All Stories

  1. Improving orthologous signal and model fit in datasets addressing the root of the animal phylogeny

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  2. FrameRate: learning the coding potential of unassembled metagenomic reads

    Article • September 2022, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  3. StORF-Reporter: Finding Genes between Genes

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  4. Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen

    Article • Microorganisms, March 2022, MDPI AG

    Dr Christopher J Creevey

  5. Using the forces of hydrodynamic countercurrent chromatography for the study of bacteriophages

    Article • Access Microbiology, February 2022, Society for General Microbiology

    Dr Christopher J Creevey

  6. Adult schistosomes have an epithelial bacterial population distinct from the surrounding mammalian host blood

    Article • PLoS ONE, January 2022, PLOS

    Dr Christopher J Creevey

  7. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study

    Article • Bioinformatics, December 2021, Oxford University Press (OUP)

    Dr Christopher J Creevey

  8. The Application of Countercurrent Chromatography for the study of Bacteriophages

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  9. On the complexity of haplotyping a microbial community

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  10. Insights into the skin of caecilian amphibians from gene expression profiles

    Article • BMC Genomics, July 2020, Springer Science + Business Media

    Dr Christopher J Creevey

  11. The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens

    Article • Frontiers in Microbiology, July 2020, Frontiers

    Dr Christopher J Creevey

  12. Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown

    Article • Frontiers in Microbiology, April 2020, Frontiers

    Dr Christopher J Creevey

  13. Rumen Virus Populations: Technological Advances Enhancing Current Understanding

    Article • Frontiers in Microbiology, March 2020, Frontiers

    Dr Christopher J Creevey

  14. Can rumen bacteria communicate to each other?

    Article • Microbiome, February 2020, Springer Science + Business Media

    Dr Christopher J Creevey

  15. Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization?

    Article • FEMS Microbiology Ecology, December 2019, Oxford University Press (OUP)

    Professor Hilario C Mantovani, Dr Christopher J Creevey

  16. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes

    Article • iScience, November 2019, Elsevier

    Dr Christopher J Creevey

  17. Improvement of Feed Efficiency in Pigs through Microbial Modulation via Fecal Microbiota Transplantation in Sows and Dietary Supplementation of Inulin in Offspring

    Article • Applied and Environmental Microbiology, September 2019, ASM Journals

    Paul Cotter, Dr Christopher J Creevey

  18. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

    Article • Genome Biology and Evolution, August 2019, Oxford University Press (OUP)

    Dr Christopher J Creevey

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

    Article • BMC Genomics, May 2019, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • Molecular Biology and Evolution, March 2019, Oxford University Press (OUP)

    Dr Christopher J Creevey

  21. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

    Article • Microbiome, January 2019, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • DNA Research, October 2018, Oxford University Press (OUP)

    Dr Christopher J Creevey

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

    Article • Frontiers in Microbiology, October 2018, Frontiers

    Dr Christopher J Creevey

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

    Article • Frontiers in Microbiology, September 2018, Frontiers

    Dr Christopher J Creevey, Rodolpho Prado, Professor Hilario C Mantovani

  25. Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria

    Article • Scientific Reports, July 2018, Springer Science + Business Media

    Dr Christopher J Creevey

  26. Assessment of Cultured Ex Vivo Equine Endometrial Explants as a Model of Uterine Inflammation Using Transcriptome Profiles

    Article • Journal of Equine Veterinary Science, July 2018, Elsevier

    Dr Christopher J Creevey

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

    Article • Frontiers in Microbiology, May 2018, Frontiers

    Dr Christopher J Creevey

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

    Article • Environmental Pollution, April 2018, Elsevier

    Dr Christopher J Creevey

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

    Article • Nature Biotechnology, March 2018, Springer Science + Business Media

    Dr Christopher J Creevey, Dr Nikos C Kyrpides

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

    Article • mSystems, March 2018, ASM Journals

    Paul Cotter, Dr Christopher J Creevey

  31. Spherical: an iterative workflow for assembling metagenomic datasets

    Article • BMC Bioinformatics, January 2018, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • npj Biofilms and Microbiomes, December 2017, Nature

    Prof Kai Hilpert, Dr Christopher J Creevey, Professor Hilario C Mantovani

  33. Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

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

    Article • BMC Genomics, November 2017, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • Frontiers in Microbiology, August 2017, Frontiers

    Dr Christopher J Creevey

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

    Article • Frontiers in Chemistry, July 2017, Frontiers

    Professor Hilario C Mantovani, Prof Kai Hilpert, Dr Christopher J Creevey

  37. Signatures of the evolution of parthenogenesis and cryptobiosis in panagrolaimid nematodes

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

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

    Article • The ISME Journal, June 2017, Springer Science + Business Media

    Dr Christopher J Creevey

  39. Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility

    Article • January 2017, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  40. Microbes carve out a niche for themselves

    Article • The ISME Journal, January 2017, Nature

    Dr Christopher J Creevey

  41. Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes

    Article • BMC Genomics, August 2016, Springer Science + Business Media

    Dr Christopher J Creevey

  42. Spherical: an iterative workflow for assembling metagenomic datasets

    Article • August 2016, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

  43. Advances in the recovery of haplotypes from the metagenome

    Article • August 2016, Cold Spring Harbor Laboratory Press

    Dr Christopher J Creevey

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

    Article • Annals of Botany, June 2016, Oxford University Press (OUP)

    Dr Christopher J Creevey

  45. De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

    Article • January 2016, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • Reproduction Fertility and Development, January 2016, CSIRO Publishing

    Dr Christopher J Creevey

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

    Article • FEMS Microbiology Ecology, November 2015, Oxford University Press (OUP)

    Dr Christopher J Creevey

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

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, August 2015, Royal Society Publishing

    Professor James McInerney, Dr Christopher J Creevey

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

    Article • Royal Society Open Science, August 2015, Royal Society Publishing

    Dr Christopher J Creevey

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

    Article • Reproduction Fertility and Development, January 2015, CSIRO Publishing

    Dr Christopher J Creevey

  51. Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods

    Article • PLoS ONE, September 2014, PLOS

    Dr Christopher J Creevey

  52. Mitochondrial data are not suitable for resolving placental mammal phylogeny

    Article • Mammalian Genome, September 2014, Springer Science + Business Media

    Dr Christopher J Creevey

  53. Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction

    Article • Systematic Biology, September 2014, Oxford University Press (OUP)

    Dr Christopher J Creevey

  54. Determining the culturability of the rumen bacterial microbiome

    Article • Microbial Biotechnology, July 2014, Wiley

    Dr Christopher J Creevey

  55. Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type

    Article • Applied and Environmental Microbiology, February 2014, ASM Journals

    Dr Christopher J Creevey

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

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • BMC Bioinformatics, January 2014, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Dr Christopher J Creevey

  59. Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Dr Christopher J Creevey

  60. eggNOG v4.0: nested orthology inference across 3686 organisms

    Article • Nucleic Acids Research, December 2013, Oxford University Press (OUP)

    Dr Christopher J Creevey

  61. Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type

    Article • Applied and Environmental Microbiology, November 2013, ASM Journals

    Dr Christopher J Creevey

  62. Consistent mutational paths predict eukaryotic thermostability

    Article • BMC Evolutionary Biology, January 2013, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Dr Christopher J Creevey

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

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Dr Christopher J Creevey

  66. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Dr Christopher J Creevey

  67. Identifying Single Copy Orthologs in Metazoa

    Article • PLoS Computational Biology, December 2011, PLOS

    Dr Christopher J Creevey

  68. Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

    Article • PLoS ONE, August 2011, PLOS

    Dr Christopher J Creevey

  69. The integration of ‘omic’ disciplines and systems biology in cattle breeding

    Article • animal, October 2010, Cambridge University Press

    Dr Christopher J Creevey

  70. Duplicate retention in signalling proteins and constraints from network dynamics

    Article • Journal of Evolutionary Biology, September 2010, Wiley

    Dr Christopher J Creevey

  71. Visualization of multiple alignments, phylogenies and gene family evolution

    Article • Nature Methods, March 2010, Nature

    Dr Christopher J Creevey, Professor Geoff Barton

  72. AQUA: automated quality improvement for multiple sequence alignments

    Article • Bioinformatics, November 2009, Oxford University Press (OUP)

    Dr Christopher J Creevey

  73. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann

    Article • January 2009, Springer Science + Business Media

    Professor James McInerney, Dr Christopher J Creevey

  74. STRING 8--a global view on proteins and their functional interactions in 630 organisms

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Dr Christopher J Creevey

  75. A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data

    Article • PLoS ONE, October 2008, PLOS

    Dr Christopher J Creevey

  76. Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

    Article • Science, November 2007, American Association for the Advancement of Science

    Dr Christopher J Creevey

  77. Toward Automatic Reconstruction of a Highly Resolved Tree of Life

    Article • Science, March 2006, American Association for the Advancement of Science

    Dr Christopher J Creevey

  78. Article • BMC Evolutionary Biology, January 2006, Springer Science + Business Media

    Dr Christopher J Creevey

  79. Genome Phylogenies Indicate a Meaningful  -Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales

    Article • Molecular Biology and Evolution, August 2005, Oxford University Press (OUP)

    Dr Christopher J Creevey

  80. Can you see the wood for the trees?

    Article • Trends in Ecology & Evolution, July 2005, Elsevier

    Dr Christopher J Creevey

  81. Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens

    Article • Journal of Molecular Evolution, June 2005, Springer Science + Business Media

    Professor James McInerney, Dr Christopher J Creevey

  82. The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods

    Article • Systematic Biology, June 2005, Oxford University Press (OUP)

    Professor James McInerney, Dr Christopher J Creevey

  83. 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

    Article • Molecular Biology and Evolution, February 2005, Oxford University Press (OUP)

    Dr Christopher J Creevey

  84. Does a tree-like phylogeny only exist at the tips in the prokaryotes?

    Article • Proceedings of the Royal Society B Biological Sciences, December 2004, Royal Society Publishing

    Dr Christopher J Creevey

  85. Clann: investigating phylogenetic information through supertree analyses

    Article • Bioinformatics, September 2004, Oxford University Press (OUP)

    Dr Christopher J Creevey

  86. CRANN: detecting adaptive evolution in protein-coding DNA sequences

    Article • Bioinformatics, September 2003, Oxford University Press (OUP)

    Dr Christopher J Creevey

  87. Fatty acid biosynthesis in Mycobacterium tuberculosis : Lateral gene transfer, adaptive evolution, and gene duplication

    Article • Proceedings of the National Academy of Sciences, August 2003, Proceedings of the National Academy of Sciences

    Dr Christopher J Creevey

  88. Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist

    Article • January 2003, Elsevier

    Dr Christopher J Creevey

  89. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences

    Article • Gene, October 2002, Elsevier

    Professor James McInerney, Dr Christopher J Creevey