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..

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.

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome (2021)
Journal Article
Harrison, X., McDevitt, A., Dunn, J., Grifftihs, S., Benvenuto, C., Birtles, R., …Antwis, R. (2021). Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proceedings of the Royal Society B: Biological Sciences, 288(1957), 20210552. https://doi.org/10.1098/rspb.2021.0552

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, compara... Read More about Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome.

Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont (2020)
Journal Article
Goodhead, I., Blow, F., Brownridge, P., Hughes, M., Kenny, J., Krishna, R., …Darby, A. (2020). Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont. Microbial Genomics, 6(1), https://doi.org/10.1099/mgen.0.000285

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutation... Read More about Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont.

Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota (2019)
Journal Article
Blow, F., Gioti, A., Goodhead, I., Kalyva, M., Kampouraki, A., Vontas, J., & Darby, A. (2020). Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota. Genome Biology and Evolution, 12(2), 3778-3791. https://doi.org/10.1093/gbe/evz258

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont “Candidatus Erwinia dacicola”. Ca. E. dacicola is thought to supplement dietary nitrogen to the host,... Read More about Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota.

Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics (2019)
Journal Article
Griffiths, S., Galambao, M., Rowntree, J., Goodhead, I., Hall, J., O'Brien, D., …Antwis, R. (2020). Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics. Journal of Ecology, 108(1), 291-309. https://doi.org/10.1111/1365-2745.13302

Tree pathogens are a major threat to forest ecosystems. Conservation management strategies can exploit natural mechanisms of resistance, such as tree genotype and host‐associated microbial communities. However, fungal and bacterial communities are ra... Read More about Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics.

Campylobacter jejuni transcriptome changes during loss of culturability in water (2017)
Journal Article
Bronowski, C., Mustafa, K., Goodhead, I., James, C., Nelson, C., Lucaci, A., …Winstanley, C. (2017). Campylobacter jejuni transcriptome changes during loss of culturability in water. PLoS ONE, 12(11), e0188936. https://doi.org/10.1371/journal.pone.0188936

Background: Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different st... Read More about Campylobacter jejuni transcriptome changes during loss of culturability in water.

Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations (2017)
Journal Article
Doudoumis, V., Blow, F., Saridaki, A., Augustinos, A., Dyer, N., Goodhead, I., …Tsiamis, G. (2017). Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations. Scientific reports, 7(4699), https://doi.org/10.1038/s41598-017-04740-3

Profiling of wild and laboratory tsetse populations using 16S rRNA gene amplicon sequencing allowed us to examine whether the “Wigglesworthia-Sodalis-Wolbachia dogma” operates across species and populations. The most abundant taxa, in wild and labora... Read More about Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations.

50 important research questions in microbial ecology (2017)
Journal Article
Antwis, R., Griffiths, S., Harrison, X., Aranega-Bou, P., Arce, A., Bettridge, A., …Sutherland, W. (2017). 50 important research questions in microbial ecology. FEMS Microbiology Ecology, 93(5), https://doi.org/10.1093/femsec/fix044

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth... Read More about 50 important research questions in microbial ecology.

ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata (2015)
Journal Article
Pieszko, M., Weir, W., Goodhead, I., Kinnaird, J., & Shiels, B. (2015). ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata. PLoS Neglected Tropical Diseases, 9(8), 1-26. https://doi.org/10.1371/journal.pntd.0003933

The ability of vector-borne Apicomplexan parasites (Babesia, Plasmodium and Theileria) to change from one life-cycle stage to the next is critical for establishment of infection and transmission to new hosts. Stage differentiation steps of both Plasm... Read More about ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata.

Taking the pseudo out of pseudogenes (2014)
Journal Article
Goodhead, I., & Darby, A. (2015). Taking the pseudo out of pseudogenes. Current Opinion in Microbiology, 23, 102-109. https://doi.org/10.1016/j.mib.2014.11.012

Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identificat... Read More about Taking the pseudo out of pseudogenes.

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes (2014)
Journal Article
IIott, N., Heward, J., Roux, B., Tsitsiou, E., Fenwick, P., Lenzi, L., …Lindsay, M. (2014). Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nature communications, 5, 3979-3979. https://doi.org/10.1038/ncomms4979

Early reports indicate that long non-coding RNAs (lncRNAs) are novel regulators of biological responses. However, their role in the human innate immune response, which provides the initial defence against infection, is largely unexplored. To address... Read More about Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence (2013)
Journal Article
Goodhead, I., Capewell, P., Bailey, J., Beament, T., Chance, M., Kay, S., …Noyes, H. (2013). Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence. mBio, 4(4), e00197. https://doi.org/10.1128/mBio.00197-13

Human African trypanosomiasis is caused by two subspecies of Trypanosoma brucei. Trypanosoma brucei rhodesiense is found in East Africa and frequently causes acute disease, while Trypanosoma brucei gambiense is found in West Africa and is associated... Read More about Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence.

Insights into hominid evolution from the gorilla genome sequence (2012)
Journal Article
Scally, A., Dutheil, J., Hillier, L., Jordan, G., Goodhead, I., Herrero, J., …Marques-Bonet, T. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-175. https://doi.org/10.1038/nature10842

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla,and compare... Read More about Insights into hominid evolution from the gorilla genome sequence.

A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice (2010)
Journal Article
Goodhead, I., Archibald, A., Amwayi, P., Brass, A., Gibson, J., Hall, N., …Kemp, S. (2010). A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice. PLoS Neglected Tropical Diseases, 4(11), e880-e880. https://doi.org/10.1371/journal.pntd.0000880

African trypanosomes are protozoan parasites that cause “sleeping sickness” in humans and a similar disease in livestock. Trypanosomes also infect laboratory mice and three major quantitative trait loci (QTL) that regulate survival time after infecti... Read More about A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.