GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
We seek to transform how new and emergent variants of pandemic-causing viruses,
specifically SARS-CoV-2, are identified and classified. By adapting large language models …
specifically SARS-CoV-2, are identified and classified. By adapting large language models …
Benchmarking machine learning robustness in COVID-19 genome sequence classification
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of
sequence data of the SARS-CoV-2 genome—millions of sequences and counting. This …
sequence data of the SARS-CoV-2 genome—millions of sequences and counting. This …
To transformers and beyond: large language models for the genome
In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool
for tackling complex computational challenges. This review focuses on the transformative …
for tackling complex computational challenges. This review focuses on the transformative …
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning
L Brierley, A Fowler - PLoS Pathogens, 2021 - journals.plos.org
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 …
coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the …
Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak
Pre‐clinical responses to fast‐moving infectious disease outbreaks heavily depend on
choosing the best isolates for animal models that inform diagnostics, vaccines and …
choosing the best isolates for animal models that inform diagnostics, vaccines and …
Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-
19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral …
19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral …
Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction …
We have performed an integrative analysis of SARS-CoV-2 genome sequences from
different countries. Apart from mutational analysis, we have predicted host antiviral miRNAs …
different countries. Apart from mutational analysis, we have predicted host antiviral miRNAs …
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
The novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we …
caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we …
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of …
respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of …
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
Background The genome of SARS-CoV-2 is susceptible to mutations during viral replication
due to the errors generated by RNA-dependent RNA polymerases. These mutations enable …
due to the errors generated by RNA-dependent RNA polymerases. These mutations enable …
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