Publications
Selected publications
- Past and future uses of text mining in ecology and evolution (Journal article - 2022)
- Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning (Journal article - 2021)
- The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape (Journal article - 2021)
- Tissue tropism and transmission ecology predict virulence of human RNA viruses (Journal article - 2019)
- Epidemiological characteristics of human-infective RNA viruses (Journal article - 2018)
2024
Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.
Maruzani, R., Brierley, L., Jorgensen, A., & Fowler, A. (2024). Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.. BMC genomics, 25(1), 827. doi:10.1186/s12864-024-10737-w
The changing landscape of text mining: a review of approaches for ecology and evolution.
Farrell, M. J., Le Guillarme, N., Brierley, L., Hunter, B., Scheepens, D., Willoughby, A., . . . Mideo, N. (2024). The changing landscape of text mining: a review of approaches for ecology and evolution.. Proceedings. Biological sciences, 291(2027), 20240423. doi:10.1098/rspb.2024.0423
Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses.
Lu, L., Zhang, F., Brierley, L., Robertson, G., Chase-Topping, M., Lycett, S., & Woolhouse, M. (2024). Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses.. Molecular biology and evolution, 41(1), msad272. doi:10.1093/molbev/msad272
2023
The International Virus Bioinformatics Meeting 2023.
Hufsky, F., Abecasis, A. B., Babaian, A., Beck, S., Brierley, L., Dellicour, S., . . . Marz, M. (2023). The International Virus Bioinformatics Meeting 2023.. Viruses, 15(10), 2031. doi:10.3390/v15102031
A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection
Hawkings, M. J., Vaselli, N. M., Charalampopoulos, D., Brierley, L., Elliot, A. J., Buchan, I., & Hungerford, D. (2023). A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection. Viruses, 15(8), 1625. doi:10.3390/v15081625
A systematic review of the prevalence of persistent gastrointestinal symptoms and incidence of new gastrointestinal illness after acute SARS-CoV-2 infection
Network embedding unveils the hidden interactions in the mammalian virome
Poisot, T., Ouellet, M. -A., Mollentze, N., Farrell, M. J., Becker, D. J., Brierley, L., . . . Carlson, C. J. (2023). Network embedding unveils the hidden interactions in the mammalian virome. PATTERNS, 4(6). doi:10.1016/j.patter.2023.100738
2022
Past and future uses of text mining in ecology and evolution
Farrell, M. J., Brierley, L., Willoughby, A., Yates, A., & Mideo, N. (2022). Past and future uses of text mining in ecology and evolution. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 289(1975). doi:10.1098/rspb.2021.2721
The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations
Carlson, C. J., Gibb, R. J., Albery, G. F., Brierley, L., Connor, R. P., Dallas, T. A., . . . Seifert, S. N. (n.d.). The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations. mBio. doi:10.1128/mbio.02985-21
Tracking changes between preprint posting and journal publication during a pandemic
Brierley, L., Nanni, F., Polka, J. K., Dey, G., Palfy, M., Fraser, N., & Coates, J. A. (2022). Tracking changes between preprint posting and journal publication during a pandemic. PLOS BIOLOGY, 20(2). doi:10.1371/journal.pbio.3001285
Benchmarking the performance of six variant callers on synthetic and real ctDNA datasets
Maruzani, R., Fowler, A., & Brierley, L. (2022). Benchmarking the performance of six variant callers on synthetic and real ctDNA datasets. In HUMAN HEREDITY Vol. VOL. (pp. 16). Retrieved from https://www.webofscience.com/
Mammal virus diversity estimates are unstable due to accelerating discovery effort
Gibb, R., Albery, G. F., Mollentze, N., Eskew, E. A., Brierley, L., Ryan, S. J., . . . Carlson, C. J. (2022). Mammal virus diversity estimates are unstable due to accelerating discovery effort. BIOLOGY LETTERS, 18(1). doi:10.1098/rsbl.2021.0427
Selecting subsets of immune repertoire features improves prediction of coeliac disease status using machine learning
Kockelbergh, H., Shoukat, M. S., Evans, S. C., Brierley, L., Jorgensen, A. L., Green, P. L., . . . Fowler, A. (2022). Selecting subsets of immune repertoire features improves prediction of coeliac disease status using machine learning. In HUMAN HEREDITY Vol. VOL. (pp. 14-15). Retrieved from https://www.webofscience.com/
2021
The science of the host–virus network
Albery, G. F., Becker, D. J., Brierley, L., Brook, C. E., Christofferson, R. C., Cohen, L. E., . . . Carlson, C. J. (2021). The science of the host–virus network. Nature Microbiology, 6(12), 1483-1492. doi:10.1038/s41564-021-00999-5
Data Proliferation, Reconciliation and Synthesis in Viral Ecology
Gibb, R., Albery, G. F., Becker, D. J., Brierley, L., Connor, R., Dallas, T. A., . . . Poisot, T. (2021). Data Proliferation, Reconciliation and Synthesis in Viral Ecology. BIOSCIENCE, 71(11), 1148-1156. doi:10.1093/biosci/biab080
Mammal virus diversity estimates are unstable due to accelerating discovery effort
The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations
Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide.
Metelmann, S., Pattni, K., Brierley, L., Cavalerie, L., Caminade, C., Blagrove, M. S. C., . . . Baylis, M. (2021). Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide.. One Health, 100221. doi:10.1016/j.onehlt.2021.100221
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
Brierley, L., & Fowler, A. (2021). Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. PLoS Pathogens, 17(4). doi:10.1371/journal.ppat.1009149
The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape
Fraser, N., Brierley, L., Dey, G., Polka, J. K., Palfy, M., Nanni, F., & Coates, J. A. (2021). The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape. PLOS BIOLOGY, 19(4). doi:10.1371/journal.pbio.3000959
Lessons from the influx of preprints during the early COVID-19 pandemic
Brierley, L. (2021). Lessons from the influx of preprints during the early COVID-19 pandemic. LANCET PLANETARY HEALTH, 5(3), E115-E117. Retrieved from https://www.webofscience.com/
Preprints in motion: tracking changes between preprint posting and journal publication during a pandemic
Brierley, L., Nanni, F., Polka, J., Dey, G., Pálfy, M., Fraser, N., & Coates, J. A. (2021). Preprints in motion: tracking changes between preprint posting and journal publication during a pandemic. doi:10.1101/2021.02.20.432090
2020
Global discovery of human-infective RNA viruses: A modelling analysis
Zhang, F., Chase-Topping, M., Guo, C. -G., van Bunnik, B. A. D., Brierley, L., & Woolhouse, M. E. J. (2020). Global discovery of human-infective RNA viruses: A modelling analysis. PLOS PATHOGENS, 16(11). doi:10.1371/journal.ppat.1009079
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
Brierley, L., & Fowler, A. (2020). Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. doi:10.1101/2020.11.02.350439
Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide
Metelmann, S., Pattni, K., Brierley, L., Cavalerie, L., Caminade, C., Blagrove, M., . . . Baylis, M. (2020). Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide. doi:10.1101/2020.07.17.20155226
Preprinting the COVID-19 pandemic
Fraser, N., Brierley, L., Dey, G., Polka, J., Pálfy, M., Nanni, F., & Coates, J. A. (2020). Preprinting the COVID-19 pandemic. doi:10.1101/2020.05.22.111294
The role of research preprints in the academic response to the COVID-19 epidemic
Brierley, L. (n.d.). The role of research preprints in the academic response to the COVID-19 epidemic. doi:10.22541/au.158516578.89167184
2019
Evolutionary origins of epidemic potential among human RNA viruses
Lu, L., Brierley, L., Robertson, G., Zhang, F., Lycett, S., Smith, D., . . . Woolhouse, M. (2019). Evolutionary origins of epidemic potential among human RNA viruses. doi:10.1101/771394
The effect of dapagliflozin on glycaemic control and other cardiovascular disease risk factors in type 2 diabetes mellitus: a real-world observational study
McGurnaghan, S. J., Brierley, L., Caparrotta, T. M., McKeigue, P. M., Blackbourn, L. A. K., Wild, S. H., . . . Colhoun, H. M. (2019). The effect of dapagliflozin on glycaemic control and other cardiovascular disease risk factors in type 2 diabetes mellitus: a real-world observational study. DIABETOLOGIA, 62(4), 621-632. doi:10.1007/s00125-018-4806-9
Tissue Tropism and Transmission Ecology Predict Virulence of Human RNA Viruses
Tissue tropism and transmission ecology predict virulence of human RNA viruses
Brierley, L., Pedersen, A. B., & Woolhouse, M. E. J. (2019). Tissue tropism and transmission ecology predict virulence of human RNA viruses. PLOS BIOLOGY, 17(11). doi:10.1371/journal.pbio.3000206
2018
Epidemiological characteristics of human-infective RNA viruses
Woolhouse, M. E. J., & Brierley, L. (2018). Epidemiological characteristics of human-infective RNA viruses. SCIENTIFIC DATA, 5. doi:10.1038/sdata.2018.17
2016
Assessing the Epidemic Potential of RNA and DNA Viruses
Woolhouse, M. E. J., Brierley, L., McCaffery, C., & Lycett, S. (2016). Assessing the Epidemic Potential of RNA and DNA Viruses. EMERGING INFECTIOUS DISEASES, 22(12), 2037-2044. doi:10.3201/eid2212.160123
Quantifying Global Drivers of Zoonotic Bat Viruses: A Process-Based Perspective
Brierley, L., Vonhof, M. J., Olival, K. J., Daszak, P., & Jones, K. E. (2016). Quantifying Global Drivers of Zoonotic Bat Viruses: A Process-Based Perspective. AMERICAN NATURALIST, 187(2), E53-E64. doi:10.1086/684391
2013
RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases.
J Woolhouse, M. E., Adair, K., & Brierley, L. (2013). RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases.. Microbiology spectrum, 1(1). doi:10.1128/microbiolspec.oh-0001-2012