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Items: 1 to 50 of 61

1.

Performance of neural network basecalling tools for Oxford Nanopore sequencing.

Wick RR, Judd LM, Holt KE.

Genome Biol. 2019 Jun 24;20(1):129. doi: 10.1186/s13059-019-1727-y.

2.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.

Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE.

PLoS Genet. 2019 Apr 15;15(4):e1008114. doi: 10.1371/journal.pgen.1008114. eCollection 2019 Apr.

3.

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15.

Lam MMC, Wyres KL, Wick RR, Judd LM, Fostervold A, Holt KE, Löhr IH.

J Antimicrob Chemother. 2019 Feb 15. pii: dkz028. doi: 10.1093/jac/dkz028. [Epub ahead of print]

4.

Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258.

Cerdeira LT, Lam MMC, Wyres KL, Wick RR, Judd LM, Lopes R, Ribas RM, Morais MM, Holt KE, Lincopan N.

Antimicrob Agents Chemother. 2019 Feb 26;63(3). pii: e02140-18. doi: 10.1128/AAC.02140-18. Print 2019 Mar. No abstract available.

5.

Overexpression of IL-11 promotes premalignant gastric epithelial hyperplasia in isolation from germline gp130-JAK-STAT driver mutations.

Buzzelli JN, O'Connor L, Scurr M, Chung Nien Chin S, Catubig A, Ng GZ, Oshima M, Oshima H, Giraud AS, Sutton P, Judd LM, Menheniott TR.

Am J Physiol Gastrointest Liver Physiol. 2019 Feb 1;316(2):G251-G262. doi: 10.1152/ajpgi.00304.2018. Epub 2018 Dec 6.

PMID:
30520693
6.

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.

Wyres KL, Hawkey J, Hetland MAK, Fostervold A, Wick RR, Judd LM, Hamidian M, Howden BP, Löhr IH, Holt KE.

J Antimicrob Chemother. 2019 Mar 1;74(3):577-581. doi: 10.1093/jac/dky492.

7.

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

Wick RR, Judd LM, Holt KE.

PLoS Comput Biol. 2018 Nov 20;14(11):e1006583. doi: 10.1371/journal.pcbi.1006583. eCollection 2018 Nov.

8.

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae.

Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE.

Genome Med. 2018 Oct 29;10(1):77. doi: 10.1186/s13073-018-0587-5.

9.

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease.

Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, Holt BJ, Kusel M, Serralha M, Troy N, Bochkov YA, Grindle K, Lemanske RF Jr, Johnston SL, Gern JE, Sly PD, Holt PG, Holt KE, Inouye M.

Cell Host Microbe. 2018 Sep 12;24(3):341-352.e5. doi: 10.1016/j.chom.2018.08.005.

PMID:
30212648
10.

Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington's disease.

Kong G, Cao KL, Judd LM, Li S, Renoir T, Hannan AJ.

Neurobiol Dis. 2018 Sep 5. pii: S0969-9961(18)30533-3. doi: 10.1016/j.nbd.2018.09.001. [Epub ahead of print]

PMID:
30194046
11.

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.

Lam MMC, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH, Hoh CH, Archuleta S, Molton JS, Kalimuddin S, Koh TH, Passet V, Brisse S, Holt KE.

Nat Commun. 2018 Jul 13;9(1):2703. doi: 10.1038/s41467-018-05114-7.

12.

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations.

Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney AWJ, Brisse S, Holt KE.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000196. Epub 2018 Jul 9.

13.

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

Hawkey J, Ascher DB, Judd LM, Wick RR, Kostoulias X, Cleland H, Spelman DW, Padiglione A, Peleg AY, Holt KE.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000165. Epub 2018 Mar 16.

14.

Test of conditions that affect in vitro production of volatile fatty acids and gases.

Judd LM, Kohn RA.

J Anim Sci. 2018 Mar 6;96(2):694-704. doi: 10.1093/jas/skx082.

15.

Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital.

Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE.

Clin Infect Dis. 2018 Jul 2;67(2):161-170. doi: 10.1093/cid/ciy027.

16.

Completing bacterial genome assemblies with multiplex MinION sequencing.

Wick RR, Judd LM, Gorrie CL, Holt KE.

Microb Genom. 2017 Sep 14;3(10):e000132. doi: 10.1099/mgen.0.000132. eCollection 2017 Oct.

17.

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

Wick RR, Judd LM, Gorrie CL, Holt KE.

PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. eCollection 2017 Jun.

18.

Loss of gastrokine-2 drives premalignant gastric inflammation and tumor progression.

Menheniott TR, O'Connor L, Chionh YT, Däbritz J, Scurr M, Rollo BN, Ng GZ, Jacobs S, Catubig A, Kurklu B, Mercer S, Minamoto T, Ong DE, Ferrero RL, Fox JG, Wang TC, Sutton P, Judd LM, Giraud AS.

J Clin Invest. 2016 Apr 1;126(4):1383-400. doi: 10.1172/JCI82655. Epub 2016 Mar 14.

19.

Altered gp130 signalling ameliorates experimental colitis via myeloid cell-specific STAT3 activation and myeloid-derived suppressor cells.

Däbritz J, Judd LM, Chalinor HV, Menheniott TR, Giraud AS.

Sci Rep. 2016 Feb 5;6:20584. doi: 10.1038/srep20584.

20.

RUNX3 methylation and anti-tumor immunity.

Menheniott TR, Judd LM, Giraud AS.

Oncoscience. 2015 Sep 12;2(10):789-90. eCollection 2015. No abstract available.

21.

Elevated IL-33 expression is associated with pediatric eosinophilic esophagitis, and exogenous IL-33 promotes eosinophilic esophagitis development in mice.

Judd LM, Heine RG, Menheniott TR, Buzzelli J, O'Brien-Simpson N, Pavlic D, O'Connor L, Al Gazali K, Hamilton O, Scurr M, Collison AM, Mattes J, Allen KJ, Giraud AS.

Am J Physiol Gastrointest Liver Physiol. 2016 Jan 1;310(1):G13-25. doi: 10.1152/ajpgi.00290.2015. Epub 2015 Oct 29.

22.

STAT3: a critical component in the response to Helicobacter pylori infection.

Menheniott TR, Judd LM, Giraud AS.

Cell Microbiol. 2015 Nov;17(11):1570-82. doi: 10.1111/cmi.12518. Epub 2015 Oct 8. Review.

PMID:
26332850
23.

The MUC1 mucin protects against Helicobacter pylori pathogenesis in mice by regulation of the NLRP3 inflammasome.

Ng GZ, Menheniott TR, Every AL, Stent A, Judd LM, Chionh YT, Dhar P, Komen JC, Giraud AS, Wang TC, McGuckin MA, Sutton P.

Gut. 2016 Jul;65(7):1087-99. doi: 10.1136/gutjnl-2014-307175. Epub 2015 Apr 8.

PMID:
26079943
24.

IL33 Is a Stomach Alarmin That Initiates a Skewed Th2 Response to Injury and Infection.

Buzzelli JN, Chalinor HV, Pavlic DI, Sutton P, Menheniott TR, Giraud AS, Judd LM.

Cell Mol Gastroenterol Hepatol. 2015 Jan 3;1(2):203-221.e3. doi: 10.1016/j.jcmgh.2014.12.003. eCollection 2015 Mar.

25.

IL-1RT1 signaling antagonizes IL-11 induced STAT3 dependent cardiac and antral stomach tumor development through myeloid cell enrichment.

Buzzelli JN, Pavlic DI, Chalinor HV, O'Connor L, Menheniott TR, Giraud AS, Judd LM.

Oncotarget. 2015 Jan 20;6(2):679-95.

26.

TFF2 deficiency exacerbates weight loss and alters immune cell and cytokine profiles in DSS colitis, and this cannot be rescued by wild-type bone marrow.

Judd LM, Chalinor HV, Walduck A, Pavlic DI, Däbritz J, Dubeykovskaya Z, Wang TC, Menheniott TR, Giraud AS.

Am J Physiol Gastrointest Liver Physiol. 2015 Jan 1;308(1):G12-24. doi: 10.1152/ajpgi.00172.2014. Epub 2014 Oct 16.

27.

Lineage-specific RUNX3 hypomethylation marks the preneoplastic immune component of gastric cancer.

Kurklu B, Whitehead RH, Ong EK, Minamoto T, Fox JG, Mann JR, Judd LM, Giraud AS, Menheniott TR.

Oncogene. 2015 May 28;34(22):2856-66. doi: 10.1038/onc.2014.233. Epub 2014 Aug 4.

28.

Inhibition of the JAK2/STAT3 pathway reduces gastric cancer growth in vitro and in vivo.

Judd LM, Menheniott TR, Ling H, Jackson CB, Howlett M, Kalantzis A, Priebe W, Giraud AS.

PLoS One. 2014 May 7;9(5):e95993. doi: 10.1371/journal.pone.0095993. eCollection 2014.

29.

Intravenous ketamine for the treatment of refractory status epilepticus: a retrospective multicenter study.

Gaspard N, Foreman B, Judd LM, Brenton JN, Nathan BR, McCoy BM, Al-Otaibi A, Kilbride R, Fernández IS, Mendoza L, Samuel S, Zakaria A, Kalamangalam GP, Legros B, Szaflarski JP, Loddenkemper T, Hahn CD, Goodkin HP, Claassen J, Hirsch LJ, Laroche SM.

Epilepsia. 2013 Aug;54(8):1498-503. doi: 10.1111/epi.12247. Epub 2013 Jun 12.

30.

Targeting STAT3 in gastric cancer.

Giraud AS, Menheniott TR, Judd LM.

Expert Opin Ther Targets. 2012 Sep;16(9):889-901. doi: 10.1517/14728222.2012.709238. Epub 2012 Jul 26. Review.

PMID:
22834702
31.

Helicobacter pylori CagA triggers expression of the bactericidal lectin REG3γ via gastric STAT3 activation.

Lee KS, Kalantzis A, Jackson CB, O'Connor L, Murata-Kamiya N, Hatakeyama M, Judd LM, Giraud AS, Menheniott TR.

PLoS One. 2012;7(2):e30786. doi: 10.1371/journal.pone.0030786. Epub 2012 Feb 1.

32.

IL-11 is a parietal cell cytokine that induces atrophic gastritis.

Howlett M, Chalinor HV, Buzzelli JN, Nguyen N, van Driel IR, Bell KM, Fox JG, Dimitriadis E, Menheniott TR, Giraud AS, Judd LM.

Gut. 2012 Oct;61(10):1398-409. doi: 10.1136/gutjnl-2011-300539. Epub 2011 Dec 16.

33.

Random mutagenesis of the mouse genome: a strategy for discovering gene function and the molecular basis of disease.

Nguyen N, Judd LM, Kalantzis A, Whittle B, Giraud AS, van Driel IR.

Am J Physiol Gastrointest Liver Physiol. 2011 Jan;300(1):G1-11. doi: 10.1152/ajpgi.00343.2010. Epub 2010 Oct 14. Review.

34.

Helicobacter pylori infection promotes methylation and silencing of trefoil factor 2, leading to gastric tumor development in mice and humans.

Peterson AJ, Menheniott TR, O'Connor L, Walduck AK, Fox JG, Kawakami K, Minamoto T, Ong EK, Wang TC, Judd LM, Giraud AS.

Gastroenterology. 2010 Dec;139(6):2005-17. doi: 10.1053/j.gastro.2010.08.043. Epub 2010 Aug 27.

35.

Loss of RegI in conjunction with gastrin deficiency in mice facilitates efficient gastric ulcer healing but is dispensable for hyperplasia and tumourigenesis.

Peterson AJ, Nguyen N, Okamoto H, Giraud AS, van Driel IR, Judd LM.

Regul Pept. 2010 Feb 25;160(1-3):9-18. doi: 10.1016/j.regpep.2009.12.001. Epub 2009 Dec 5.

PMID:
19969026
36.

A33 antigen-deficient mice have defective colonic mucosal repair.

Pereira-Fantini PM, Judd LM, Kalantzis A, Peterson A, Ernst M, Heath JK, Giraud AS.

Inflamm Bowel Dis. 2010 Apr;16(4):604-12. doi: 10.1002/ibd.21114.

PMID:
19856415
37.

Cytokine signalling via gp130 in gastric cancer.

Howlett M, Menheniott TR, Judd LM, Giraud AS.

Biochim Biophys Acta. 2009 Nov;1793(11):1623-33. doi: 10.1016/j.bbamcr.2009.07.009. Epub 2009 Aug 7. Review.

38.

The interleukin-6 family cytokine interleukin-11 regulates homeostatic epithelial cell turnover and promotes gastric tumor development.

Howlett M, Giraud AS, Lescesen H, Jackson CB, Kalantzis A, Van Driel IR, Robb L, Van der Hoek M, Ernst M, Minamoto T, Boussioutas A, Oshima H, Oshima M, Judd LM.

Gastroenterology. 2009 Mar;136(3):967-77. doi: 10.1053/j.gastro.2008.12.003. Epub 2008 Dec 3.

PMID:
19121317
39.

Cytokine signalling by gp130 regulates gastric mucosal healing after ulceration and, indirectly, antral tumour progression.

Judd LM, Ulaganathan M, Howlett M, Giraud AS.

J Pathol. 2009 Mar;217(4):552-62. doi: 10.1002/path.2479.

PMID:
19097069
40.

Augmented gp130-mediated cytokine signalling accompanies human gastric cancer progression.

Jackson CB, Judd LM, Menheniott TR, Kronborg I, Dow C, Yeomans ND, Boussioutas A, Robb L, Giraud AS.

J Pathol. 2007 Oct;213(2):140-51.

PMID:
17724739
41.

STAT3 activation regulates growth, inflammation, and vascularization in a mouse model of gastric tumorigenesis.

Judd LM, Bredin K, Kalantzis A, Jenkins BJ, Ernst M, Giraud AS.

Gastroenterology. 2006 Oct;131(4):1073-85. Epub 2006 Jul 24.

PMID:
17030178
42.

Differentiation of the Gastric Mucosa IV. Role of trefoil peptides and IL-6 cytokine family signaling in gastric homeostasis.

Giraud AS, Jackson C, Menheniott TR, Judd LM.

Am J Physiol Gastrointest Liver Physiol. 2007 Jan;292(1):G1-5. Epub 2006 Aug 24. Review.

43.

Differential regulation of gastric tumor growth by cytokines that signal exclusively through the coreceptor gp130.

Howlett M, Judd LM, Jenkins B, La Gruta NL, Grail D, Ernst M, Giraud AS.

Gastroenterology. 2005 Sep;129(3):1005-18.

PMID:
16143138
44.

Gastric achlorhydria in H/K-ATPase-deficient (Atp4a(-/-)) mice causes severe hyperplasia, mucocystic metaplasia and upregulation of growth factors.

Judd LM, Andringa A, Rubio CA, Spicer Z, Shull GE, Miller ML.

J Gastroenterol Hepatol. 2005 Aug;20(8):1266-78.

PMID:
16048577
45.

Hyperactivation of Stat3 in gp130 mutant mice promotes gastric hyperproliferation and desensitizes TGF-beta signaling.

Jenkins BJ, Grail D, Nheu T, Najdovska M, Wang B, Waring P, Inglese M, McLoughlin RM, Jones SA, Topley N, Baumann H, Judd LM, Giraud AS, Boussioutas A, Zhu HJ, Ernst M.

Nat Med. 2005 Aug;11(8):845-52. Epub 2005 Jul 24.

PMID:
16041381
46.

Reciprocal changes in trefoil 1 and 2 expression in stomachs of mice with gastric unit hypertrophy and inflammation.

Franic TV, van Driel IR, Gleeson PA, Giraud AS, Judd LM.

J Pathol. 2005 Sep;207(1):43-52.

PMID:
15983982
47.

Growth factors associated with gastric mucosal hypertrophy in autoimmune gastritis.

Franic TV, Judd LM, Nguyen NV, Samuelson LC, Loveland KL, Giraud AS, Gleeson PA, van Driel IR.

Am J Physiol Gastrointest Liver Physiol. 2004 Oct;287(4):G910-8. Epub 2004 Jun 17.

48.

TFF-2 inhibits iNOS/NO in monocytes, and nitrated protein in healing colon after colitis.

Giraud AS, Pereira PM, Thim L, Parker LM, Judd LM.

Peptides. 2004 May;25(5):803-9.

PMID:
15177875
49.

Mice with a targeted disruption of the AE2 Cl-/HCO3- exchanger are achlorhydric.

Gawenis LR, Ledoussal C, Judd LM, Prasad V, Alper SL, Stuart-Tilley A, Woo AL, Grisham C, Sanford LP, Doetschman T, Miller ML, Shull GE.

J Biol Chem. 2004 Jul 16;279(29):30531-9. Epub 2004 Apr 30.

50.

Abnormal Paneth cell granule dissolution and compromised resistance to bacterial colonization in the intestine of CF mice.

Clarke LL, Gawenis LR, Bradford EM, Judd LM, Boyle KT, Simpson JE, Shull GE, Tanabe H, Ouellette AJ, Franklin CL, Walker NM.

Am J Physiol Gastrointest Liver Physiol. 2004 Jun;286(6):G1050-8. Epub 2004 Jan 8.

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