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Management of Brain Metastases in Epidermal Growth Factor Receptor Mutant Non-Small-Cell Lung Cancer.

Kelly WJ, Shah NJ, Subramaniam DS.

Front Oncol. 2018 Jul 3;8:208. doi: 10.3389/fonc.2018.00208. eCollection 2018. Review.


Bifidobacterium pseudolongum has characteristics of a keystone species in bifidobacterial blooms in the ceca of rats fed Hi-Maize starch.

Centanni M, Lawley B, Butts CA, Roy N, Lee J, Kelly WJ, Tannock GW.

Appl Environ Microbiol. 2018 May 25. pii: AEM.00547-18. doi: 10.1128/AEM.00547-18. [Epub ahead of print]


Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators, Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ.

Nat Biotechnol. 2018 Apr;36(4):359-367. doi: 10.1038/nbt.4110. Epub 2018 Mar 19.


Clinical activity of nivolumab in patients with non-clear cell renal cell carcinoma.

Koshkin VS, Barata PC, Zhang T, George DJ, Atkins MB, Kelly WJ, Vogelzang NJ, Pal SK, Hsu J, Appleman LJ, Ornstein MC, Gilligan T, Grivas P, Garcia JA, Rini BI.

J Immunother Cancer. 2018 Jan 29;6(1):9. doi: 10.1186/s40425-018-0319-9.


Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria.

Gilbert RA, Kelly WJ, Altermann E, Leahy SC, Minchin C, Ouwerkerk D, Klieve AV.

Front Microbiol. 2017 Dec 5;8:2340. doi: 10.3389/fmicb.2017.02340. eCollection 2017.


The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.

Palevich N, Kelly WJ, Leahy SC, Altermann E, Rakonjac J, Attwood GT.

Stand Genomic Sci. 2017 Dec 4;12:72. doi: 10.1186/s40793-017-0285-8. eCollection 2017.


Product review on the Anti-PD-L1 antibody atezolizumab.

Shah NJ, Kelly WJ, Liu SV, Choquette K, Spira A.

Hum Vaccin Immunother. 2018 Feb 1;14(2):269-276. doi: 10.1080/21645515.2017.1403694. Epub 2017 Dec 20.


Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

Kim CC, Kelly WJ, Patchett ML, Tannock GW, Jordens Z, Stoklosinski HM, Taylor JW, Sims IM, Bell TJ, Rosendale DI.

Int J Syst Evol Microbiol. 2017 Dec;67(12):4992-4998. doi: 10.1099/ijsem.0.002395. Epub 2017 Oct 17.


Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

Kamke J, Soni P, Li Y, Ganesh S, Kelly WJ, Leahy SC, Shi W, Froula J, Rubin EM, Attwood GT.

BMC Res Notes. 2017 Aug 8;10(1):367. doi: 10.1186/s13104-017-2671-0.


Draft Genome Sequences of 24 Lactococcus lactis Strains.

Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SA, Bachmann H.

Genome Announc. 2017 Mar 30;5(13). pii: e01737-16. doi: 10.1128/genomeA.01737-16.


Differential growth of bowel commensal Bacteroides species on plant xylans of differing structural complexity.

Centanni M, Hutchison JC, Carnachan SM, Daines AM, Kelly WJ, Tannock GW, Sims IM.

Carbohydr Polym. 2017 Feb 10;157:1374-1382. doi: 10.1016/j.carbpol.2016.11.017. Epub 2016 Nov 8.


The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales.

Li Y, Leahy SC, Jeyanathan J, Henderson G, Cox F, Altermann E, Kelly WJ, Lambie SC, Janssen PH, Rakonjac J, Attwood GT.

Stand Genomic Sci. 2016 Sep 6;11(1):59. doi: 10.1186/s40793-016-0183-5. eCollection 2016.


The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9.

Kelly WJ, Pacheco DM, Li D, Attwood GT, Altermann E, Leahy SC.

Stand Genomic Sci. 2016 Aug 17;11:49. doi: 10.1186/s40793-016-0171-9. eCollection 2016.


Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract.

Kelly WJ, Cookson AL, Altermann E, Lambie SC, Perry R, Teh KH, Otter DE, Shapiro N, Woyke T, Leahy SC.

Sci Rep. 2016 Jul 29;6:30768. doi: 10.1038/srep30768.


Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1.

Kelly WJ, Li D, Lambie SC, Cox F, Attwood GT, Altermann E, Leahy SC.

Genome Announc. 2016 Apr 7;4(2). pii: e00232-16. doi: 10.1128/genomeA.00232-16.


Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen.

Kelly WJ, Li D, Lambie SC, Jeyanathan J, Cox F, Li Y, Attwood GT, Altermann E, Leahy SC.

Genome Announc. 2016 Apr 7;4(2). pii: e00221-16. doi: 10.1128/genomeA.00221-16.


The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen.

Kelly WJ, Henderson G, Pacheco DM, Li D, Reilly K, Naylor GE, Janssen PH, Attwood GT, Altermann E, Leahy SC.

Stand Genomic Sci. 2016 Mar 15;11:26. doi: 10.1186/s40793-016-0147-9. eCollection 2016.


The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus.

Dunne JC, Kelly WJ, Leahy SC, Li D, Bond JJ, Peng L, Attwood GT, Jordan TW.

Proteomes. 2015 Oct 27;3(4):347-368. doi: 10.3390/proteomes3040347.


The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.

Lambie SC, Kelly WJ, Leahy SC, Li D, Reilly K, McAllister TA, Valle ER, Attwood GT, Altermann E.

Stand Genomic Sci. 2015 Aug 19;10:57. doi: 10.1186/s40793-015-0038-5. eCollection 2015.


RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis.

McAllister TA, Meale SJ, Valle E, Guan LL, Zhou M, Kelly WJ, Henderson G, Attwood GT, Janssen PH.

J Anim Sci. 2015 Apr;93(4):1431-49. doi: 10.2527/jas.2014-8329.


Utilization of grasses for potential biofuel production and phytoremediation of heavy metal contaminated soils.

Balsamo RA, Kelly WJ, Satrio JA, Ruiz-Felix MN, Fetterman M, Wynn R, Hagel K.

Int J Phytoremediation. 2015;17(1-6):448-55. doi: 10.1080/15226514.2014.922918.


Determining the culturability of the rumen bacterial microbiome.

Creevey CJ, Kelly WJ, Henderson G, Leahy SC.

Microb Biotechnol. 2014 Sep;7(5):467-79. doi: 10.1111/1751-7915.12141. Epub 2014 Jul 1.


Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.

Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM.

Genome Res. 2014 Sep;24(9):1517-25. doi: 10.1101/gr.168245.113. Epub 2014 Jun 6.


Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium.

Lambie SC, Altermann E, Leahy SC, Kelly WJ.

Genome Announc. 2014 Mar 6;2(2). pii: e00107-14. doi: 10.1128/genomeA.00107-14.


The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9.

Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E.

Stand Genomic Sci. 2014 Dec 8;9:15. doi: 10.1186/1944-3277-9-15. eCollection 2014.


Interaction between the genomes of Lactococcus lactis and phages of the P335 species.

Kelly WJ, Altermann E, Lambie SC, Leahy SC.

Front Microbiol. 2013 Aug 30;4:257. doi: 10.3389/fmicb.2013.00257. eCollection 2013.


The Complete Genome Sequence of Methanobrevibacter sp. AbM4.

Leahy SC, Kelly WJ, Li D, Li Y, Altermann E, Lambie SC, Cox F, Attwood GT.

Stand Genomic Sci. 2013 May 25;8(2):215-27. doi: 10.4056/sigs.3977691. eCollection 2013.


Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies.

Leahy SC, Kelly WJ, Ronimus RS, Wedlock N, Altermann E, Attwood GT.

Animal. 2013 Jun;7 Suppl 2:235-43. doi: 10.1017/S1751731113000700. Review.


Lactic acid bacteria convert glucosinolates to nitriles efficiently yet differently from enterobacteriaceae.

Mullaney JA, Kelly WJ, McGhie TK, Ansell J, Heyes JA.

J Agric Food Chem. 2013 Mar 27;61(12):3039-46. doi: 10.1021/jf305442j. Epub 2013 Mar 15.


Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus.

Till M, Goldstone DC, Attwood GT, Moon CD, Kelly WJ, Arcus VL.

Proteins. 2013 May;81(5):911-7. doi: 10.1002/prot.24254. Epub 2013 Feb 25.


Rumen microbial (meta)genomics and its application to ruminant production.

Morgavi DP, Kelly WJ, Janssen PH, Attwood GT.

Animal. 2013 Mar;7 Suppl 1:184-201. doi: 10.1017/S1751731112000419. Epub 2012 Mar 1.


Carbohydrate transporting membrane proteins of the rumen bacterium, Butyrivibrio proteoclasticus.

Bond JJ, Dunne JC, Kwan FY, Li D, Zhang K, Leahy SC, Kelly WJ, Attwood GT, Jordan TW.

J Proteomics. 2012 Jun 18;75(11):3138-44. doi: 10.1016/j.jprot.2011.12.013. Epub 2011 Dec 20.


Extracellular polysaccharide-degrading proteome of Butyrivibrio proteoclasticus.

Dunne JC, Li D, Kelly WJ, Leahy SC, Bond JJ, Attwood GT, Jordan TW.

J Proteome Res. 2012 Jan 1;11(1):131-42. doi: 10.1021/pr200864j. Epub 2011 Nov 29.


The large episomes of Butyrivibrio proteoclasticus B316T have arisen through intragenomic gene shuttling from the chromosome to smaller Butyrivibrio-specific plasmids.

Yeoman CJ, Kelly WJ, Rakonjac J, Leahy SC, Altermann E, Attwood GT.

Plasmid. 2011 Jul;66(2):67-78. doi: 10.1016/j.plasmid.2011.05.002. Epub 2011 Jun 12.


Transposition of Tn916 in the four replicons of the Butyrivibrio proteoclasticus B316(T) genome.

Cookson AL, Noel S, Hussein H, Perry R, Sang C, Moon CD, Leahy SC, Altermann E, Kelly WJ, Attwood GT.

FEMS Microbiol Lett. 2011 Mar;316(2):144-51. doi: 10.1111/j.1574-6968.2010.02204.x. Epub 2011 Jan 18.


Lactobacillus plantarum MB452 enhances the function of the intestinal barrier by increasing the expression levels of genes involved in tight junction formation.

Anderson RC, Cookson AL, McNabb WC, Park Z, McCann MJ, Kelly WJ, Roy NC.

BMC Microbiol. 2010 Dec 9;10:316. doi: 10.1186/1471-2180-10-316.


Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures.

Kelly WJ, Ward LJ, Leahy SC.

Genome Biol Evol. 2010;2:729-44. doi: 10.1093/gbe/evq056. Epub 2010 Sep 16.


The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment.

Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, Kong Z, Pacheco DM, Li D, Noel SJ, Moon CD, Cookson AL, Attwood GT.

PLoS One. 2010 Aug 3;5(8):e11942. doi: 10.1371/journal.pone.0011942.


Modeling shear-induced CHO cell damage in a rotary positive displacement pump.

Kamaraju H, Wetzel K, Kelly WJ.

Biotechnol Prog. 2010 Nov-Dec;26(6):1606-15. doi: 10.1002/btpr.479.


Lactobacillus plantarum DSM 2648 is a potential probiotic that enhances intestinal barrier function.

Anderson RC, Cookson AL, McNabb WC, Kelly WJ, Roy NC.

FEMS Microbiol Lett. 2010 Aug 1;309(2):184-92. doi: 10.1111/j.1574-6968.2010.02038.x. Epub 2010 Jun 16.


The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.

Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT.

PLoS One. 2010 Jan 28;5(1):e8926. doi: 10.1371/journal.pone.0008926.


Structural and functional characterization of a promiscuous feruloyl esterase (Est1E) from the rumen bacterium Butyrivibrio proteoclasticus.

Goldstone DC, Villas-Bôas SG, Till M, Kelly WJ, Attwood GT, Arcus VL.

Proteins. 2010 May 1;78(6):1457-69. doi: 10.1002/prot.22662.


Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium.

Moon CD, Pacheco DM, Kelly WJ, Leahy SC, Li D, Kopecny J, Attwood GT.

Int J Syst Evol Microbiol. 2008 Sep;58(Pt 9):2041-5. doi: 10.1099/ijs.0.65845-0.


Using computational fluid dynamics to characterize and improve bioreactor performance.

Kelly WJ.

Biotechnol Appl Biochem. 2008 Apr;49(Pt 4):225-38. doi: 10.1042/BA20070177.


Phenotypic characterization of transposon-inserted mutants of Clostridium proteoclasticum B316T using extracellular metabolomics.

Villas-Bôas SG, Moon CD, Noel S, Hussein H, Kelly WJ, Cao M, Lane GA, Cookson AL, Attwood GT.

J Biotechnol. 2008 Mar 20;134(1-2):55-63. doi: 10.1016/j.jbiotec.2008.01.010. Epub 2008 Jan 19.


Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.

Rademaker JL, Herbet H, Starrenburg MJ, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JE.

Appl Environ Microbiol. 2007 Nov;73(22):7128-37. Epub 2007 Sep 21.


Natural diversity and adaptive responses of Lactococcus lactis.

van Hylckama Vlieg JE, Rademaker JL, Bachmann H, Molenaar D, Kelly WJ, Siezen RJ.

Curr Opin Biotechnol. 2006 Apr;17(2):183-90. Epub 2006 Mar 6. Review.


Optimal operation of high-pressure homogenization for intracellular product recovery.

Kelly WJ, Muske KR.

Bioprocess Biosyst Eng. 2004 Dec;27(1):25-37. Epub 2004 Oct 7.


Audiological findings in Usher syndrome types IIa and II (non-IIa).

Sadeghi M, Cohn ES, Kelly WJ, Kimberling WJ, Tranebjoerg L, Möller C.

Int J Audiol. 2004 Mar;43(3):136-43.


The use of PCR for the identification and characterisation of bacteriocin genes from bacterial strains isolated from rumen or caecal contents of cattle and sheep.

Cookson AL, Noel SJ, Kelly WJ, Attwood GT.

FEMS Microbiol Ecol. 2004 May 1;48(2):199-207. doi: 10.1016/j.femsec.2004.01.003.

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