randomized protein-encoding libraries using error-prone PCR. In J. A. Gerrard (Ed.), Protein nanotechnology: Protocols, instrumentation, and applications. (2nd ed.) (pp. 251-267). Humana Press. doi: 10.1007/978-1-62703-354-1-15

Merriman, T. R., & Flynn, T. J. (2013). Molecular genetics of hyperuricaemia and gout. In eLS. Chichester: John Wiley & Sons. doi: 10.1002/9780470015902.a0025153

Merriman, T. R., & McKinney, C. (2013). An update on the genetic causes of hyperuricemia and gout. In N. Dalbeth, F. Perez-Ruiz & N. Schlesinger (Eds.), Gout. (pp. 54-69). London, UK: Future Medicine. doi: 10.2217/ebo.12.256

Picard, K., Lee, R., Hellens, R., & Macknight, R. (2013). Transient gene expression in Medicago truncatula leaves via agroinfiltration. In R. J. Rose (Ed.), Legume genomics: Methods and protocols: Methods in molecular biology (Vol. 1069). (pp. 215-226). New York: Springer. doi: 10.1007/978-1-62703-613-9_15

Macknight, R. C., Herridge, R. P., & Day, R. C. (2012). Using transcriptomics to reveal gene networks of seed development in Arabidopsis. In G. K. Agrawal & R. Rakwal (Eds.), Seed development: OMICS technologies toward Improvement of seed quality and crop yield. (pp. 99-110). Dordrecht, The Netherlands: Springer. doi: 10.1007/978-94-007-4749-4_6

McConnell, I. L., Eaton-Rye, J. J., & van Rensen, J. J. S. (2012). Regulation of Photosystem II electron transport by bicarbonate. In J. J. Eaton-Rye, B. C. Tripathy & T. D. Sharkey (Eds.), Photosynthesis: Plastid biology, energy conversion and carbon assimilation. (pp. 475-500). New York: Springer. doi: 10.1007/978-94-007-1579-0

Collins, L. J., Schönfeld, B., & Chen, X. S. (2011). The epigenetics of non-coding RNA. In T. Tollefsbol (Ed.), Handbook of epigenetics: The new molecular and medical genetics. (pp. 49-61). London: Academic Press. doi: 10.1016/B978-0-12-375709-8.00004-6

Daly, T., Chen, X. S., & Penny, D. (2011). How old are RNA networks? In L. J. Collins (Ed.), RNA infrastructure and networks: Advances in experimental medicine and biology (Vol. 722). (pp. 255-273). New York: Springer Science+Business Media. doi: 10.1007/978-1-4614-0332-6

Day, R. C. (2010). Laser microdissection of paraffin-embedded plant tissues for transcript profiling. In L. Hennig & C. Köhler (Eds.), Plant developmental biology: Methods and protocols. (pp. 321-346). New York: Spinger. doi: 10.1007/978-1-60761-765-5_22

Dearden, P. K., Duncan, E. J., & Wilson, M. J. (2010). The honeybee Apis mellifera. In Emerging model organisms: A laboratory manual (Vol. 2). (pp. 223-246). Cold Spring Harbor, NY: Cold Spring Harbor Press.

Eaton-Rye, J. (2010). Construction of gene interruptions and gene deletions in the cyanobacterium Synechocystis sp. strain PCC 6803. In R. Carpentier (Ed.), Photosynthesis Research Protocols. (2nd ed.) (pp. 295-312). NY: Springer. doi: 10.1007/978-1-60761-925-3_22

von Zychlinski, A., & Gruissem, W. (2009). Preparation and analysis of plastid proteomes by 2DE. In D. Sheehan & R. Tyther (Eds.), Two-dimensional electrophoresis protocols: Methods in molecular biology (Vol. 519). (pp. 205-220). Totowa, NJ: Humana Press. doi: 10.1007/978-1-59745-281-6_13

von Zychilinski, A., Reiland, S., Gruissem, W., & Baginsky, S. (2008). Etioplast. In G. K. Agrawal & R. Rakwal (Eds.), Plant Proteomics: Technologies, strategies, and applications. (pp. 351-360). Hoboken, NJ: John Wiley & Sons. doi: 10.1002/9780470369630.ch24

Hastings, J. W., & Krause, K. L. (2006). Luciferases and light-emitting accessory proteins: Structural biology. In Encyclopedia of Life Sciences. New York: John Wiley & Sons. doi: 10.1038/npg.els.0003064

Hastings, J. W., & Krause, K. L. (2005). Luciferase and light-emitting accessory proteins: Structural biology. In Encyclopedia of life sciences. John Wiley & Sons. doi: 10.1038/npg.els.0003064

Eaton-Rye, J. J. (2004). The construction of gene knockouts in the Cyanobacterium Synechocystis sp. PCC 6803. In R. Carpentier (Ed.), Methods in molecular biology, vol. 274: Photosynthesis research protocols. (pp. 309-324). Totowa, USA: Humana Press.

Poole, E. S., Major, L. L., Cridge, A. G., & Tate, W. P. (2004). The mechanism of recoding in pro- and eukaryotes. In K. H. Nierhaus & D. N. Wilson (Eds.), Protein synthesis and ribosome structure: Translating the genome. (pp. 397-428). Weinheim, Germany: Wiley-VCH.

Eccles, M. R., Bockett, N., & Stayner, C.-A. K. (2003). PAX2 and Renal-Coloboma Syndrome. In P. D. Vize, A. S. Woolf & J. B. L. Bard (Eds.), The kidney. (pp. 411-432). San Diego, USA: Elsevier Science.

McCormick, S. P. A., Liu, C. Y.-Y., Young, S. G., & Nielsen, L. B. (2003). Manipulating large insert clones for transgenesis. In M. H. Hofker & J. van Deursen (Eds.), Methods in molecular biology: Transgenic mouse methods and protocols. (pp. 105-123). Totowa, NJ: Humana Press.

Dunbier, A. K., & Guilford, P. J. (2002). Gastric cancer: Inherited predisposition. In J. R. Bertino (Ed.), Encyclopedia of cancer. (2nd ed.) (pp. 253-258). Academic Press. [Encyclopaedia/Dictionary Entry].

Dunbier, A. K., & Guilford, P. J. (2002). Gastric cancer: Inherited predisposition. In S. R. Hamilton & L. A. Aaltonen (Eds.), Encyclopedia of Cancer, Volume 2. (2nd ed.) (pp. 253-258). USA: Elsevier Science.

Brown, C., Schreiber, M., Chapman, B., & Jacobs, G. (2000). Information Science and Bioinformatics. In N. Kasabov (Ed.), Future Directions for Intelligent Systems and Information Science. (pp. 251-287). Heidelberg, Germany: Springer.

Fenoglio-Preiser, C., Carneiro, F., Correa, P., Guilford, P., & et al (2000). Gastric carcinoma. In S. R. Hamilton & L. A. Aaltonen (Eds.), World Health Organization classification of tumours: Pathology and genetics of tumours of the digestive system. (pp. 39-52). Lyon, France: IARC Press.

Ha, J.-H., Johnson, E. R., McKay, D. B., Sousa, M. C., Takeda, S., & Wilbanks, S. M. (1999). Structure and mechanism of the Hsp70s. In B. Bukau (Ed.), Molecular Biology of Chaperones and Folding Catalysts. (pp. 573-607). London: Harwood Academic Publishers.

Ledgerwood, E. C., & Prins, J. B. (1999). Tumour necrosis factor alpha. In S. M. Marshall, P. D. Home & R. A. Rizza (Eds.), The Diabetes Annual. (12 ed.) (pp. 161-180). Amsterdam: Elsevier.

Broom, M. F. (1998). N-Formylmethionyl Peptidase. In A. J. Barrett, N. D. Rawlings & J. F. Woessner (Eds.), The Handbook of Proteolytic Enzymes. (pp. 1567-1568). San Diego: Academic Press.

Ha, J.-H., Johnson, E. R., McKay, D. B., Sousa, M. C., Takeda, S., & Wilbanks, S. (1998). Structure and properties of the seventy Kilodalton heat shock proteins. In A. L. Fink & Y. Goto (Eds.), Structure and functions of molecular chaperones: The role of chaperones in the life of proteins. (pp. 95-122). USA: Marcel Dekker.

McCormick, S. P. A., Allan, C. M., Taylor, J. M., & Young, S. G. (1997). The use of P1 bacteriophage clones to generate transgenic animals. In L. M. Houdebine (Ed.), Transgenic Animals: Generation and Use. (pp. 273-281). Amsterdam: Harwood Academic Publishers.

Montgomery, G. W., & Crawford, A. M. (1997). The Sheep Linkage Map. In L. Piper & A. Rubinsky (Eds.), The Genetics of Sheep. (pp. 297-351). CAB International.

Wilbanks, S. (1997). 3-D structure of Hsp70 proteins. In M.-J. Gething (Ed.), Guidebook to molecular chaperones and protein folding factors. (pp. 13-18). Oxford University Press.

Broad, T. E., Hill, D. F., Maddox, J. F., Nicholas, F. W., & Powell, B. C. (1996). Mapped loci and other genetic systems (Category 4). In J. J. Lauvergne, C. H. S. Dolling & C. Renieri (Eds.), Mendelian Inheritance in Sheep 1996 (MIS 96). (pp. 155-158). Clamart, France: COGOVICA/COGNOSAG.

Schwaiger, F.-W., Maddox, J. F., Ballingall, K., Buitkamp, J., Crawford, A. M., Dutia, B. M., … Wright, H. (1996). The ovine major histocompatibility complex. In L. B. Schook & S. J. Lamont (Eds.), The Major Histocompatibility Complex Region of Domestic Animal Species. (pp. 121-176). Boca Raton: CRC Press.

Swarbrick, P. A., & Crawford, A. M. (1996). The cervine major histocompatibility complex: Genetic structure and function of the cervine DRB genes. In L. B. Schook & S. J. Lamont (Eds.), The Major Histocompatibility Complex Region of Domestic Animal Species. (pp. 177-186). Boca Raton: CRC Press.

Tate, W. P., Dalphin, M. E., Pel, H. J., & Mannering, S. A. (1996). Decoding efficiencies of translational stop signals: a new facet of cellular regulation. In J. K. Setlow (Ed.), Genetic Engineering, Principles and Methods, Volume 18. (pp. 157-182). New York: Plenum Press.

Clarke, S. M., & Eaton-Rye, J. J. (1995). Oligonucleotide-directed complementation of a lethal deletion within the large hydrophilic domain of CP47. In P. Mathis (Ed.), Photosynthesis: From Light to Biosphere: Proceedings of the Xth International Photosynthesis Congress, Vol. 3. (pp. 469-472). Dordrecht: Kluwer.

Murphy, M. P., & O' Neill, L. A. J. (1995). What is life? The next fifty years an introduction. In M. P. Murphy & L. A. J. O'Neill (Eds.), What is Life? The Next Fifty Years: Speculations on the Future of Biology. (pp. 1-4). Cambridge: Cambridge University Press.

Reeve, A. E. (1995). Genomic imprinting in embryonal and overgrowth disorders. In R. Ohlsson, K. Hall & M. Ritzen (Eds.), Nobel Symposium: Parental Imprinting: Causes and Consequences. (pp. 209-223). Cambridge: Cambridge University Press.

Chapter in Book - Other

Eaton-Rye, J. J. (2012). Contributions of Govindjee, 1970-1999. In J. J. Eaton-Rye, B. C. Tripathy & T. D. Sharkey (Eds.), Photosynthesis: Plastid biology, energy conversion and carbon assimilation. New York: Springer. doi: 10.1007/978-94-007-1579-0

Hastings, J. W., & Krause, K. L. (2007). Luciferases and light-emitting accessory proteins: Structural biology. In Encyclopedia of Life Sciences. New York: John Wiley & Sons.

Intellectual Property

Koepke, M., Patrick, W., Maddock, D. J., & Gerth, M. (2015). Enzyme-altered metabolic activity. (9,550,979). United States.

Sowerby, S. J. (2015). Apparatus for the detection and analysis of particles in fluids. (8,961,907). United States.

Sowerby, S. J., Petersen, G. B., Broom, M. F., & Jones, M. D. (2012). Detecting, measuring and controlling particles and electromagnetic radiation. (8,247,214). United States.

Anjomshoaa, A., Reeve, A. E., Lin, Y.-H., & Black, M. A. (2011). Proliferation signature and prognosis for gastrointestinal cancer. (562237).

Guilford, P. J., & Holyoake, A. J. (2011). Markers for detection of gastric cancer. (EP 1 649 064).

Guilford, P. J., Kerr, N. J., & Pollock, R. C. (2011). Urine markers for detection of bladder cancer. (553297).

Cardno, T. S., & Tate, W. P. (2010). Dual-fluorescent reporter construct and assay for measuring translational recoding. (EP 1 929 015).

Reeve, A. E., Black, M. A., McCall, J. L., Nekarda, H., Rosenberg, R., Friederichs, J., … Lin, Y.-H., & Pollock, R. C. (2009). Prognosis prediction for colorectal cancer. (544432).

Reeve, A. E., Futschik, M. E., Sullivan, M. J., Kasabov, N. K., & Guilford, P. J. (2008). Medical applications of adaptive learning systems using gene expression data. (US 7,370,021).

Sowerby, S. J., & Broom, M. F. (2008). Method of sample analysis and apparatus therefor. (555390).

Kasabov, N. K., Futschik, M. E., Sullivan, M. J., & Reeve, A. E. (2005). Medical decision support systems utilizing gene expression and clinical information and method for use. (23910).

Poulter, R. T. M., & Butler, M. I. (2005). Detection of cryptococcus in a sample by detecting a mini-intein encoding region of the PRP8 gene. International Application Published Under the Patent Cooperation Treaty (PCT) (WO 2005/056821).

Butler, M., & Poulter, R. (2004). Cosmos atrosanguineus (Hook) Voss. European Community Plant Variety Office Patent (13436). Retrieved from http://www.cpvo.fr

Poulter, R. T. M., & Butler, M. I. (2004). Inteins within fungal PRP8 genes, uses thereof and assays. International Application Published Under the Patent Cooperation Treaty (PCT) (WO 2005/056587).

University of Otago, Poulter, R. T. M., Goodwin, T. J. D., Butler, M. I., Adams, M. D., & et al (2002). A novel intein and uses thereof. International Application Published Under the Patent Cooperation Treaty (PCT) [Revised version] (WO 02/095036).

Janssen Pharmaceutica N.V., Luyten, W. H. M. L., De Backer, M. D., Nelissen, B. J. M., Poulter, R. T. M., Hawkins, M. H., & et al (2000). An unusual retrotransposon from the yeast candida albicans. International Application Published Under the Patent Cooperation Treaty (PCT) (WO 00/26397).

Poulter, R., & Butler, M. (1997). Grant of plant variety rights in respect of the cosmos variety Pinot Noir. New Zealand Plant Variety Rights (1243).

Reeve, A. E., & Guilford, P. J. (1997). Method of Testing. number 328994. Cancer Genetics Laboratory Biochemistry Department.

Software

Stockwell, P. A. (2009). SSEdit: Single (Short) Sequence Editor: For MacOS X (Version 6.04) [Computer Software]. Dunedin, New Zealand: Biochemistry Department, University of Otago.

Stockwell, P. A. (2008). HOMED: HOMologous Sequence EDitor: For MacOS X (Version 6.76) [Computer Software]. Dunedin, New Zealand: Department of Biochemistry, University of Otago.

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