Jeremy Ratcliff
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View article: Evaluating the Effectiveness of Parameter-Efficient Fine-Tuning in Genomic Classification Tasks
Evaluating the Effectiveness of Parameter-Efficient Fine-Tuning in Genomic Classification Tasks Open
Foundation models are increasingly being leveraged for biological tasks. To address the high memory requirements of fine-tuning large pre-trained language models, parameter efficient fine-tuning (PEFT) methods are also being increasingly u…
View article: TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection
TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection Open
Motivation TaxTriage is a comprehensive pathogen identification workflow designed for both short– and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative patho…
View article: Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry
Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry Open
Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmissi…
View article: Transformer model generated bacteriophage genomes are compositionally distinct from natural sequences
Transformer model generated bacteriophage genomes are compositionally distinct from natural sequences Open
Novel applications of language models in genomics promise to have a large impact on the field. The megaDNA model is the first publicly available generative model for creating synthetic viral genomes. To evaluate megaDNA’s ability to recapi…
View article: Transformer Model Generated Bacteriophage Genomes are Compositionally Distinct from Natural Sequences
Transformer Model Generated Bacteriophage Genomes are Compositionally Distinct from Natural Sequences Open
Novel applications of language models in genomics promise to have a large impact on the field. The megaDNA model is the first publicly available generative model for creating synthetic viral genomes. To evaluate megaDNA’s ability to recapi…
View article: Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents
Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents Open
Introduction The key to understanding the COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Young people are at a lower risk of COVID-19 mortality, females are at a lower risk than mal…
View article: Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry
Improved Resolution of Highly Pathogenic Avian Influenza Virus Haemagglutinin Cleavage Site Using Oxford Nanopore R10 Sequencing Chemistry Open
Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmissi…
View article: On the Mark: Modeling and Forecasting for Public Health Impact
On the Mark: Modeling and Forecasting for Public Health Impact Open
View article: Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents
Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents Open
Key to understanding COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Sex- and age-specific immune differences have a wide impact on outcomes from infections and immunisations. Typica…
View article: The roles of nucleic acid editing in adaptation of zoonotic viruses to humans
The roles of nucleic acid editing in adaptation of zoonotic viruses to humans Open
View article: Exposed seronegative: Cellular immune responses to SARS-CoV-2 in the absence of seroconversion
Exposed seronegative: Cellular immune responses to SARS-CoV-2 in the absence of seroconversion Open
The factors determining whether infection will occur following exposure to SARS-CoV-2 remain elusive. Certain SARS-CoV-2-exposed individuals mount a specific T-cell response but fail to seroconvert, representing a population that may provi…
View article: Coronavirus disease 2019 subphenotypes and differential treatment response to convalescent plasma in critically ill adults: secondary analyses of a randomized clinical trial
Coronavirus disease 2019 subphenotypes and differential treatment response to convalescent plasma in critically ill adults: secondary analyses of a randomized clinical trial Open
View article: The Johns Hopkins University Center for Systems Science and Engineering COVID-19 Dashboard: data collection process, challenges faced, and lessons learned
The Johns Hopkins University Center for Systems Science and Engineering COVID-19 Dashboard: data collection process, challenges faced, and lessons learned Open
View article: Detection frequencies and viral load distribution of parvovirus <scp>B19 DNA</scp> in blood and plasma donations in <scp>E</scp>ngland
Detection frequencies and viral load distribution of parvovirus <span>B19 DNA</span> in blood and plasma donations in <span>E</span>ngland Open
Background and Objectives Infections with human parvovirus B19 (B19V) are transmissible by blood components and plasma‐derived medicines. The European Pharmacopoeia regulates maximum levels of virus allowed in manufacturers' plasma pools. …
View article: Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses
Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses Open
The role of immune responses to previously seen endemic coronavirus epitopes in severe acute respiratory coronavirus 2 (SARS-CoV-2) infection and disease progression has not yet been determined. Here, we show that a key characteristic of f…
View article: Highly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR
Highly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR Open
Tools to detect SARS-CoV-2 variants of concern and track the ongoing evolution of the virus are necessary to support public health efforts and the design and evaluation of novel COVID-19 therapeutics and vaccines. Although next-generation …
View article: Effects of Severe Acute Respiratory Syndrome Coronavirus 2 Strain Variation on Virus Neutralization Titers: Therapeutic Use of Convalescent Plasma
Effects of Severe Acute Respiratory Syndrome Coronavirus 2 Strain Variation on Virus Neutralization Titers: Therapeutic Use of Convalescent Plasma Open
We compared neutralizing antibody titers of convalescent samples collected before and after the emergence of novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), against the wild-type virus and Alpha (B.1.1.7) and…
View article: Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction Open
Introduction Tools to detect SARS-Coronavirus-2 variants of concern and track the ongoing evolution of the virus are necessary to support public health efforts and the design and evaluation of novel COVID-19 therapeutics and vaccines. Alth…
View article: Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil
Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil Open
View article: Clinical validation of optimised RT-LAMP for the diagnosis of SARS-CoV-2 infection
Clinical validation of optimised RT-LAMP for the diagnosis of SARS-CoV-2 infection Open
View article: Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil; an exploratory analysis of a randomised controlled trial
Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil; an exploratory analysis of a randomised controlled trial Open
Background Emerging evidence shows the substantial real-world impact of authorised vaccines against COVID-19 and provides insight into the potential role of vaccines in curbing the pandemic. However, there remains uncertainty about the eff…
View article: Virological Characterization of Critically Ill Patients With COVID-19 in the United Kingdom: Interactions of Viral Load, Antibody Status, and B.1.1.7 Infection
Virological Characterization of Critically Ill Patients With COVID-19 in the United Kingdom: Interactions of Viral Load, Antibody Status, and B.1.1.7 Infection Open
Background Convalescent plasma containing neutralizing antibody to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is under investigation for coronavirus disease 2019 (COVID-19) treatment. We report diverse virological charact…
View article: Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses
Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses Open
Summary It is unclear whether prior endemic coronavirus infections affect COVID-19 severity. Here, we show that in cases of fatal COVID-19, antibody responses to the SARS-COV-2 spike are directed against epitopes shared with endemic beta-c…
View article: T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses
T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses Open
View article: Virological and serological characterization of critically ill patients with COVID-19 in the UK: a special focus on variant detection
Virological and serological characterization of critically ill patients with COVID-19 in the UK: a special focus on variant detection Open
Background Treatment of COVID-19 patients with convalescent plasma containing neutralising antibody to SARS-CoV-2 is under investigation as a means of reducing viral loads, ameliorating disease outcomes, and reducing mortality. However, it…
View article: Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution
Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution Open
Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coron…
View article: Fatal COVID-19 Outcomes are Associated with an Antibody Response Targeting Epitopes Shared with Endemic Coronaviruses
Fatal COVID-19 Outcomes are Associated with an Antibody Response Targeting Epitopes Shared with Endemic Coronaviruses Open
View article: Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020
Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020 Open
Background The progression and geographical distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the United Kingdom (UK) and elsewhere is unknown because typically only symptomatic individuals are diagn…
View article: SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus
SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus Open
Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of…
View article: Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19
Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19 Open