Liam Brierley
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View article: An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning
An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning Open
Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cases have resulted from the current epizootic outbreak, the wide diversity of influenza vir…
View article: Predicting High Confidence ctDNA Somatic Variants with Ensemble Machine Learning Models
Predicting High Confidence ctDNA Somatic Variants with Ensemble Machine Learning Models Open
Circulating tumour DNA (ctDNA) is a minimally invasive cancer biomarker that can be used to inform treatment of cancer patients. The utility of ctDNA as a cancer biomarker depends on the ability to accurately detect somatic variants associ…
View article: Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification
Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification Open
Insights gained through interpretation of models trained on the T-cell receptor (TCR) repertoire contribute to advances in understanding of immune-mediated disease. This has the potential to improve diagnostic tests and treatments, particu…
View article: Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection
Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection Open
Background Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collectin…
View article: The changing landscape of text mining: a review of approaches for ecology and evolution
The changing landscape of text mining: a review of approaches for ecology and evolution Open
In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data fro…
View article: Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe
Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe Open
Highly pathogenic avian influenza (HPAI) represents a threat to animal and human health, with the ongoing H5N1 outbreak within the H5 2.3.4.4b clade being the largest on record. However, it remains unclear what factors have contributed to …
View article: The changing landscape of text mining - a review of approaches for ecology and evolution
The changing landscape of text mining - a review of approaches for ecology and evolution Open
In ecology and evolutionary biology, synthesis and modelling of data from published literature is a common practice for generating insight and testing theories across systems. However, the tasks of searching, screening, and extracting data…
View article: Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses
Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses Open
Transmissibility, the ability to spread within host populations, is a prerequisite for a pathogen to have epidemic or pandemic potential. Here, we estimate the phylogenies of human infectivity and transmissibility using 1,408 genome sequen…
View article: Benchmarking UMI-aware and standard variant callers on synthetic and real ctDNA datasets
Benchmarking UMI-aware and standard variant callers on synthetic and real ctDNA datasets Open
Background Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collectin…
View article: The International Virus Bioinformatics Meeting 2023
The International Virus Bioinformatics Meeting 2023 Open
The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific enviro…
View article: A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection
A Systematic Review of the Prevalence of Persistent Gastrointestinal Symptoms and Incidence of New Gastrointestinal Illness after Acute SARS-CoV-2 Infection Open
It is known that SARS-CoV-2 infection can result in gastrointestinal symptoms. For some, these symptoms may persist beyond acute infection, in what is known as ‘post-COVID syndrome’. We conducted a systematic review to examine the prevalen…
View article: A systematic review of the prevalence of persistent gastrointestinal symptoms and incidence of new gastrointestinal illness after acute SARS-CoV-2 infection
A systematic review of the prevalence of persistent gastrointestinal symptoms and incidence of new gastrointestinal illness after acute SARS-CoV-2 infection Open
It is known that SARS-CoV-2 infection can result in gastrointestinal symptoms. For some, these symptoms may persist beyond acute infection, in what is known as ‘post-COVID syndrome’. We conducted a systematic review to examine the prevalen…
View article: Past and future uses of text mining in ecology and evolution
Past and future uses of text mining in ecology and evolution Open
Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant lit…
View article: The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations
The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations Open
Animals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in differe…
View article: Tracking changes between preprint posting and journal publication during a pandemic
Tracking changes between preprint posting and journal publication during a pandemic Open
Amid the Coronavirus Disease 2019 (COVID-19) pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press, and policymakers for the first t…
View article: Mammal virus diversity estimates are unstable due to accelerating discovery effort
Mammal virus diversity estimates are unstable due to accelerating discovery effort Open
Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by hi…
View article: Mammal virus diversity estimates are unstable due to accelerating discovery effort
Mammal virus diversity estimates are unstable due to accelerating discovery effort Open
Host-virus association data form the backbone of research into eco-evolutionary drivers of viral diversity and host-level zoonotic risk. However, knowledge of the wildlife virome is inherently constrained by historical discovery effort, an…
View article: The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations
The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations Open
Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this p…
View article: Data Proliferation, Reconciliation, and Synthesis in Viral Ecology
Data Proliferation, Reconciliation, and Synthesis in Viral Ecology Open
The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic ri…
View article: Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning Open
The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging t…
View article: Ranking the risk of animal-to-human spillover for newly discovered viruses
Ranking the risk of animal-to-human spillover for newly discovered viruses Open
Significance The recent emergence and spread of zoonotic viruses, including Ebola virus and severe acute respiratory syndrome coronavirus 2, demonstrate that animal-sourced viruses are a very real threat to global public health. Virus disc…
View article: The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape
The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape Open
The world continues to face a life-threatening viral pandemic. The virus underlying the Coronavirus Disease 2019 (COVID-19), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has caused over 98 million confirmed cases and 2.2 m…
View article: preprinting-a-pandemic/pandemic_preprints: Version 3.0
preprinting-a-pandemic/pandemic_preprints: Version 3.0 Open
preprint now available (version 3):
View article: Lessons from the influx of preprints during the early COVID-19 pandemic
Lessons from the influx of preprints during the early COVID-19 pandemic Open
Approximately 1 year since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recognised, the COVID-19 pandemic has been characterised by widespread transmission, substantial strains on health infrastructure, and global…
View article: Data proliferation, reconciliation, and synthesis in viral ecology
Data proliferation, reconciliation, and synthesis in viral ecology Open
The fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic preventi…