Outputs (34)

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. (2024)
Journal Article
Krishnamurthi, R., González-Tortuero, E., Plahe, G., Goodhead, I. B., Fothergill, J. L., James, C. E., & Allison, H. E. (in press). Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. Journal of Visualized Experiments, 10.3791/64945. https://doi.org/10.3791/64945

Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, but others are active and can be triggered into a replicative form either spontaneously or by e... Read More about Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics..

Identification of constrained sequence elements across 239 primate genomes. (2023)
Journal Article
Kuderna, L. F., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., …Farh, K. K. (2023). Identification of constrained sequence elements across 239 primate genomes. Nature, 36, https://doi.org/10.1038/s41586-023-06798-8

Noncoding DNA is central to our understanding of human gene regulation and complex diseases , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome . Identifying... Read More about Identification of constrained sequence elements across 239 primate genomes..

Determining management strategies to control ash dieback disease through molecular and environmental interactions (2023)
Thesis
Raykova, A. (2023). Determining management strategies to control ash dieback disease through molecular and environmental interactions. (Thesis). University of Salford

Forest trees have been increasingly threatened by invasive pathogens, endangering associated biodiversity, and reducing ecosystems. Such an alien pathogen, Hymenoscyphus fraxineus, has had considerable impacts on the common ash tree (Fraxinus exce... Read More about Determining management strategies to control ash dieback disease through molecular and environmental interactions.

The landscape of tolerated genetic variation in humans and primates. (2023)
Journal Article
Gao, H., Hamp, T., Ede, J., Schraiber, J. G., McRae, J., Singer-Berk, M., …Jolly, C. J. (2023). The landscape of tolerated genetic variation in humans and primates. Science, 380(6648), https://doi.org/10.1126/science.abn8197

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtain... Read More about The landscape of tolerated genetic variation in humans and primates..

A global catalog of whole-genome diversity from 233 primate species. (2023)
Journal Article
Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., …Jolly, C. J. (2023). A global catalog of whole-genome diversity from 233 primate species. Science, 380(6648), 906-913. https://doi.org/10.1126/science.abn7829

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into lon... Read More about A global catalog of whole-genome diversity from 233 primate species..

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches (2022)
Journal Article
Beck, R., de Vries, D., Janiak, M., Goodhead, I., & Boubli, J. (2022). Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. Journal of Human Evolution, 174, https://doi.org/10.1016/j.jhevol.2022.103293

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we pr... Read More about Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates (2022)
Journal Article
Janiak, M. C., Silva, F. E., Beck, R. M. D., de Vries, D., Kuderna, L. F. K., Torosin, N. S., …Boubli, J. P. (2022). Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14), 3888-3902. https://doi.org/10.1111/mec.16554

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these ar... Read More about Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.

Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages (2022)
Journal Article
Gonzalez Tortuero, E., Krishnamurthi, R., Goodhead, I., Allison, H., & James, C. (2022). Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages. Access Microbiology, 4(5), https://doi.org/10.1099/acmi.ac2021.po0318

Pseudomonas aeruginosais an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased... Read More about Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages.

Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production (2021)
Journal Article
Monahan, T., Baker, J. A., Krabben, P., Davies, E. T., Jenkinson, E. R., Goodhead, I. B., …Shepherd, M. (2021). Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production. Microbial Biotechnology, 15(5), 1574-1585. https://doi.org/10.1111/1751-7915.13990

SummaryThe development and advent of mutagenesis tools for solventogenic clostridial species in recent years has allowed for the increased refinement of industrially relevant strains. In this study we have utilised CLEAVE™, a CRISPR/Cas genome editin... Read More about Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production.

Comparative analysis of gene prediction tools for viral genome annotation (2021)
Journal Article
Gonzalez-Tortuero, E., Krishnamurthi, R., Allison, H., Goodhead, I., & James, C. Comparative analysis of gene prediction tools for viral genome annotation. https://doi.org/10.1101/2021.12.11.472104. Manuscript submitted for publication

The number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and genome analysis tools. Bioinformatic annotation pipelines are largely based on open reading fram... Read More about Comparative analysis of gene prediction tools for viral genome annotation.