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Outputs (24)

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation (2024)
Journal Article
Kosch, T. A., Torres-Sánchez, M., Liedtke, H. C., Summers, K., Yun, M. H., Crawford, A. J., Maddock, S. T., Ahammed, M. S., Araújo, V. L., Bertola, L. V., Bucciarelli, G. M., Carné, A., Carneiro, C. M., Chan, K. O., Chen, Y., Crottini, A., da Silva, J. M., Denton, R. D., Dittrich, C., Espregueira Themudo, G., …Wogan, G. O. (2024). The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BMC Genomics, 25(1), Article 1025. https://doi.org/10.1186/s12864-024-10899-7

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal cla... Read More about The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Understanding conceptus-maternal interactions: what tools do we need to develop? (2023)
Journal Article
Butt, Z., Tinning, H., O'Connell, M. J., Fenn, J., Alberio, R., & Forde, N. (2023). Understanding conceptus-maternal interactions: what tools do we need to develop?. Reproduction, Fertility and Development, 36(2), 81-92. https://doi.org/10.1071/RD23181

Communication between the maternal endometrium and developing embryo/conceptus is critical to support successful pregnancy to term. Studying the peri-implantation period of pregnancy is critical as this is when most pregnancy loss occurs in cattle. O... Read More about Understanding conceptus-maternal interactions: what tools do we need to develop?.

Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians (2023)
Journal Article
Ovchinnikov, V., Uliano-Silva, M., Wilkinson, M., Wood, J., Smith, M., Oliver, K., Sims, Y., Torrance, J., Suh, A., McCarthy, S. A., Durbin, R., & O’Connell, M. J. (2023). Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians. Molecular Biology and Evolution, 40(5), 1-11. https://doi.org/10.1093/molbev/msad102

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. Mo... Read More about Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.

A burst of genomic innovation at the origin of placental mammals mediated embryo implantation (2023)
Journal Article
Taylor, A. S., Tinning, H., Ovchinnikov, V., Edge, J., Smith, W., Pullinger, A. L., Sutton, R. A., Constantinides, B., Wang, D., Forbes, K., Forde, N., & O'Connell, M. J. (2023). A burst of genomic innovation at the origin of placental mammals mediated embryo implantation. Communications Biology, 6, Article 459. https://doi.org/10.1038/s42003-023-04809-y

The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although progesterone receptor signalling predates... Read More about A burst of genomic innovation at the origin of placental mammals mediated embryo implantation.

MicroRNAs emerging coordinate with placental mammals alter pathways in endometrial epithelia important for endometrial function (2023)
Journal Article
Hume, L., Edge, J. C., Tinning, H., Wang, D., Taylor, A. S., Ovchinnikov, V., Geijer-Simpson, A., Vrljicak, P., Brosens, J. J., Lucas, E. S., Simson, N. A., Shillito, J., Forbes, K., O’Connell, M. J., & Forde, N. (2023). MicroRNAs emerging coordinate with placental mammals alter pathways in endometrial epithelia important for endometrial function. iScience, 26(4), Article 106339. https://doi.org/10.1016/j.isci.2023.106339


We tested the hypothesis that conserved placental mammal-specific microRNAs and their targets facilitate endometrial receptivity to implantation. Expression of miR-340-5p, -542-3p, and -671-5p was regulated by exposure of endometri... Read More about MicroRNAs emerging coordinate with placental mammals alter pathways in endometrial epithelia important for endometrial function.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny (2023)
Journal Article
McCarthy, C. G., Mulhair, P. O., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2023). Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Molecular Biology and Evolution, 40(1), Article msac276. https://doi.org/10.1093/molbev/msac276

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of mode... Read More about Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.

Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life (2022)
Journal Article
Mulhair, P. O., McCarthy, C. G., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2022). Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Current Biology, 32(23), 5180-5188.e3. https://doi.org/10.1016/j.cub.2022.10.036

Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum or within Deuterostomia, sister to Ambulacraria. Although their placement... Read More about Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life.

Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling (2021)
Journal Article
Hyland, E. M., Webb, A. E., Kennedy, K. F., Gerek Ince, Z. N., Loscher, C. E., & O'Connell, M. J. (2021). Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling. Genome Biology and Evolution, 13(12), Article evab268. https://doi.org/10.1093/gbe/evab268

The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven disti... Read More about Adaptive Evolution in TRIF Leads to Discordance between Human and Mouse Innate Immune Signaling.

Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation (2021)
Journal Article
DOUKA, K., BIRDS, I., WANG, D., KOSTELETOS, A., CLAYTON, S., BYFORD, A., VASCONCELOS, E. J., O'CONNELL, M. J., DEUCHARS, J., WHITEHOUSE, A., & ASPDEN, J. L. (2021). Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation. RNA, 27(9), 1082-1101. https://doi.org/10.1261/rna.078782.121

The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand... Read More about Cytoplasmic long noncoding rnas are differentially regulated and translated during human neuronal differentiation.