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The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk (2023)
Journal Article
Lei, C. L., Whittaker, D. G., & Mirams, G. R. (2024). The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk. British Journal of Pharmacology, 181(7), 987-1004. https://doi.org/10.1111/bph.16250

Background and Purpose Drug-induced reduction of the rapid delayed rectifier potassium current carried by the human Ether-à-go-go-Related Gene (hERG) channel is associated with increased risk of arrhythmias. Recent updates to drug safety regulatory... Read More about The impact of uncertainty in hERG binding mechanism on in silico predictions of drug-induced proarrhythmic risk.

A Cell-Based Optimised Approach for Rapid and Efficient Gene Editing of Human Pluripotent Stem Cells (2023)
Journal Article
Cuevas-Ocaña, S., Yang, J. Y., Aushev, M., Schlossmacher, G., Bear, C. E., Hannan, N. R., …Gray, M. A. (2023). A Cell-Based Optimised Approach for Rapid and Efficient Gene Editing of Human Pluripotent Stem Cells. International Journal of Molecular Sciences, 24(12), Article 10266. https://doi.org/10.3390/ijms241210266

Introducing or correcting disease-causing mutations through genome editing in human pluripotent stem cells (hPSCs) followed by tissue-specific differentiation provide sustainable models of multiorgan diseases, such as cystic fibrosis (CF). However, l... Read More about A Cell-Based Optimised Approach for Rapid and Efficient Gene Editing of Human Pluripotent Stem Cells.

Ion channel model reduction using manifold boundaries (2022)
Journal Article
Whittaker, D. G., Wang, J., Shuttleworth, J., Venkateshappa, R., Kemp, J. M., Claydon, T. W., & Mirams, G. R. (2022). Ion channel model reduction using manifold boundaries. Journal of the Royal Society, Interface, 19(193), Article 20220193. https://doi.org/10.1098/rsif.2022.0193

Mathematical models of voltage-gated ion channels are used in basic research, industrial and clinical settings. These models range in complexity, but typically contain numerous variables representing the proportion of channels in a given state, and p... Read More about Ion channel model reduction using manifold boundaries.

Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids (2022)
Journal Article
Babaei-Jadidi, R., Kashfi, H., Alelwani, W., Bakhtiari, A., Kattan, S. W., Mansouri, O. A., …Nateri, A. S. (2022). Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids. Oncogenesis, 11, Article 4. https://doi.org/10.1038/s41389-021-00376-1

Little is known about the role of microRNAs (miRNAs) in rewiring the metabolism within tumours and adjacent non-tumour bearing normal tissue and their potential in cancer therapy. This study aimed to investigate the relationship between deregulated m... Read More about Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids.

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae (2019)
Journal Article
Overbey, E. G., Paul, A. M., da Silveira, W. A., Tahimic, C. G., Reinsch, S. S., Szewczyk, N., …Mao, X. W. (2019). Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae. International Journal of Molecular Sciences, 20(17), Article 4094. https://doi.org/10.3390/ijms20174094

Spaceflight poses many challenges for humans. Ground-based analogs typically focus on single parameters of spaceflight and their associated acute effects. This study assesses the long-term transcriptional effects following single and combination spac... Read More about Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae.

Mitochondrial dysfunction causes Ca2+ overload and ECM degradation–mediated muscle damage in C. elegans (2019)
Journal Article
Sudevan, S., Takiura, M., Kubota, Y., Higashitani, N., Cooke, M., Ellwood, R. A., …Higashitani, A. (2019). Mitochondrial dysfunction causes Ca2+ overload and ECM degradation–mediated muscle damage in C. elegans. FASEB Journal, 33(8), 9540-9550. https://doi.org/10.1096/fj.201802298r

Mitochondrial dysfunction impairs muscle health and causes subsequent muscle wasting. This study explores the role of mitochondrial dysfunction as an intramuscular signal for the extracellular matrix (ECM)–based proteolysis and, consequentially, musc... Read More about Mitochondrial dysfunction causes Ca2+ overload and ECM degradation–mediated muscle damage in C. elegans.

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa (2019)
Journal Article
Monnahan, P., Kolář, F., Baduel, P., Sailer, C., Koch, J., Horvath, R., …Yant, L. (2019). Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nature Ecology and Evolution, 3(3), 457-468. https://doi.org/10.1038/s41559-019-0807-4

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical d... Read More about Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep (2019)
Journal Article
Ahbara, A., Bahbahani, H., Almathen, F., Al Abri, M., Agoub, M. O., Abeba, A., …Mwacharo, J. M. (2019). Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontiers in Genetics, 9, Article 699. https://doi.org/10.3389/fgene.2018.00699

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, whic... Read More about Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity (2018)
Journal Article
Schurink, A., da Silva, V. H., Velie, B. D., Dibbits, B. W., Crooijmans, R. P., Franҫois, L., …Ducro, B. J. (2018). Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genetics, 19, Article 49. https://doi.org/10.1186/s12863-018-0657-0

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of man... Read More about Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity.

The fecal metabolome as a functional readout of the gut microbiome (2018)
Journal Article
Zierer, J., Jackson, M. A., Kastenmüller, G., Mangino, M., Long, T., Telenti, A., …Menni, C. (2018). The fecal metabolome as a functional readout of the gut microbiome. Nature Genetics, 50(6), 790-795. https://doi.org/10.1038/s41588-018-0135-7

© 2018 The Author(s). The human gut microbiome plays a key role in human health 1 , but 16S characterization lacks quantitative functional annotation 2 . The fecal metabolome provides a functional readout of microbial activity and can be used as an... Read More about The fecal metabolome as a functional readout of the gut microbiome.

Murine systemic thrombophilia and hemolytic uremic syndrome from a factor H point mutation (2017)
Journal Article
Ueda, Y., Mohammed, I., Song, D., Gullipalli, D., Zhou, L., Sato, S., …Song, W. (2017). Murine systemic thrombophilia and hemolytic uremic syndrome from a factor H point mutation. Blood, 129(9), 1184-1196. https://doi.org/10.1182/blood-2016-07-728253

Complement plays a key role in host defense, but its dysregulation can cause autologous tissue injury. Complement activation is normally controlled by regulatory proteins, including factor H (FH) in plasma and membrane cofactor protein (MCP) on the c... Read More about Murine systemic thrombophilia and hemolytic uremic syndrome from a factor H point mutation.

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways (2016)
Journal Article
Archer, N., Walsh, M. D., Shahrezaei, V., & Hebenstreit, D. (2016). Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways. Cell Systems, 3(5), 467-479. https://doi.org/10.1016/j.cels.2016.10.012

© 2016 The Author(s) Experimental procedures for preparing RNA-seq and single-cell (sc) RNA-seq libraries are based on assumptions regarding their underlying enzymatic reactions. Here, we show that the fairness of these assumptions varies within libr... Read More about Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.