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John Parkinson

TitleSenior Scientist
InstitutionThe Hospital for Sick Children
DepartmentMolecular Medicine
Address555 University Avenue
Toronto ON M5G 1X8
Phone416-813-1500
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Zou A, Sharif S, Parkinson J. Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome. NPJ Biofilms Microbiomes. 2018; 4:27. PMID: 30455975.
      View in: PubMed
    2. Yitbarek A, Taha-Abdelaziz K, Hodgins DC, Read L, Nagy É, Weese JS, Caswell JL, Parkinson J, Sharif S. Author Correction: Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Sci Rep. 2018 Oct 31; 8(1):16367. PMID: 30382111.
      View in: PubMed
    3. Nursimulu N, Xu LL, Wasmuth JD, Krukov I, Parkinson J. Improved enzyme annotation with EC-specific cutoffs using DETECT v2. Bioinformatics. 2018 Oct 01; 34(19):3393-3395. PMID: 29722785.
      View in: PubMed
    4. Yitbarek A, Taha-Abdelaziz K, Hodgins DC, Read L, Nagy É, Weese JS, Caswell JL, Parkinson J, Sharif S. Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Sci Rep. 2018 Sep 04; 8(1):13189. PMID: 30181578.
      View in: PubMed
    5. Swapna LS, Molinaro AM, Lindsay-Mosher N, Pearson BJ, Parkinson J. Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. Genome Biol. 2018 08 24; 19(1):124. PMID: 30143032.
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    6. Piñas GE, DeSantis MD, Parkinson JS. Noncritical Signaling Role of a Kinase-Receptor Interaction Surface in the Escherichia coli Chemosensory Core Complex. J Mol Biol. 2018 Mar 30; 430(7):1051-1064. PMID: 29453948.
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    7. Yitbarek A, Alkie T, Taha-Abdelaziz K, Astill J, Rodriguez-Lecompte JC, Parkinson J, Nagy É, Sharif S. Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2. Benef Microbes. 2018 Apr 25; 9(3):417-427. PMID: 29380643.
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    8. Yitbarek A, Weese JS, Alkie TN, Parkinson J, Sharif S. Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens. FEMS Microbiol Ecol. 2018 Jan 01; 94(1). PMID: 29228270.
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    9. Popovic A, Parkinson J. Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing. Methods Mol Biol. 2018; 1849:29-48. PMID: 30298246.
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    10. Adeolu M, Parkinson J, Xiong X. Analyzing Metabolic Pathways in Microbiomes. Methods Mol Biol. 2018; 1849:291-307. PMID: 30298261.
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    11. Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Global landscape of cell envelope protein complexes in Escherichia coli. Nat Biotechnol. 2018 Jan; 36(1):103-112. PMID: 29176613.
      View in: PubMed
    12. Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-?B Signaling. Cell Syst. 2017 Dec 27; 5(6):564-577.e12. PMID: 29128334.
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    13. Xiong X, Bales ES, Ir D, Robertson CE, McManaman JL, Frank DN, Parkinson J. Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome. 2017 09 06; 5(1):117. PMID: 28877764.
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    14. Zhang J, Khan A, Kennard A, Grigg ME, Parkinson J. PopNet: A Markov Clustering Approach to Study Population Genetic Structure. Mol Biol Evol. 2017 07 01; 34(7):1799-1811. PMID: 28383661.
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    15. Vetere G, Kenney JW, Tran LM, Xia F, Steadman PE, Parkinson J, Josselyn SA, Frankland PW. Chemogenetic Interrogation of a Brain-wide Fear Memory Network in Mice. Neuron. 2017 Apr 19; 94(2):363-374.e4. PMID: 28426969.
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    16. Bertschi NL, Toenhake CG, Zou A, Niederwieser I, Henderson R, Moes S, Jenoe P, Parkinson J, Bartfai R, Voss TS. Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA. Nat Microbiol. 2017 Mar 13; 2:17033. PMID: 28288093.
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    17. Swapna LS, Parkinson J. Genomics of apicomplexan parasites. Crit Rev Biochem Mol Biol. 2017 06; 52(3):254-273. PMID: 28276701.
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    18. Lai RZ, Gosink KK, Parkinson JS. Signaling Consequences of Structural Lesions that Alter the Stability of Chemoreceptor Trimers of Dimers. J Mol Biol. 2017 03 24; 429(6):823-835. PMID: 28215934.
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    19. Frank V, Piñas GE, Cohen H, Parkinson JS, Vaknin A. Networked Chemoreceptors Benefit Bacterial Chemotaxis Performance. MBio. 2016 12 20; 7(6). PMID: 27999161.
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    20. Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol. 2016 Nov 21; 2:16216. PMID: 27869790.
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    21. Ames P, Hunter S, Parkinson JS. Evidence for a Helix-Clutch Mechanism of Transmembrane Signaling in a Bacterial Chemoreceptor. J Mol Biol. 2016 09 25; 428(19):3776-88. PMID: 27019297; PMCID: PMC5023463 [Available on 09/25/17].
    22. Cromar GL, Zhao A, Xiong X, Swapna LS, Loughran N, Song H, Parkinson J. PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. Database (Oxford). 2016; 2016. PMID: 26980519; PMCID: PMC4792532.
    23. McCartney G, Bouttell J, Craig N, Craig P, Graham L, Lakha F, Lewsey J, McAdams R, MacPherson M, Minton J, Parkinson J, Robinson M, Shipton D, Taulbut M, Walsh D, Beeston C. Explaining trends in alcohol-related harms in Scotland 1991-2011 (II): policy, social norms, the alcohol market, clinical changes and a synthesis. Public Health. 2016 Mar; 132:24-32. PMID: 26921977.
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    24. McCartney G, Bouttell J, Craig N, Craig P, Graham L, Lakha F, Lewsey J, McAdams R, MacPherson M, Minton J, Parkinson J, Robinson M, Shipton D, Taulbut M, Walsh D, Beeston C. Explaining trends in alcohol-related harms in Scotland, 1991-2011 (I): the role of incomes, effects of socio-economic and political adversity and demographic change. Public Health. 2016 Mar; 132:13-23. PMID: 26917268.
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    25. Jiang Y, Xiong X, Danska J, Parkinson J. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. Microbiome. 2016 Jan 12; 4:2. PMID: 26757703; PMCID: PMC4710996.
    26. Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep. 2016 Jan 26; 14(3):648-661. PMID: 26774489.
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    27. Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nat Commun. 2016 Jan 07; 7:10147. PMID: 26738725; PMCID: PMC4729833.
    28. Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data Brief. 2016 Mar; 6:715-21. PMID: 26870755; PMCID: PMC4738005.
    29. Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Panorama of ancient metazoan macromolecular complexes. Nature. 2015 Sep 17; 525(7569):339-44. PMID: 26344197; PMCID: PMC5036527.
    30. Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G. Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One. 2015; 10(7):e0134759. PMID: 26218289; PMCID: PMC4517915.
    31. Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G. Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One. 2015; 10(6):e0130902. PMID: 26125937; PMCID: PMC4509574.
    32. Cromar GL, Zhao A, Yang A, Parkinson J. Hyperscape: visualization for complex biological networks. Bioinformatics. 2015 Oct 15; 31(20):3390-1. PMID: 26108529.
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    33. Kitanovic S, Ames P, Parkinson JS. A Trigger Residue for Transmembrane Signaling in the Escherichia coli Serine Chemoreceptor. J Bacteriol. 2015 Aug 01; 197(15):2568-79. PMID: 26013490; PMCID: PMC4518824.
    34. Blazejewski T, Nursimulu N, Pszenny V, Dangoudoubiyam S, Namasivayam S, Chiasson MA, Chessman K, Tonkin M, Swapna LS, Hung SS, Bridgers J, Ricklefs SM, Boulanger MJ, Dubey JP, Porcella SF, Kissinger JC, Howe DK, Grigg ME, Parkinson J. Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle. MBio. 2015 Feb 10; 6(1). PMID: 25670772; PMCID: PMC4337577.
    35. Bundalovic-Torma C, Parkinson J. Comparative Genomics and Evolutionary Modularity of Prokaryotes. Adv Exp Med Biol. 2015; 883:77-96. PMID: 26621462.
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    36. Wetzel J, Herrmann S, Swapna LS, Prusty D, John Peter AT, Kono M, Saini S, Nellimarla S, Wong TW, Wilcke L, Ramsay O, Cabrera A, Biller L, Heincke D, Mossman K, Spielmann T, Ungermann C, Parkinson J, Gilberger TW. The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite. J Biol Chem. 2015 Jan 16; 290(3):1712-28. PMID: 25425642; PMCID: PMC4340414.
    37. Celaj A, Markle J, Danska J, Parkinson J. Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. Microbiome. 2014; 2:39. PMID: 25411636; PMCID: PMC4236897.
    38. Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, Parkinson J. New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biol Evol. 2014 Oct 15; 6(10):2897-917. PMID: 25323955; PMCID: PMC4224354.
    39. Lai RZ, Parkinson JS. Functional suppression of HAMP domain signaling defects in the E. coli serine chemoreceptor. J Mol Biol. 2014 Oct 23; 426(21):3642-55. PMID: 25134756; PMCID: PMC4188812.
    40. Alniss HY, Salvia MV, Sadikov M, Golovchenko I, Anthony NG, Khalaf AI, MacKay SP, Suckling CJ, Parkinson JA. Recognition of the DNA minor groove by thiazotropsin analogues. Chembiochem. 2014 Sep 05; 15(13):1978-90. PMID: 25045155.
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    41. Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res. 2014 Oct; 24(10):1676-85. PMID: 25015382; PMCID: PMC4199364.
    42. Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. 2014 Feb; 10(2):e1004120. PMID: 24586182; PMCID: PMC3930520.
    43. Song C, Chiasson MA, Nursimulu N, Hung SS, Wasmuth J, Grigg ME, Parkinson J. Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii. Mol Syst Biol. 2013 Nov 19; 9:708. PMID: 24247825; PMCID: PMC4039375.
    44. Nishiyama S, Garzón A, Parkinson JS. Mutational analysis of the P1 phosphorylation domain in Escherichia coli CheA, the signaling kinase for chemotaxis. J Bacteriol. 2014 Jan; 196(2):257-64. PMID: 24163342; PMCID: PMC3911240.
    45. Briegel A, Ames P, Gumbart JC, Oikonomou CM, Parkinson JS, Jensen GJ. The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state. Mol Microbiol. 2013 Sep; 89(5):831-41. PMID: 23802570; PMCID: PMC3763515.
    46. Leung HC, Yiu SM, Parkinson J, Chin FY. IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology. J Comput Biol. 2013 Jul; 20(7):540-50. PMID: 23829653.
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    47. Salvia MV, Addison F, Alniss HY, Buurma NJ, Khalaf AI, Mackay SP, Anthony NG, Suckling CJ, Evstigneev MP, Santiago AH, Waigh RD, Parkinson JA. Thiazotropsin aggregation and its relationship to molecular recognition in the DNA minor groove. Biophys Chem. 2013 Sep; 179:1-11. PMID: 23714424.
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    48. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai X, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PWH, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y, Cai J, Soberón X, Olson PD, Laclette JP, Brehm K, Berriman M. The genomes of four tapeworm species reveal adaptations to parasitism. Nature. 2013 Apr 04; 496(7443):57-63. PMID: 23485966.
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    49. Khoshraftar S, Hung S, Khan S, Gong Y, Tyagi V, Parkinson J, Sain M, Moses AM, Christendat D. Sequencing and annotation of the Ophiostoma ulmi genome. BMC Genomics. 2013 Mar 12; 14:162. PMID: 23496816; PMCID: PMC3618308.
    50. Wheeler AL, Teixeira CM, Wang AH, Xiong X, Kovacevic N, Lerch JP, McIntosh AR, Parkinson J, Frankland PW. Identification of a functional connectome for long-term fear memory in mice. PLoS Comput Biol. 2013; 9(1):e1002853. PMID: 23300432; PMCID: PMC3536620.
    51. Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nat Commun. 2013; 4:2881. PMID: 24335957; PMCID: PMC4310728.
    52. Parkinson J, Wasmuth JD, Salinas G, Bizarro CV, Sanford C, Berriman M, Ferreira HB, Zaha A, Blaxter ML, Maizels RM, Fernández C. A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PLoS Negl Trop Dis. 2012; 6(11):e1897. PMID: 23209850.
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    53. Wasmuth JD, Pszenny V, Haile S, Jansen EM, Gast AT, Sher A, Boyle JP, Boulanger MJ, Parkinson J, Grigg ME. Integrated bioinformatic and targeted deletion analyses of the SRS gene superfamily identify SRS29C as a negative regulator of Toxoplasma virulence. MBio. 2012 Nov 13; 3(6). PMID: 23149485; PMCID: PMC3509429.
    54. He D, Miao M, Sitarz EE, Muiznieks LD, Reichheld S, Stahl RJ, Keeley FW, Parkinson J. Polymorphisms in the human tropoelastin gene modify in vitro self-assembly and mechanical properties of elastin-like polypeptides. PLoS One. 2012; 7(9):e46130. PMID: 23049958; PMCID: PMC3458006.
    55. Urban D, Li L, Christensen H, Pluthero FG, Chen SZ, Puhacz M, Garg PM, Lanka KK, Cummings JJ, Kramer H, Wasmuth JD, Parkinson J, Kahr WH. The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet a-granule biogenesis. Blood. 2012 Dec 13; 120(25):5032-40. PMID: 23002115; PMCID: PMC3538988.
    56. Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One. 2012; 7(4):e36009. PMID: 22558305; PMCID: PMC3338770.
    57. Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A, Wastling JM. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog. 2012; 8(3):e1002567. PMID: 22457617; PMCID: PMC3310773.
    58. Kostjukov VV, Hernandez Santiago AA, Rojas Rodriguez F, Rosas Castilla S, Parkinson JA, Evstigneev MP. Energetics of ligand binding to the DNA minor groove. Phys Chem Chem Phys. 2012 Apr 28; 14(16):5588-600. PMID: 22419053.
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    59. Kono M, Herrmann S, Loughran NB, Cabrera A, Engelberg K, Lehmann C, Sinha D, Prinz B, Ruch U, Heussler V, Spielmann T, Parkinson J, Gilberger TW. Evolution and architecture of the inner membrane complex in asexual and sexual stages of the malaria parasite. Mol Biol Evol. 2012 Sep; 29(9):2113-32. PMID: 22389454.
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    60. Song H, Parkinson J. Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures. PLoS Comput Biol. 2012; 8(3):e1002406. PMID: 22396636; PMCID: PMC3291537.
    61. Cromar GL, Xiong X, Chautard E, Ricard-Blum S, Parkinson J. Toward a systems level view of the ECM and related proteins: a framework for the systematic definition and analysis of biological systems. Proteins. 2012 Jun; 80(6):1522-44. PMID: 22275077.
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    62. Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011 Nov; 7(11):e1002377. PMID: 22125496; PMCID: PMC3219608.
    63. Kahr WH, Hinckley J, Li L, Schwertz H, Christensen H, Rowley JW, Pluthero FG, Urban D, Fabbro S, Nixon B, Gadzinski R, Storck M, Wang K, Ryu GY, Jobe SM, Schutte BC, Moseley J, Loughran NB, Parkinson J, Weyrich AS, Di Paola J. Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome. Nat Genet. 2011 Jul 17; 43(8):738-40. PMID: 21765413.
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    64. Xiong X, Song H, On T, Lochovsky L, Provart NJ, Parkinson J. PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya. Bioinformatics. 2011 Mar 15; 27(6):877-8. PMID: 21252074.
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    65. Massazza DA, Parkinson JS, Studdert CA. Cross-linking evidence for motional constraints within chemoreceptor trimers of dimers. Biochemistry. 2011 Feb 08; 50(5):820-7. PMID: 21174433; PMCID: PMC3042772.
    66. Hung SS, Parkinson J. Post-genomics resources and tools for studying apicomplexan metabolism. Trends Parasitol. 2011 Mar; 27(3):131-40. PMID: 21145790.
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    67. Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ. Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PLoS One. 2010 Nov 29; 5(11):e14122. PMID: 21124763; PMCID: PMC2993927.
    68. Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, Wodak SJ. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res. 2011 Jan; 39(Database issue):D889-94. PMID: 20876685; PMCID: PMC3013761.
    69. Wittayanarakul K, Anthony NG, Treesuwan W, Hannongbua S, Alniss H, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP. Ranking ligand affinity for the DNA minor groove by experiment and simulation. ACS Med Chem Lett. 2010 Nov 11; 1(8):376-80. PMID: 24900221; PMCID: PMC4007966.
    70. On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 2010 Jul; 78(9):2075-89. PMID: 20455264.
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    71. Yu Z, Reichheld SE, Savchenko A, Parkinson J, Davidson AR. A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators. J Mol Biol. 2010 Jul 23; 400(4):847-64. PMID: 20595046.
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    72. Hung SS, Wasmuth J, Sanford C, Parkinson J. DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum. Bioinformatics. 2010 Jul 15; 26(14):1690-8. PMID: 20513663.
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    73. Cardozo MJ, Massazza DA, Parkinson JS, Studdert CA. Disruption of chemoreceptor signalling arrays by high levels of CheW, the receptor-kinase coupling protein. Mol Microbiol. 2010 Mar; 75(5):1171-81. PMID: 20487303.
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    74. Shan S, Ellis T, Fenwick S, Edwards J, O'Dea M, Parkinson J. Biological and genetic characterization of a low-pathogenicity avian influenza H6N2 virus originating from a healthy Eurasian coot. Arch Virol. 2010 Mar; 155(3):403-9. PMID: 20112121.
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    75. Parkinson JS. Signaling mechanisms of HAMP domains in chemoreceptors and sensor kinases. Annu Rev Microbiol. 2010; 64:101-22. PMID: 20690824.
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    76. Persaud A, Alberts P, Amsen EM, Xiong X, Wasmuth J, Saadon Z, Fladd C, Parkinson J, Rotin D. Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Mol Syst Biol. 2009; 5:333. PMID: 19953087; PMCID: PMC2824488.
    77. Chong YT, Gidda SK, Sanford C, Parkinson J, Mullen RT, Goring DR. Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies. New Phytol. 2010 Jan; 185(2):401-19. PMID: 19895414.
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    78. Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J. The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol. 2009 Oct; 5(10):e1000523. PMID: 19798435; PMCID: PMC2739439.
    79. Treesuwan W, Wittayanarakul K, Anthony NG, Huchet G, Alniss H, Hannongbua S, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP. A detailed binding free energy study of 2:1 ligand-DNA complex formation by experiment and simulation. Phys Chem Chem Phys. 2009 Dec 07; 11(45):10682-93. PMID: 20145812.
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    80. González S, Fló M, Margenat M, Durán R, González-Sapienza G, Graña M, Parkinson J, Maizels RM, Salinas G, Alvarez B, Fernández C. A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk. PLoS One. 2009 Sep 17; 4(9):e7009. PMID: 19759914.
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    81. Peregrín-Alvarez JM, Sanford C, Parkinson J. The conservation and evolutionary modularity of metabolism. Genome Biol. 2009; 10(6):R63. PMID: 19523219; PMCID: PMC2718497.
    82. Samiric T, Parkinson J, Ilic MZ, Cook J, Feller JA, Handley CJ. Changes in the composition of the extracellular matrix in patellar tendinopathy. Matrix Biol. 2009 May; 28(4):230-6. PMID: 19371780.
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    83. Wasmuth J, Daub J, Peregrín-Alvarez JM, Finney CA, Parkinson J. The origins of apicomplexan sequence innovation. Genome Res. 2009 Jul; 19(7):1202-13. PMID: 19363216; PMCID: PMC2704437.
    84. Diakos CI, Messerle BA, Murdoch Pdel S, Parkinson JA, Sadler PJ, Fenton RR, Hambley TW. Identification by NMR spectroscopy of the two stereoisomers of the platinum complex [PtCl2(S-ahaz)] (S-ahaz = 3(S)-aminohexahydroazepine) bound to a DNA 14-mer oligonucleotide. NMR evidence of structural alteration of a platinated A x T-rich 14-mer DNA duplex. Inorg Chem. 2009 Apr 06; 48(7):3047-56. PMID: 19265406.
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    85. Anthony NG, Breen D, Donoghue G, Khalaf AI, Mackay SP, Parkinson JA, Suckling CJ. A new synthesis of alkene-containing minor-groove binders and essential hydrogen bonding in binding to DNA and in antibacterial activity. Org Biomol Chem. 2009 May 07; 7(9):1843-50. PMID: 19590779.
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    86. Peregrín-Alvarez JM, Parkinson J. Phylogenomic analysis of EST datasets. Methods Mol Biol. 2009; 533:257-76. PMID: 19277568.
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    87. Parkinson J, Blaxter M. Expressed sequence tags: an overview. Methods Mol Biol. 2009; 533:1-12. PMID: 19277571.
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    88. Mowery P, Ostler JB, Parkinson JS. Different signaling roles of two conserved residues in the cytoplasmic hairpin tip of Tsr, the Escherichia coli serine chemoreceptor. J Bacteriol. 2008 Dec; 190(24):8065-74. PMID: 18931127; PMCID: PMC2593199.
    89. Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res. 2008 Aug; 18(8):1247-58. PMID: 18456862; PMCID: PMC2493427.
    90. He D, Parkinson J. SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. Bioinformatics. 2008 Apr 01; 24(7):1016-7. PMID: 18304932.
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    91. Hazelbauer GL, Falke JJ, Parkinson JS. Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci. 2008 Jan; 33(1):9-19. PMID: 18165013; PMCID: PMC2890293.
    92. Anthony NG, Breen D, Clarke J, Donoghue G, Drummond AJ, Ellis EM, Gemmell CG, Helesbeux JJ, Hunter IS, Khalaf AI, Mackay SP, Parkinson JA, Suckling CJ, Waigh RD. Antimicrobial lexitropsins containing amide, amidine, and alkene linking groups. J Med Chem. 2007 Nov 29; 50(24):6116-25. PMID: 17960927.
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    93. Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J. Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res. 2008 Jan; 36(Database issue):D632-6. PMID: 17942431; PMCID: PMC2238847.
    94. Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007 Sep 21; 317(5845):1756-60. PMID: 17885136; PMCID: PMC2613796.
    95. Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D. Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol. 2007; 3:116. PMID: 17551511; PMCID: PMC1911201.
    96. He D, Chung M, Chan E, Alleyne T, Ha KC, Miao M, Stahl RJ, Keeley FW, Parkinson J. Comparative genomics of elastin: Sequence analysis of a highly repetitive protein. Matrix Biol. 2007 Sep; 26(7):524-40. PMID: 17628459.
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    97. Tait KM, Parkinson JA, Gibson DI, Richardson PR, Ebenezer WJ, Hutchings MG, Jones AC. Structural characterisation of the photoisomers of reactive sulfonated azo dyes by NMR spectroscopy and DFT calculations. Photochem Photobiol Sci. 2007 Sep; 6(9):1010-8. PMID: 17721601.
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    98. Parkinson JS. Ancient chemoreceptors retain their flexibility. Proc Natl Acad Sci U S A. 2007 Feb 20; 104(8):2559-60. PMID: 17301220; PMCID: PMC1815221.
    99. Peregrín-Alvarez JM, Parkinson J. The global landscape of sequence diversity. Genome Biol. 2007; 8(11):R238. PMID: 17996061; PMCID: PMC2258180.
    100. Liu HK, Berners-Price SJ, Wang F, Parkinson JA, Xu J, Bella J, Sadler PJ. Diversity in guanine-selective DNA binding modes for an organometallic ruthenium arene complex. Angew Chem Int Ed Engl. 2006 Dec 11; 45(48):8153-6. PMID: 17120267.
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    101. Sanford C, Yip ML, White C, Parkinson J. Cell++--simulating biochemical pathways. Bioinformatics. 2006 Dec 01; 22(23):2918-25. PMID: 17038347.
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    102. Chung MI, Miao M, Stahl RJ, Chan E, Parkinson J, Keeley FW. Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: Clues to the evolutionary history of elastins. Matrix Biol. 2006 Oct; 25(8):492-504. PMID: 16982180.
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    103. Liu HK, Wang F, Parkinson JA, Bella J, Sadler PJ. Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes. Chemistry. 2006 Aug 07; 12(23):6151-65. PMID: 16807967.
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    104. Ames P, Parkinson JS. Conformational suppression of inter-receptor signaling defects. Proc Natl Acad Sci U S A. 2006 Jun 13; 103(24):9292-7. PMID: 16751275; PMCID: PMC1482603.
    105. Zhao J, Parkinson JS. Mutational analysis of the chemoreceptor-coupling domain of the Escherichia coli chemotaxis signaling kinase CheA. J Bacteriol. 2006 May; 188(9):3299-307. PMID: 16621823; PMCID: PMC1447439.
    106. Gosink KK, Burón-Barral MC, Parkinson JS. Signaling interactions between the aerotaxis transducer Aer and heterologous chemoreceptors in Escherichia coli. J Bacteriol. 2006 May; 188(10):3487-93. PMID: 16672602; PMCID: PMC1482851.
    107. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30; 440(7084):637-43. PMID: 16554755.
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    108. Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biol. 2006; 7(8):R75. PMID: 26271136; PMCID: PMC1779591.
    109. Anthony NG, Huchet G, Johnston BF, Parkinson JA, Suckling CJ, Waigh RD, Mackay SP. In silico footprinting of ligands binding to the minor groove of DNA. J Chem Inf Model. 2005 Nov-Dec; 45(6):1896-907. PMID: 16309297.
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    110. Soares DC, Gerloff DL, Syme NR, Coulson AF, Parkinson J, Barlow PN. Large-scale modelling as a route to multiple surface comparisons of the CCP module family. Protein Eng Des Sel. 2005 Aug; 18(8):379-88. PMID: 15976010.
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    111. Parkinson JS, Ames P, Studdert CA. Collaborative signaling by bacterial chemoreceptors. Curr Opin Microbiol. 2005 Apr; 8(2):116-21. PMID: 15802240.
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    112. Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005 Feb 03; 433(7025):531-7. PMID: 15690043.
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    113. Peregrín-Alvarez JM, Yam A, Sivakumar G, Parkinson J. PartiGeneDB--collating partial genomes. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D303-7. PMID: 15608203; PMCID: PMC540063.
    114. Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter ML. A transcriptomic analysis of the phylum Nematoda. Nat Genet. 2004 Dec; 36(12):1259-67. PMID: 15543149.
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    115. Anthony NG, Johnston BF, Khalaf AI, MacKay SP, Parkinson JA, Suckling CJ, Waigh RD. Short lexitropsin that recognizes the DNA minor groove at 5'-ACTAGT-3': understanding the role of isopropyl-thiazole. J Am Chem Soc. 2004 Sep 15; 126(36):11338-49. PMID: 15355117.
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    116. Harcus YM, Parkinson J, Fernández C, Daub J, Selkirk ME, Blaxter ML, Maizels RM. Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites. Genome Biol. 2004; 5(6):R39. PMID: 15186490; PMCID: PMC463072.
    117. Anthony NG, Fox KR, Johnston BF, Khalaf AI, Mackay SP, McGroarty IS, Parkinson JA, Skellern GG, Suckling CJ, Waigh RD. DNA binding of a short lexitropsin. Bioorg Med Chem Lett. 2004 Mar 08; 14(5):1353-6. PMID: 14980697.
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    118. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M. PartiGene--constructing partial genomes. Bioinformatics. 2004 Jun 12; 20(9):1398-404. PMID: 14988115.
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    119. Studdert CA, Parkinson JS. Crosslinking snapshots of bacterial chemoreceptor squads. Proc Natl Acad Sci U S A. 2004 Feb 17; 101(7):2117-22. PMID: 14769919; PMCID: PMC357061.
    120. Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M. NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D427-30. PMID: 14681449; PMCID: PMC308753.
    121. Parkinson J, Blaxter M. Expressed sequence tags: analysis and annotation. Methods Mol Biol. 2004; 270:93-126. PMID: 15153624.
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    122. Dabos KJ, Nelson LJ, Hewage CH, Parkinson JA, Howie AF, Sadler IH, Hayes PC, Plevris JN. Comparison of bioenergetic activity of primary porcine hepatocytes cultured in four different media. Cell Transplant. 2004; 13(3):213-29. PMID: 15191159.
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    123. Chen H, Parkinson JA, Nováková O, Bella J, Wang F, Dawson A, Gould R, Parsons S, Brabec V, Sadler PJ. Induced-fit recognition of DNA by organometallic complexes with dynamic stereogenic centers. Proc Natl Acad Sci U S A. 2003 Dec 09; 100(25):14623-8. PMID: 14657383; PMCID: PMC299748.
    124. Liang X, Weishäupl M, Parkinson JA, Parsons S, McGregor PA, Sadler PJ. Selective recognition of configurational substates of zinc cyclam by carboxylates: implications for the design and mechanism of action of anti-HIV agents. Chemistry. 2003 Oct 06; 9(19):4709-17. PMID: 14566877.
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    125. Parkinson J, Mitreva M, Hall N, Blaxter M, McCarter JP. 400000 nematode ESTs on the Net. Trends Parasitol. 2003 Jul; 19(7):283-6. PMID: 12855373.
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    126. Kenyon F, Welsh M, Parkinson J, Whitton C, Blaxter ML, Knox DP. Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis--allergens, proteases and free-radical scavengers. Parasitology. 2003 May; 126(Pt 5):451-60. PMID: 12793649.
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    127. Dabos KJ, Parkinson JA, Nelson LJ, Sadler IH, Hayes PC, Plevris JN. The effect of hypothermia on primary porcine hepatocyte metabolism monitored by (1H) nuclear magnetic resonance spectroscopy. Eur J Gastroenterol Hepatol. 2003 Mar; 15(3):283-93. PMID: 12610324.
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    128. Parkinson J, Blaxter M. SimiTri--visualizing similarity relationships for groups of sequences. Bioinformatics. 2003 Feb 12; 19(3):390-5. PMID: 12584125.
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    129. Müller P, Schröder B, Parkinson JA, Kratochwil NA, Coxall RA, Parkin A, Parsons S, Sadler PJ. Nucleotide cross-linking induced by photoreactions of platinum(IV)-azide complexes. Angew Chem Int Ed Engl. 2003 Jan 20; 42(3):335-9. PMID: 12548693.
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    130. Chen H, Parkinson JA, Morris RE, Sadler PJ. Highly selective binding of organometallic ruthenium ethylenediamine complexes to nucleic acids: novel recognition mechanisms. J Am Chem Soc. 2003 Jan 08; 125(1):173-86. PMID: 12515520.
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    131. Parkinson J, Guiliano DB, Blaxter M. Making sense of EST sequences by CLOBBing them. BMC Bioinformatics. 2002 Oct 25; 3:31. PMID: 12398795; PMCID: PMC137596.
    132. Blindauer CA, Harrison MD, Robinson AK, Parkinson JA, Bowness PW, Sadler PJ, Robinson NJ. Multiple bacteria encode metallothioneins and SmtA-like zinc fingers. Mol Microbiol. 2002 Sep; 45(5):1421-32. PMID: 12207707.
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    133. Wang F, Chen H, Parkinson JA, Murdoch Pdel S, Sadler PJ. Reactions of a ruthenium(II) arene antitumor complex with cysteine and methionine. Inorg Chem. 2002 Aug 26; 41(17):4509-23. PMID: 12184769.
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    134. Liang X, Parkinson JA, Parsons S, Weishäupl M, Sadler PJ. Cadmium cyclam complexes: interconversion of cis and trans configurations and fixation of CO(2). Inorg Chem. 2002 Aug 26; 41(17):4539-47. PMID: 12184772.
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    135. Liang X, Parkinson JA, Weishäupl M, Gould RO, Paisey SJ, Park HS, Hunter TM, Blindauer CA, Parsons S, Sadler PJ. Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor. J Am Chem Soc. 2002 Aug 07; 124(31):9105-12. PMID: 12149014.
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    136. Loke P, Nair MG, Parkinson J, Guiliano D, Blaxter M, Allen JE. IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype. BMC Immunol. 2002 Jul 04; 3:7. PMID: 12098359; PMCID: PMC117781.
    137. Dabos KJ, Parkinson JA, Hewage C, Nelson LJ, Sadler IH, Hayes PC, Plevris JN. 1H NMR spectroscopy as a tool to evaluate key metabolic functions of primary porcine hepatocytes after cryopreservation. NMR Biomed. 2002 May; 15(3):241-50. PMID: 11968140.
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    138. Chen H, Parkinson JA, Parsons S, Coxall RA, Gould RO, Sadler PJ. Organometallic ruthenium(II) diamine anticancer complexes: arene-nucleobase stacking and stereospecific hydrogen-bonding in guanine adducts. J Am Chem Soc. 2002 Mar 27; 124(12):3064-82. PMID: 11902898.
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    139. Zhong W, Parkinson JA, Guo M, Sadler PJ. Unusual features for zirconium(IV) binding to human serum transferrin. J Biol Inorg Chem. 2002 Jun; 7(6):589-99. PMID: 12072964.
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    140. Blaxter M, Daub J, Guiliano D, Parkinson J, Whitton C. The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans R Soc Trop Med Hyg. 2002 Jan-Feb; 96(1):7-17. PMID: 11925998.
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    141. Parkinson J, Whitton C, Guiliano D, Daub J, Blaxter M. 200000 nematode expressed sequence tags on the Net. Trends Parasitol. 2001 Aug 01; 17(8):394-396. PMID: 11700236.
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    142. Loukas A, Hintz M, Linder D, Mullin NP, Parkinson J, Tetteh KK, Maizels RM. A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs. J Biol Chem. 2000 Dec 15; 275(50):39600-7. PMID: 10950959.
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    143. Smith SA, Mullin NP, Parkinson J, Shchelkunov SN, Totmenin AV, Loparev VN, Srisatjaluk R, Reynolds DN, Keeling KL, Justus DE, Barlow PN, Kotwal GJ. Conserved surface-exposed K/R-X-K/R motifs and net positive charge on poxvirus complement control proteins serve as putative heparin binding sites and contribute to inhibition of molecular interactions with human endothelial cells: a novel mechanism for evasion of host defense. J Virol. 2000 Jun; 74(12):5659-66. PMID: 10823874; PMCID: PMC112054.
    144. Bibikov SI, Barnes LA, Gitin Y, Parkinson JS. Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):5830-5. PMID: 10811894; PMCID: PMC18519.
    145. Cho HS, Lee SY, Yan D, Pan X, Parkinson JS, Kustu S, Wemmer DE, Pelton JG. NMR structure of activated CheY. J Mol Biol. 2000 Mar 31; 297(3):543-51. PMID: 10731410.
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    146. Kirkitadze MD, Henderson C, Price NC, Kelly SM, Mullin NP, Parkinson J, Dryden DT, Barlow PN. Central modules of the vaccinia virus complement control protein are not in extensive contact. Biochem J. 1999 Nov 15; 344 Pt 1:167-75. PMID: 10548547; PMCID: PMC1220627.
    147. Parkinson J, Brechet Y, Gordon R. Centric diatom morphogenesis: a model based on a DLA algorithm investigating the potential role of microtubules. Biochim Biophys Acta. 1999 Oct 13; 1452(1):89-102. PMID: 10525163.
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    148. Kratochwil NA, Parkinson JA, Bednarski PJ, Sadler PJ. Nucleotide Platination Induced by Visible Light. Angew Chem Int Ed Engl. 1999 May 17; 38(10):1460-1463. PMID: 29711587.
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    149. Parkinson J, Gordon R. Beyond micromachining: the potential of diatoms. Trends Biotechnol. 1999 May; 17(5):190-6. PMID: 10322443.
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    150. Parkinson J, Sadat-Ebrahimi S, Wilton A, McKie JH, Andrews J, Douglas KT. Predictability of designing specific binding interactions for DNA minor groove ligands from NMR spectroscopy and molecular modeling: a copper(II)-activated DNA cleaver based on Hoechst 33258. Biochemistry. 1995 Dec 19; 34(50):16240-4. PMID: 8845347.
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    151. Lux R, Jahreis K, Bettenbrock K, Parkinson JS, Lengeler JW. Coupling the phosphotransferase system and the methyl-accepting chemotaxis protein-dependent chemotaxis signaling pathways of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Dec 05; 92(25):11583-7. PMID: 8524808; PMCID: PMC40446.
    152. Sanatinia H, Kofoid EC, Morrison TB, Parkinson JS. The smaller of two overlapping cheA gene products is not essential for chemotaxis in Escherichia coli. J Bacteriol. 1995 May; 177(10):2713-20. PMID: 7751280; PMCID: PMC176941.
    153. Ames P, Parkinson JS. Constitutively signaling fragments of Tsr, the Escherichia coli serine chemoreceptor. J Bacteriol. 1994 Oct; 176(20):6340-8. PMID: 7929006; PMCID: PMC196976.
    154. Fahrner KA, Block SM, Krishnaswamy S, Parkinson JS, Berg HC. A mutant hook-associated protein (HAP3) facilitates torsionally induced transformations of the flagellar filament of Escherichia coli. J Mol Biol. 1994 Apr 29; 238(2):173-86. PMID: 8158647.
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    155. Liu JD, Parkinson JS. Genetic evidence for interaction between the CheW and Tsr proteins during chemoreceptor signaling by Escherichia coli. J Bacteriol. 1991 Aug; 173(16):4941-51. PMID: 1860813; PMCID: PMC208182.
    156. Kofoid EC, Parkinson JS. Tandem translation starts in the cheA locus of Escherichia coli. J Bacteriol. 1991 Mar; 173(6):2116-9. PMID: 2002011; PMCID: PMC207748.
    157. Parkinson JA, Barber J, Douglas KT, Rosamond J, Sharples D. Minor-groove recognition of the self-complementary duplex d(CGCGAATTCGCG)2 by Hoechst 33258: a high-field NMR study. Biochemistry. 1990 Nov 06; 29(44):10181-90. PMID: 1703003.
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    158. Wolff C, Parkinson JS. Aspartate taxis mutants of the Escherichia coli tar chemoreceptor. J Bacteriol. 1988 Oct; 170(10):4509-15. PMID: 3049535; PMCID: PMC211483.
    159. Parkinson JS, Parker SR, Talbert PB, Houts SE. Interactions between chemotaxis genes and flagellar genes in Escherichia coli. J Bacteriol. 1983 Jul; 155(1):265-74. PMID: 6305913; PMCID: PMC217677.
    160. Parkinson JS, Huskey RJ. Deletion mutants of bacteriophage lambda. I. Isolation and initial characterization. J Mol Biol. 1971 Mar 14; 56(2):369-84. PMID: 4323931.
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    161. Parkinson JS. Deletion mutants of bacteriophage lambda. II. Genetic properties of att-defective mutants. J Mol Biol. 1971 Mar 14; 56(2):385-401. PMID: 5551395.
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    162. Davis RW, Parkinson JS. Deletion mutants of bacteriophage lambda. 3. Physical structure of att-phi. J Mol Biol. 1971 Mar 14; 56(2):403-23. PMID: 5551396.
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    163. Parkinson JS, Davis RW. A physical map of the left arm of the lambda chromosome. J Mol Biol. 1971 Mar 14; 56(2):425-8. PMID: 5551397.
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