Chris J. Creevey, B.Sc. M.Sc. Ph.D. - Publications

2013-2018 Institute of Biological, Environmental and Rural Sciences Aberystwyth University, Cymru, United Kingdom 
 2018- School of Biological Sciences / Institute for Global Food Security Queen's University Belfast, Belfast, Northern Ireland, United Kingdom 
Computational Biology, Evolution, Phylogenetics, Microbiology

65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Torres-Sánchez M, Wilkinson M, Gower DJ, Creevey CJ, San Mauro D. Insights into the skin of caecilian amphibians from gene expression profiles. Bmc Genomics. 21: 515. PMID 32718305 DOI: 10.1186/S12864-020-06881-8  1
2020 Williams CL, Thomas BJ, McEwan NR, Rees Stevens P, Creevey CJ, Huws SA. Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown. Frontiers in Microbiology. 11: 720. PMID 32411103 DOI: 10.3389/Fmicb.2020.00720  1
2020 Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Frontiers in Microbiology. 11: 450. PMID 32273870 DOI: 10.3389/Fmicb.2020.00450  0.88
2020 Won MY, Oyama LB, Courtney SJ, Creevey CJ, Huws SA. Can rumen bacteria communicate to each other? Microbiome. 8: 23. PMID 32085816 DOI: 10.1186/S40168-020-00796-Y  1
2019 Moreira SM, Mendes TAO, Santanta MF, Huws SA, Creevey CJ, Mantovani HC. Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization? Fems Microbiology Ecology. PMID 31825517 DOI: 10.1093/Femsec/Fiz198  1
2019 Am M, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, Mj O. Gene Fusions derived by transcriptional readthrough are Driven by Segmental Duplication in Human. Genome Biology and Evolution. PMID 31400206 DOI: 10.1093/Gbe/Evz163  1
2019 Torres-Sánchez M, Gower DJ, Alvarez-Ponce D, Creevey CJ, Wilkinson M, San Mauro D. What lies beneath? Molecular evolution during the radiation of caecilian amphibians. Bmc Genomics. 20: 354. PMID 31072350 DOI: 10.1186/S12864-019-5694-1  1
2019 Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connell MJ, Creevey CJ. Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics. Molecular Biology and Evolution. PMID 30903171 DOI: 10.1093/Molbev/Msz067  1
2019 Li F, Hitch TCA, Chen Y, Creevey CJ, Guan LL. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. Microbiome. 7: 6. PMID 30642389 DOI: 10.1186/S40168-019-0618-5  0.88
2018 Torres-Sánchez M, Creevey CJ, Kornobis E, Gower DJ, Wilkinson M, San Mauro D. Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 30351380 DOI: 10.1093/Dnares/Dsy034  1
2018 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, et al. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Frontiers in Microbiology. 9: 2161. PMID 30319557 DOI: 10.3389/Fmicb.2018.02161  1
2018 Wilkinson TJ, Huws SA, Edwards JE, Kingston-Smith AH, Siu-Ting K, Hughes M, Rubino F, Friedersdorff M, Creevey CJ. CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software. Frontiers in Microbiology. 9: 1095. PMID 29887853 DOI: 10.3389/Fmicb.2018.01095  1
2018 Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D, Perry R, Henderson G, Creevey CJ, et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology. PMID 29553575 DOI: 10.1038/Nbt.4110  1
2018 Hitch TCA, Creevey CJ. Spherical: an iterative workflow for assembling metagenomic datasets. Bmc Bioinformatics. 19: 20. PMID 29361904 DOI: 10.1186/S12859-018-2028-2  0.88
2018 Hitch TCA, Thomas BJ, Friedersdorff JCA, Ougham H, Creevey CJ. Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genes. Environmental Pollution (Barking, Essex : 1987). 235: 571-575. PMID 29331890 DOI: 10.1016/J.Envpol.2017.12.067  0.88
2017 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, ... ... Creevey CJ, et al. The rumen microbiome: an underexplored resource for novel antimicrobial discovery. Npj Biofilms and Microbiomes. 3: 33. PMID 29214045 DOI: 10.1038/s41522-017-0042-1  1
2017 Matthews D, Diskin MG, Kenny DA, Creevey CJ, Keogh K, Waters SM. Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology. Bmc Genomics. 18: 857. PMID 29121875 DOI: 10.1186/S12864-017-4265-6  1
2017 Dougal K, Harris PA, Girdwood SE, Creevey CJ, Curtis GC, Barfoot CF, Argo CM, Newbold CJ. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks. Frontiers in Microbiology. 8: 1502. PMID 28848517 DOI: 10.3389/Fmicb.2017.01502  1
2017 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. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Frontiers in Chemistry. 5: 51. PMID 28748180 DOI: 10.3389/Fchem.2017.00051  1
2017 Rubino F, Carberry C, Waters SM, Kenny D, McCabe MS, Creevey CJ. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. The Isme Journal. 11: 1510. PMID 28507336 DOI: 10.1038/ismej.2017.34  1
2017 Rubino F, Carberry C, M Waters S, Kenny D, McCabe MS, Creevey CJ. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. The Isme Journal. PMID 28085156 DOI: 10.1038/Ismej.2016.172  1
2016 Moran B, Cummins SB, Creevey CJ, Butler ST. Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. Bmc Genomics. 17: 603. PMID 27514375 DOI: 10.1186/S12864-016-2938-1  1
2016 Velmurugan J, Mollison E, Barth S, Marshall D, Milne L, Creevey CJ, Lynch B, Meally H, McCabe M, Milbourne D. An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. Annals of Botany. PMID 27268483 DOI: 10.1093/Aob/Mcw081  1
2015 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, et al. Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle. Reproduction, Fertility, and Development. 28: 11-24. PMID 27062871 DOI: 10.1071/Rd15354  1
2015 Huws SA, Edwards JE, Creevey CJ, Stevens PR, Lin W, Girdwood SE, Pachebat JA, Kingston-Smith AH. Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass. Fems Microbiology Ecology. PMID 26542074 DOI: 10.1093/Femsec/Fiv137  1
2015 Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D. Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. Royal Society Open Science. 2: 140436. PMID 26361544 DOI: 10.1098/Rsos.140436  1
2015 Akanni WA, Siu-Ting K, Creevey CJ, McInerney JO, Wilkinson M, Foster PG, Pisani D. Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370: 20140337. PMID 26323767 DOI: 10.1098/Rstb.2014.0337  1
2015 Moran B, Butler ST, Moore SG, MacHugh DE, Creevey CJ. Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits. Reproduction, Fertility, and Development. PMID 26304020 DOI: 10.1071/Rd15128  0.36
2015 Siu-Ting K, Pisani D, Creevey CJ, Wilkinson M. Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction. Systematic Biology. 64: 137-43. PMID 25183706 DOI: 10.1093/Sysbio/Syu066  1
2014 Doran AG, Berry DP, Creevey CJ. Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle. Bmc Genomics. 15: 837. PMID 25273628 DOI: 10.1186/1471-2164-15-837  1
2014 Snelling TJ, Genç B, McKain N, Watson M, Waters SM, Creevey CJ, Wallace RJ. Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods. Plos One. 9: e106491. PMID 25250654 DOI: 10.1371/Journal.Pone.0106491  1
2014 Morgan CC, Creevey CJ, O'Connell MJ. Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 25: 636-47. PMID 25239304 DOI: 10.1007/S00335-014-9544-9  1
2014 Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology. 7: 467-79. PMID 24986151 DOI: 10.1111/1751-7915.12141  1
2014 Akanni WA, Creevey CJ, Wilkinson M, Pisani D. L.U.St: a tool for approximated maximum likelihood supertree reconstruction. Bmc Bioinformatics. 15: 183. PMID 24925766 DOI: 10.1186/1471-2105-15-183  1
2014 Ciric M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagic D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. Bmc Genomics. 15: 356. PMID 24886150 DOI: 10.1186/1471-2164-15-356  1
2014 Rudder S, Doohan F, Creevey CJ, Wendt T, Mullins E. Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. Bmc Genomics. 15: 268. PMID 24708309 DOI: 10.1186/1471-2164-15-268  1
2014 Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 42: D231-9. PMID 24297252 DOI: 10.1093/Nar/Gkt1253  1
2014 Carberry CA, Waters SM, Waters SM, Kenny DA, Creevey CJ. Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type. Applied and Environmental Microbiology. 80: 586-94. PMID 24212580 DOI: 10.1128/Aem.03131-13  1
2013 Doran AG, Creevey CJ. Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. Bmc Bioinformatics. 14: 45. PMID 23390980 DOI: 10.1186/1471-2105-14-45  1
2013 van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. Bmc Evolutionary Biology. 13: 7. PMID 23305080 DOI: 10.1186/1471-2148-13-7  1
2012 Foley C, Chapwanya A, Creevey CJ, Narciandi F, Morris D, Kenny EM, Cormican P, Callanan JJ, O'Farrelly C, Meade KG. Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows. Bmc Genomics. 13: 489. PMID 22985206 DOI: 10.1186/1471-2164-13-489  1
2012 McCabe M, Waters S, Morris D, Kenny D, Lynn D, Creevey C. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance Bmc Genomics. 13. PMID 22607119 DOI: 10.1186/1471-2164-13-193  1
2012 Mullen MP, Creevey CJ, Berry DP, McCabe MS, Magee DA, Howard DJ, Killeen AP, Park SD, McGettigan PA, Lucy MC, Machugh DE, Waters SM. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. Bmc Genomics. 13: 16. PMID 22235840 DOI: 10.1186/1471-2164-13-16  1
2011 Berry DP, Meade KG, Mullen MP, Butler S, Diskin MG, Morris D, Creevey CJ. The integration of 'omic' disciplines and systems biology in cattle breeding. Animal : An International Journal of Animal Bioscience. 5: 493-505. PMID 22439945 DOI: 10.1017/S1751731110002120  1
2011 Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. Identifying single copy orthologs in Metazoa. Plos Computational Biology. 7: e1002269. PMID 22144877 DOI: 10.1371/Journal.Pcbi.1002269  1
2011 Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. Plos One. 6: e22099. PMID 21850220 DOI: 10.1371/Journal.Pone.0022099  1
2010 Soyer OS, Creevey CJ. Duplicate retention in signalling proteins and constraints from network dynamics. Journal of Evolutionary Biology. 23: 2410-21. PMID 20825548 DOI: 10.1111/J.1420-9101.2010.02101.X  1
2010 Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods. 7: S16-25. PMID 20195253 DOI: 10.1038/Nmeth.1434  1
2010 Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P. AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics (Oxford, England). 26: 263-5. PMID 19926669 DOI: 10.1093/Bioinformatics/Btp651  1
2009 Creevey CJ, McInerney JO. Trees from trees: construction of phylogenetic supertrees using clann. Methods in Molecular Biology (Clifton, N.J.). 537: 139-61. PMID 19378143 DOI: 10.1007/978-1-59745-251-9_7  1
2009 Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/Nar/Gkn760  1
2008 Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P. A computational screen for type I polyketide synthases in metagenomics shotgun data. Plos One. 3: e3515. PMID 18953415 DOI: 10.1371/Journal.Pone.0003515  1
2007 Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. Genome-wide experimental determination of barriers to horizontal gene transfer. Science (New York, N.Y.). 318: 1449-52. PMID 17947550 DOI: 10.1126/Science.1147112  1
2006 Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. Bmc Evolutionary Biology. 6: 29. PMID 16563161 DOI: 10.1186/1471-2148-6-29  1
2006 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science (New York, N.Y.). 311: 1283-7. PMID 16513982 DOI: 10.1126/Science.1123061  1
2006 Fitzpatrick DA, Creevey CJ, McInerney JO. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Molecular Biology and Evolution. 23: 74-85. PMID 16151187 DOI: 10.1093/Molbev/Msj009  1
2005 Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D, Thorley JL. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Systematic Biology. 54: 419-31. PMID 16012108 DOI: 10.1080/10635150590949832  1
2005 Fitzpatrick DA, Creevey CJ, McInerney JO. Evidence of positive Darwinian selection in putative meningococcal vaccine antigens. Journal of Molecular Evolution. 61: 90-8. PMID 16007491 DOI: 10.1007/S00239-004-0290-6  1
2005 Philip GK, Creevey CJ, McInerney JO. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Molecular Biology and Evolution. 22: 1175-84. PMID 15703245 DOI: 10.1093/Molbev/Msi102  1
2005 Creevey CJ, McInerney JO. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics (Oxford, England). 21: 390-2. PMID 15374874 DOI: 10.1093/Bioinformatics/Bti020  1
2004 Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings. Biological Sciences / the Royal Society. 271: 2551-8. PMID 15615680 DOI: 10.1098/Rspb.2004.2864  1
2003 Creevey CJ, McInerney JO. CRANN: detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics (Oxford, England). 19: 1726. PMID 15593409 DOI: 10.1093/Bioinformatics/Btg225  1
2003 McInerney JO, Littlewood DT, Creevey CJ. Detecting adaptive molecular evolution: additional tools for the parasitologist. Advances in Parasitology. 54: 359-79. PMID 14711091 DOI: 10.1016/S0065-308X(03)54009-X  1
2003 Kinsella RJ, Fitzpatrick DA, Creevey CJ, McInerney JO. Fatty acid biosynthesis in Mycobacterium tuberculosis: lateral gene transfer, adaptive evolution, and gene duplication. Proceedings of the National Academy of Sciences of the United States of America. 100: 10320-5. PMID 12917487 DOI: 10.1073/Pnas.1737230100  1
2002 Creevey CJ, McInerney JO. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene. 300: 43-51. PMID 12468084 DOI: 10.1016/S0378-1119(02)01039-9  1
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