89. M Rousseau, T Oulavallickal, A Williamson, V Arcus, WM Patrick, J Hicks (2024). Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus. Nucleic Acids Research, 52, 3924-3937.
88. JC Mainwaring, JNA Vink & ML Gerth (2023). Plant-pathogen management in a native forest ecosystem. Current Biology, 33, R500-R505.
87. CJ Matthews & WM Patrick (2023). An enzyme-centric approach for constructing an amperometric L-malate biosensor with a long and programmable linear range. Protein Science, 32, e4743.
86. KA Ramsay, A Rehman, ST Wardell, LW Martin, SC Bell, WM Patrick, C Winstanley & IL Lamont (2023). Ceftazidime resistance in Pseudomonas aeruginosa is multigenic and complex. PLoS One, 18, e0285856.
85. JNA Vink, M Hayhurst & ML Gerth (2023). Harnessing CRISPR-Cas for oomycete genome editing. Trends in Microbiology, 31, 947-958.
84. I Matsumura & WM Patrick (2023). Dan Tawfik’s lessons for protein engineers about enzymes adapting to new substrates. Biochemistry, 62, 158-162.
83. LJ Stevenson, KJ Robins, JK Sharma, EM Williams, AV Sharrock, AK Williamson, VL Arcus, WM Patrick & DF Ackerley (2023). Development of a compartmentalised self-replication protocol for selection of superior blunt-end DNA ligases. Enzyme and Microbial Technology, 163, 110153.
82. MJ Fairhurst, JNA Vink, JR Deslippe & ML Gerth (2023). A method for quantifying Phytophthora oospore viability using fluorescent dyes and automated image analysis. Phytofrontiers, 3, 497-505.
81. MP Cox, Y Guo, DJ Winter, D Sen, NC Cauldron, J Shiller, EL Bradley, AR Ganley, ML Gerth, RF Lacey, RL McDougal, P Panda, NM Williams, NJ Grunwald, CH Mesarich, RE Bradshaw (2022). Phytophthora agathidicida genome reveals adaptation in effector gene families, Frontiers in Microbiology, 13, 1038444.
80. E Noor, AI Flamholz, V Jayaraman, BL Ross, Y Cohen, WM Patrick, I Gruic-Sovulj & DS Tawfik (2022). Uniform binding and negative catalysis at the origin of enzymes. Protein Science, 31, e4381.
79. A Romero-Rivera, M Corbella, A Parracino, WM Patrick & SCL Kamerlin (2022). Complex loop dynamics underpin activity, specificity and evolvability in the (βα)8 barrels of histidine and tryptophan biosynthesis. JACS Au, 4, 943-960.
78. ESV Andrews & WM Patrick (2022). The hypothesized role of YbeZ in 16S rRNA maturation. Archives of Microbiology, 204, 114.
77. CH Miller, C Taylor, JG Owen, WM Patrick & CJ Vickers (2022). Draft genome sequence of a novel Rhizobium species isolated from the marine macroalga Codium fragile (oyster thief). Microbial Resource Announcements, e00030-22.
76. RF Lacey, MJ Fairhurst, KJ Daley, TA Ngata-Aerengamate, HR Patterson, WM Patrick & ML Gerth (2021). Assessing the effectiveness of oxathiapiprolin toward Phytophthora agathidicida, the causal agent of kauri dieback disease. FEMS Microbes, 2, xtab016.
75. MKG Ehrhardt, ML Gerth & JM Johnston (2021) Structure of a double CACHE chemoreceptor ligand-binding domain from Pseudomonas syringae provides insights into the basis of proline recognition. Biochemical and Biophysical Research Communications, 549, 194-199.
74. SA Murugayah, GB Evans, JDA Tyndall & ML Gerth (2021) A single point mutation converts a glutaryl-7-aminocephalosporanic acid acylase into an N-acyl-homoserine lactone acylase. Biotechnology Letters, 43, 1467-1473.
73. RF Lacey, BA Sullivan-Hill, JR Deslippe, RA Keyzers & ML Gerth (2021)The Fatty Acid Methyl Ester (FAME) profile of Phytophthora agathidicida and its potential use as a diagnostic tool. FEMS Microbiology Letters, 368, fnab113.
72. MC Summers, VV Nowak, MJ Fairhurst, JG Owen, ML Gerth & WM Patrick (2021). Complete genome sequence of a novel Pseudomonas fluorescens strain isolated from the flower of kūmarahou (Pomaderris kumeraho). Microbial Resource Announcements, 10, e00629-21.
71. A Srivastava, DEM Saavedra, B Thomson, JAL García, Z Zhao, WM Patrick, GJ Herndl & F Baltar (2021). Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean. ISME Journal, 15, 3375-3383.
70. MH Elias, JS Fraser, SCL Kamerlin, WM Patrick & CJ Jackson (2021). Dan Salah Tawfik (1955-2021)—a giant of protein evolution. EMBO Reports, 22, e53256.
69. JL Brewster, P Pachl, JLO McKellar, M Selmer, CJ Squire & WM Patrick (2021). Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis. Journal of Biological Chemistry, 296, 100797.
68. CJ Vickers, D Fraga & WM Patrick (2021). Quantifying the taxonomic bias in enzymology. Protein Science, 30, 914-921.
67. MKG Ehrhardt, ML Gerth & JM Johnston (2021). Structure of a double CACHE chemoreceptor ligand-binding domain from Pseudomonas syringae provides insight into the basis of proline recognition. Biochemical and Biophysical Research Communications, 549, 194-199.
66. SA Lawrence, HF Robinson, DP Furkert, MA Brimble & ML Gerth (2021). Screening a natural product-inspired library for anti-Phytophthora activities. Molecules, 26, 1819.
65. CJ Matthews, ESV Andrews & WM Patrick (2021). Enzyme-based amperometric biosensors for malate – a review. Analytica Chimica Acta, 1156, 338218.
64. KR Hall, KJ Robins, EM Williams, MH Rich, MJ Calcott, JN Copp, RF Little, R Schwörer, GB Evans, WM Patrick, & DF Ackerley (2020). Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active site residues. eLife, 9, e59081.
63. A Söderholm, MS Newton, WM Patrick & M Selmer (2020). Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa – decarboxylation is not essential for indole formation. Journal of Biological Chemistry 295, 15948-15956.
62. RE Bradshaw, SE Bellgard, A Black, BR Burns, ML Gerth, RL McDougal, PM Scott, NW Waipara, BS Weir, NM Williams, RC Winkworth, T Ashcroft, EL Bradley, PP Dijkwel, Y Guo, RF Lacey, CH Mesarich, P Panda & IJ Horner (2020). Phytophthora agathidicida: research progress, cultural perspectives and knowledge gaps in the control and management of kauri dieback in New Zealand. Plant Pathology, 69, 3-16.
61. JK Sharma, LJ Stevenson, KJ Robins, AK Williamson, WM Patrick & DF Ackerley (2020). Methods for competitive enrichment and evaluation of superior DNA ligases. Methods in Enzymology, 644, 209-225.
60. KA Davies, C Fitzgibbon [and 10 others], WM Patrick, N Kannan, EJ Petrie, PE Czabotar & JM Murphy (2020). Distinct pseudokinase domain conformations underlie divergent activation mechanisms among vertebrate MLKL orthologues. Nature Communications, 11, 3060.
59. EJ Dunkley, JD Chalmers, S Cho, TJ Finn & WM Patrick (2019). Assessment of Phenotype Microarray plates for rapid and high-throughput analysis of collateral sensitivity networks. PLoS One, e0219879.
58. J Bracegirdle, Z Sohail, MJ Fairhurst, ML Gerth, GC Zuccarello, MA Hashmi & RA Keyzers (2019). Costatone C – a new halogenated monoterpene from the New Zealand red alga Plocamium angustum. Marine Drugs, 17, 418.
57. SJT Wardell, A Rehman, LW Martin, C Winstanley, WM Patrick & IL Lamont (2019). A large-scale whole-genome comparison shows that experimental evolution in response to antibiotics predicts changes in naturally evolved clinical Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy, 63, e01619-19.
56. KA Ramsay, SJT Wardell, WM Patrick, B Brockway, DW Reid, C Winstanley, SC Bell & IL Lamont (2019). Genomic and phenotypic comparison of environmental and patient-derived isolates of Pseudomonas aeruginosa suggest that antimicrobial resistance is rare within the environment. Journal of Medical Microbiology, 68, 1591-1595.
55. B Mohanty, P Hanson-Manful, TJ Finn, CR Chambers, JLO McKellar, I Macindoe, S Helder, S Setiyaputra, JY Zhong, JP Mackay & WM Patrick (2019). The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G. Proteins: Structure, Function and Bioinformatics, 87, 699-705.
54. SL Lawrence, EJ Burgess, C Pairama, A Black, WM Patrick, I Mitchell, NB Perry & ML Gerth (2019) Mātauranga-guided screening of New Zealand native plants reveals flavonoids from kānuka (Kunzea robusta) with anti-Phytophthora activity. Journal of the Royal Society of New Zealand, 49, 137-154.
53. SA Murugayah & ML Gerth (2019). Engineering quorum quenching enzymes: progress and perspectives. Biochemical Society Transactions, 47, 793-800.
52. SA Murugayah, SL Warring & ML Gerth (2019). Optimisation of a high-throughput fluorescamine assay for detection of N-acyl-L-homoserine lactone acylase activity. Analytical Biochemistry, 566, 10-12.
51. A Rehman, WM Patrick & IL Lamont (2019). Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. Journal of Medical Microbiology, 68, 1-10.
50. I Mutreja, SL Warring, KS Lim, T Swadi, K Clinch, JM Mason, CR Sheen, DR Thompson, RG Ducati, ST Chambers, GB Evans, ML Gerth, AG Miller & TBF Woodfield (2019). Biofilm inhibition via delivery of novel methylthioadenosine nucleosidase inhibitors from PVA-tyramine hydrogels while supporting mesenchymal stromal cell viability. ACS Biomaterials Science & Engineering, 5, 748-758.
49. BE Clifton, JA Kaczmarski, PD Carr, ML Gerth, N Tokuriki & CJ Jackson (2018). Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nature Chemical Biology 14, 542-547.
48. MS Newton, VL Arcus, ML Gerth & WM Patrick (2018). Enzyme evolution: innovation is easy, optimization is complicated. Current Opinion in Structural Biology, 48, 110-116.
47. A Black, N Waipara & ML Gerth (2018). Calling time on New Zealand’s oldest tree species. Nature, 561, 177.
46. MKG Ehrhardt, SL Warring & ML Gerth (2018). A thermal shift assay for screening chemoreceptor ligand interactions. Methods in Molecular Biology, 1729, 281-290.
45. DCC Wai, TN Szyszka, AE Campbell, C Kwong, LE Wilkinson-White, APG Silva, JKK Low, AH Kwan, R Gamsjaeger, JD Chalmers, WM Patrick, B Lu, CR Vakoc, GA Blobel & JP Mackay (2018). The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. Journal of Biological Chemistry, 293, 7160-7175.
44. DJ Maddock, ML Gerth & WM Patrick (2017). An engineered glycerol dehydratase with improved activity for the conversion of meso-2,3-butanediol to butanone. Biotechnology Journal, 12, 1700480.
43. T Oulavallickal, JL Brewster, JLO McKellar, MJ Fairhurst, NA Tenci & ML Gerth (2017). The Pseudomonas syringae pv. actinidiae chemoreceptor protein F (PscF) periplasmic sensor domain: cloning, purification and X-ray crystallographic analysis. Acta Crystallographica Section F, 73, 701-705.
42. MP Ferla, JL Brewster, KR Hall, GB Evans & WM Patrick (2017). Primordial-like enzymes from bacteria with reduced genomes. Molecular Microbiology, 105, 508-524.
41. ML Gerth, Y Liu, W Jiao, X-X Zhang, EN Baker, JS Lott, PB Rainey & JM Johnston (2017). Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas. Proteins: Structure, Function and Bioinformatics, 85, 1580-1588.
40. WM Patrick (2017). Biochemical evolution: the pursuit of perfection (second edition). Quarterly Review of Biology, 92, 332-333.
39. SA Lawrence, CB Armstrong, WM Patrick & ML Gerth (2017). High-throughput chemical screening identifies compounds that inhibit different stages of the Phytophthora agathidicida and Phytophthora cinnamomi life cycles. Frontiers in Microbiology, 8, 1340.
38. MS Newton, X Guo, A Söderholm, J Näsvall, P Lundström, DI Andersson, M Selmer & WM Patrick (2017). Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes. Proceedings of the National Academy of Sciences USA, 114, 4727-4732.
37. CH Mesarich, J Rees-George, PP Gardner, FA Ghomi, ML Gerth, MT Andersen, EHA Rikkerink, PC Fineran & MD Templeton (2017). Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE, 12, e0172790.
36. JL Brewster, JLO McKellar, TJ Finn, J Newman, TS Peat & ML Gerth (2016). Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Scientific Reports, 6, 35198.
35. VWC Soo, Y Yosaatmadja, CJ Squire & WM Patrick (2016). Mechanistic and evolutionary insights from the reciprocal promiscuity of two pyridoxal phosphate-dependent enzymes. Journal of Biological Chemistry, 291, 19873-19887.
34. JL Brewster, TJ Finn, MA Ramirez & WM Patrick (2016). Whither life? Conjectures on the future evolution of biochemistry. Biology Letters, 12, 20160269.
33. HM Read, G Mills, S Johnson, P Tsai, J Dalton, L Barquist, CG Print, WM Patrick & S Wiles (2016). The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium. PeerJ, 4, e2130.
32. A Söderholm, X Guo, MS Newton, GB Evans, J Näsvall, WM Patrick & M Selmer (2015). Two-step ligand binding in a (βα)8 barrel enzyme – substrate-bound structures shed new light on the catalytic cycle of HisA. Journal of Biological Chemistry, 290, 24657-24668.
31. DJ Maddock, WM Patrick & ML Gerth (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design and Selection, 28, 251-258.
30. CR Chambers & WM Patrick (2015). Archaeal nucleic acid ligases and their potential in biotechnology. Archaea, 2015, 170571.
29. JLO McKellar, JJ Minnell & ML Gerth (2015). A high-throughput screen for ligand binding reveals the specificities of three amino acid chemoreceptors from Pseudomonas syringae pv. actinidiae. Molecular Microbiology, 96, 694-707.
28. MS Newton, VL Arcus & WM Patrick (2015). Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. Journal of the Royal Society Interface, 12, 20150036.
27. WM Patrick & ML Gerth (2014). ITCHY: Incremental truncation for the creation of hybrid enzymes. Methods in Molecular Biology, 1179, 225-244.
26. JN Copp, P Hanson-Manful, DF Ackerley & WM Patrick (2014). Error-prone PCR and effective generation of gene variant libraries for directed evolution. Methods in Molecular Biology, 1179, 3-22.
25. MP Ferla & WM Patrick (2014). Bacterial methionine biosynthesis. Microbiology, 160, 1571-1584.
24. HS Bernhardt & WM Patrick (2014). Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids. Journal of Molecular Evolution, 78, 307-309.
23. M Köpke, ML Gerth, DJ Maddock, AP Mueller, F Liew, SD Simpson & WM Patrick (2014). Reconstruction of an acetogenic 2,3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase. Applied and Environmental Microbiology, 80, 3394-3403.
22. MP Ferla, JC Thrash, SJ Giovannoni & WM Patrick (2013). New rRNA gene-based phylogenies of the Alphaproteobacteriaprovide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS ONE, 8, e83383.
21. RH Wilson, SK Morton, H Deiderick, ML Gerth, HA Paul, I Gerber, A Patel, AD Ellington, SP Hunicke-Smith & WM Patrick (2013). Engineered DNA ligases with improved activities in vitro. Protein Engineering, Design and Selection, 26, 471-478.
20. M Saraswat, RS Grand & WM Patrick (2013). Desalting DNA by drop dialysis increases library size upon transformation. Bioscience, Biotechnology and Biochemistry, 77, 402-404.
19. P Hanson-Manful & WM Patrick (2013). Construction and analysis of randomized protein-encoding libraries using error-prone PCR. Methods in Molecular Biology, 996, 251-267.
18. ML Gerth, MP Ferla & PB Rainey (2012). The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1. Environmental Microbiology, 14, 1929-1940.
17. ML Gerth, LV Nigon & WM Patrick (2012). Characterization of the indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa PAO1. The Protein Journal, 31, 359-365.
16. S Setiyaputra, JP Mackay & WM Patrick (2011). The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold. Journal of Molecular Biology, 408, 291-303.
15. VWC Soo, P Hanson-Manful & WM Patrick (2011). Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proceedings of the National Academy of Sciences USA, 108, 1484-1489.
14. WM Patrick, Y Nakatani, SM Cutfield, ML Sharpe, RJ Ramsay & JF Cutfield (2010). Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe ‘clamp’ at the active site entrance. FEBS Journal, 277, 4549-4561.
13. AE Firth & WM Patrick (2008). GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Research, 36, W281-W285.
12. WM Patrick & I Matsumura (2008). A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. Journal of Molecular Biology, 377, 323-336.
11. ML Gerth & S Lutz (2007). Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. Journal of Molecular Biology, 370, 742-751.
10. WM Patrick, EM Quandt, DB Swartzlander & I Matsumura (2007). Multicopy suppression underpins metabolic evolvability. Molecular Biology and Evolution, 24, 2716-2722.
9. ML Gerth & S Lutz (2007). Mutagenesis of non-conserved active site residues improves the activity and narrows the specificity of human thymidine kinase 2. Biochemical and Biophysical Research Communications, 354, 802-807.
8. TL O’Loughlin, WM Patrick & I Matsumura (2006). Natural history as a predictor of protein evolvability. Protein Engineering, Design and Selection, 19, 439-442.
7. AE Firth & WM Patrick (2005). Statistics of protein library construction. Bioinformatics, 21, 3314-3315.
6. WM Patrick & JM Blackburn (2005). In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase. FEBS Journal, 272, 3684-3697.
5. WM Patrick & AE Firth (2005). Strategies and computational tools for improving randomized protein libraries. Biomolecular Engineering, 22, 105-112.
4. ML Gerth, WM Patrick & S Lutz (2004). A second-generation system for unbiased reading frame selection. Protein Engineering, Design and Selection, 17, 595-602.
3. S Lutz & WM Patrick (2004). Novel methods for directed evolution of enzymes: quality, not quantity. Current Opinion in Biotechnology, 15, 291-297.
2. WM Patrick, AE Firth & JM Blackburn (2003). User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Engineering, 16, 451-457.
1. WM Patrick, J Weisner & JM Blackburn (2002). Site-directed mutagenesis of Tyr354 of Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance. ChemBioChem, 3, 789-792.