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What lies beneath? Molecular evolution during the radiation of caecilian amphibians.

Torres-Sánchez M, Gower DJ, Alvarez-Ponce D, Creevey CJ, Wilkinson M, San Mauro D.

BMC Genomics. 2019 May 9;20(1):354. doi: 10.1186/s12864-019-5694-1.


Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.

Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connell MJ, Creevey CJ.

Mol Biol Evol. 2019 Jun 1;36(6):1344-1356. doi: 10.1093/molbev/msz067.


Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats.

Abecia L, Martínez-Fernandez G, Waddams K, Martín-García AI, Pinloche E, Creevey CJ, Denman SE, Newbold CJ, Yáñez-Ruiz DR.

Front Microbiol. 2018 Oct 9;9:2227. doi: 10.3389/fmicb.2018.02227. eCollection 2018.


Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families.

Torres-Sánchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M, San Mauro D.

DNA Res. 2019 Feb 1;26(1):13-20. doi: 10.1093/dnares/dsy034.


Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future.

Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP.

Front Microbiol. 2018 Sep 25;9:2161. doi: 10.3389/fmicb.2018.02161. eCollection 2018. Review.


CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software.

Wilkinson TJ, Huws SA, Edwards JE, Kingston-Smith AH, Siu-Ting K, Hughes M, Rubino F, Friedersdorff M, Creevey CJ.

Front Microbiol. 2018 May 25;9:1095. doi: 10.3389/fmicb.2018.01095. eCollection 2018.


Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring.

McCormack UM, Curião T, Wilkinson T, Metzler-Zebeli BU, Reyer H, Ryan T, Calderon-Diaz JA, Crispie F, Cotter PD, Creevey CJ, Gardiner GE, Lawlor PG.

mSystems. 2018 Mar 13;3(3). pii: e00134-17. doi: 10.1128/mSystems.00134-17. eCollection 2018 May-Jun.


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.


Spherical: an iterative workflow for assembling metagenomic datasets.

Hitch TCA, Creevey CJ.

BMC Bioinformatics. 2018 Jan 24;19(1):20. doi: 10.1186/s12859-018-2028-2.


Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genes.

Hitch TCA, Thomas BJ, Friedersdorff JCA, Ougham H, Creevey CJ.

Environ Pollut. 2018 Apr;235:571-575. doi: 10.1016/j.envpol.2017.12.067. Epub 2018 Jan 11.


The rumen microbiome: an underexplored resource for novel antimicrobial discovery.

Oyama LB, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Privé F, Vallin HE, Wilkinson TJ, Golyshin PN, Golyshina OV, Mikut R, Hilpert K, Richards J, Wootton M, Edwards JE, Maresca M, Perrier J, Lundy FT, Luo Y, Zhou M, Hess M, Mantovani HC, Creevey CJ, Huws SA.

NPJ Biofilms Microbiomes. 2017 Dec 1;3:33. doi: 10.1038/s41522-017-0042-1. eCollection 2017.


Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology.

Matthews D, Diskin MG, Kenny DA, Creevey CJ, Keogh K, Waters SM.

BMC Genomics. 2017 Nov 9;18(1):857. doi: 10.1186/s12864-017-4265-6.


Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks.

Dougal K, Harris PA, Girdwood SE, Creevey CJ, Curtis GC, Barfoot CF, Argo CM, Newbold CJ.

Front Microbiol. 2017 Aug 11;8:1502. doi: 10.3389/fmicb.2017.01502. eCollection 2017.


Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis.

Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA.

Front Chem. 2017 Jul 12;5:51. doi: 10.3389/fchem.2017.00051. eCollection 2017.


Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.

Rubino F, Carberry C, Waters SM, Kenny D, McCabe MS, Creevey CJ.

ISME J. 2017 Jun;11(6):1510. doi: 10.1038/ismej.2017.34. No abstract available.


Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome.

Rubino F, Carberry C, M Waters S, Kenny D, McCabe MS, Creevey CJ.

ISME J. 2017 Apr;11(4):932-944. doi: 10.1038/ismej.2016.172. Epub 2017 Jan 13. Erratum in: ISME J. 2017 Jun;11(6):1510.


An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly.

Velmurugan J, Mollison E, Barth S, Marshall D, Milne L, Creevey CJ, Lynch B, Meally H, McCabe M, Milbourne D.

Ann Bot. 2016 Jul;118(1):71-87. doi: 10.1093/aob/mcw081. Epub 2016 Jun 6.


Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass.

Huws SA, Edwards JE, Creevey CJ, Rees Stevens P, Lin W, Girdwood SE, Pachebat JA, Kingston-Smith AH.

FEMS Microbiol Ecol. 2016 Jan;92(1). pii: fiv137. doi: 10.1093/femsec/fiv137. Epub 2015 Nov 4.


Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics.

Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D.

R Soc Open Sci. 2015 Aug 5;2(8):140436. doi: 10.1098/rsos.140436. eCollection 2015 Aug.


Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.

Akanni WA, Siu-Ting K, Creevey CJ, McInerney JO, Wilkinson M, Foster PG, Pisani D.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140337. doi: 10.1098/rstb.2014.0337.


Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits.

Moran B, Butler ST, Moore SG, MacHugh DE, Creevey CJ.

Reprod Fertil Dev. 2017 Feb;29(2):274-282. doi: 10.1071/RD15128.


Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.

McGettigan PA, Browne JA, Carrington SD, Crowe MA, Fair T, Forde N, Loftus BJ, Lohan A, Lonergan P, Pluta K, Mamo S, Murphy A, Roche J, Walsh SW, Creevey CJ, Earley B, Keady S, Kenny DA, Matthews D, McCabe M, Morris D, O'Loughlin A, Waters S, Diskin MG, Evans AC.

Reprod Fertil Dev. 2016;28(1-2):11-24. doi: 10.1071/RD15354.


Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.

Snelling TJ, Genç B, McKain N, Watson M, Waters SM, Creevey CJ, Wallace RJ.

PLoS One. 2014 Sep 24;9(9):e106491. doi: 10.1371/journal.pone.0106491. eCollection 2014.


Mitochondrial data are not suitable for resolving placental mammal phylogeny.

Morgan CC, Creevey CJ, O'Connell MJ.

Mamm Genome. 2014 Dec;25(11-12):636-47. doi: 10.1007/s00335-014-9544-9. Epub 2014 Sep 20.


Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction.

Siu-Ting K, Pisani D, Creevey CJ, Wilkinson M.

Syst Biol. 2015 Jan;64(1):137-43. doi: 10.1093/sysbio/syu066. Epub 2014 Sep 2. No abstract available.


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.


L.U.St: a tool for approximated maximum likelihood supertree reconstruction.

Akanni WA, Creevey CJ, Wilkinson M, Pisani D.

BMC Bioinformatics. 2014 Jun 12;15:183. doi: 10.1186/1471-2105-15-183.


Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community.

Ciric M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagic D.

BMC Genomics. 2014 May 12;15:356. doi: 10.1186/1471-2164-15-356.


Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.

Rudder S, Doohan F, Creevey CJ, Wendt T, Mullins E.

BMC Genomics. 2014 Apr 7;15:268. doi: 10.1186/1471-2164-15-268.


Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type.

Carberry CA, Waters SM, Kenny DA, Creevey CJ.

Appl Environ Microbiol. 2014 Jan;80(2):586-94. doi: 10.1128/AEM.03131-13. Epub 2013 Nov 8. Erratum in: Appl Environ Microbiol. 2014 Mar;80(6):2039. Waters, Sinead M [corrected to Waters, Sinéad M].


Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.

Doran AG, Creevey CJ.

BMC Bioinformatics. 2013 Feb 8;14:45. doi: 10.1186/1471-2105-14-45.


Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows.

Foley C, Chapwanya A, Creevey CJ, Narciandi F, Morris D, Kenny EM, Cormican P, Callanan JJ, O'Farrelly C, Meade KG.

BMC Genomics. 2012 Sep 18;13:489. doi: 10.1186/1471-2164-13-489.


The integration of 'omic' disciplines and systems biology in cattle breeding.

Berry DP, Meade KG, Mullen MP, Butler S, Diskin MG, Morris D, Creevey CJ.

Animal. 2011 Feb;5(4):493-505. doi: 10.1017/S1751731110002120.


Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples.

Mullen MP, Creevey CJ, Berry DP, McCabe MS, Magee DA, Howard DJ, Killeen AP, Park SD, McGettigan PA, Lucy MC, Machugh DE, Waters SM.

BMC Genomics. 2012 Jan 11;13:16. doi: 10.1186/1471-2164-13-16.


Identifying single copy orthologs in Metazoa.

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P.

PLoS Comput Biol. 2011 Dec;7(12):e1002269. doi: 10.1371/journal.pcbi.1002269. Epub 2011 Dec 1.


Universally distributed single-copy genes indicate a constant rate of horizontal transfer.

Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P.

PLoS One. 2011;6(8):e22099. doi: 10.1371/journal.pone.0022099. Epub 2011 Aug 5.


Duplicate retention in signalling proteins and constraints from network dynamics.

Soyer OS, Creevey CJ.

J Evol Biol. 2010 Nov;23(11):2410-21. doi: 10.1111/j.1420-9101.2010.02101.x. Epub 2010 Sep 6.


AQUA: automated quality improvement for multiple sequence alignments.

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P.

Bioinformatics. 2010 Jan 15;26(2):263-5. doi: 10.1093/bioinformatics/btp651. Epub 2009 Nov 19.


Trees from trees: construction of phylogenetic supertrees using clann.

Creevey CJ, McInerney JO.

Methods Mol Biol. 2009;537:139-61. doi: 10.1007/978-1-59745-251-9_7.


A computational screen for type I polyketide synthases in metagenomics shotgun data.

Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P.

PLoS One. 2008;3(10):e3515. doi: 10.1371/journal.pone.0003515. Epub 2008 Oct 27.


Genome-wide experimental determination of barriers to horizontal gene transfer.

Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM.

Science. 2007 Nov 30;318(5855):1449-52. Epub 2007 Oct 18.


Toward automatic reconstruction of a highly resolved tree of life.

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P.

Science. 2006 Mar 3;311(5765):1283-7. Erratum in: Science. 2006 May 5;312(5774):697.


Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.

Fitzpatrick DA, Creevey CJ, McInerney JO.

Mol Biol Evol. 2006 Jan;23(1):74-85. Epub 2005 Sep 8.


Evidence of positive Darwinian selection in putative meningococcal vaccine antigens.

Fitzpatrick DA, Creevey CJ, McInerney JO.

J Mol Evol. 2005 Jul;61(1):90-8. Epub 2005 Jun 29.


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