All Stories

  1. Improving orthologous signal and model fit in datasets addressing the root of the animal phylogeny
  2. FrameRate: learning the coding potential of unassembled metagenomic reads
  3. StORF-Reporter: Finding Genes between Genes
  4. Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen
  5. Using the forces of hydrodynamic countercurrent chromatography for the study of bacteriophages
  6. Adult schistosomes have an epithelial bacterial population distinct from the surrounding mammalian host blood
  7. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study
  8. The Application of Countercurrent Chromatography for the study of Bacteriophages
  9. On the complexity of haplotyping a microbial community
  10. Insights into the skin of caecilian amphibians from gene expression profiles
  11. The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens
  12. Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown
  13. Rumen Virus Populations: Technological Advances Enhancing Current Understanding
  14. Can rumen bacteria communicate to each other?
  15. Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization?
  16. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes
  17. Improvement of Feed Efficiency in Pigs through Microbial Modulation via Fecal Microbiota Transplantation in Sows and Dietary Supplementation of Inulin in Offspring
  18. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human
  19. What lies beneath? Molecular evolution during the radiation of caecilian amphibians
  20. Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics
  21. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle
  22. Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families
  23. Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats
  24. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
  25. Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria
  26. Assessment of Cultured Ex Vivo Equine Endometrial Explants as a Model of Uterine Inflammation Using Transcriptome Profiles
  27. CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
  28. Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genes
  29. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
  30. Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring
  31. Spherical: an iterative workflow for assembling metagenomic datasets
  32. The rumen microbiome: an underexplored resource for novel antimicrobial discovery
  33. Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities
  34. Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology
  35. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks
  36. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis
  37. Signatures of the evolution of parthenogenesis and cryptobiosis in panagrolaimid nematodes
  38. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome
  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
  40. Microbes carve out a niche for themselves
  41. Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes
  42. Spherical: an iterative workflow for assembling metagenomic datasets
  43. Advances in the recovery of haplotypes from the metagenome
  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
  45. De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass
  46. Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle
  47. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass
  48. Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis
  49. Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics
  50. Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits
  51. Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
  52. Mitochondrial data are not suitable for resolving placental mammal phylogeny
  53. Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction
  54. Determining the culturability of the rumen bacterial microbiome
  55. Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type
  56. Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes
  57. L.U.St: a tool for approximated maximum likelihood supertree reconstruction
  58. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community
  59. Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle
  60. eggNOG v4.0: nested orthology inference across 3686 organisms
  61. Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type
  62. Consistent mutational paths predict eukaryotic thermostability
  63. Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms
  64. Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows
  65. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples
  66. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance
  67. Identifying Single Copy Orthologs in Metazoa
  68. Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
  69. The integration of ‘omic’ disciplines and systems biology in cattle breeding
  70. Duplicate retention in signalling proteins and constraints from network dynamics
  71. Visualization of multiple alignments, phylogenies and gene family evolution
  72. AQUA: automated quality improvement for multiple sequence alignments
  73. Trees from Trees: Construction of Phylogenetic Supertrees Using Clann
  74. STRING 8--a global view on proteins and their functional interactions in 630 organisms
  75. A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
  76. Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
  77. Reconstructing the Tree of Life
  78. Toward Automatic Reconstruction of a Highly Resolved Tree of Life
  79. Genome Phylogenies Indicate a Meaningful  -Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales
  80. Can you see the wood for the trees?
  81. Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens
  82. The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods
  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
  84. Does a tree-like phylogeny only exist at the tips in the prokaryotes?
  85. Clann: investigating phylogenetic information through supertree analyses
  86. CRANN: detecting adaptive evolution in protein-coding DNA sequences
  87. Fatty acid biosynthesis in Mycobacterium tuberculosis : Lateral gene transfer, adaptive evolution, and gene duplication
  88. Detecting Adaptive Molecular Evolution: Additional Tools for the Parasitologist
  89. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences