Adi Stern
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View article: Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients Open
In rare individuals with a severely immunocompromised system, chronic infections of SARS-CoV-2 may develop, where the virus replicates in the body for months. Sequencing of some chronic infections has uncovered dramatic adaptive evolution …
View article: Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle
Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle Open
Cheater viruses cannot replicate on their own yet replicate faster than the wild type (WT) when the 2 viruses coinfect the same cell. Cheaters must possess dual genetic features: a defect, which leads to their inability to infect cells on …
View article: Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients
Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients Open
In rare individuals with a severely immunocompromised system, chronic infections of SARS-CoV-2 may develop, where the virus replicates in the body for months. Sequencing of some chronic infections has uncovered dramatic adaptive evolution …
View article: Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle
Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle Open
Cheater viruses, alternatively denoted as defective interfering viruses, cannot replicate on their own yet replicate faster than the wild type (WT) when the two viruses coinfect the same cell. Cheaters must possess dual genetic features: a…
View article: Using big sequencing data to identify chronic SARS-Coronavirus-2 infections
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections Open
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised …
View article: Using big sequencing data to identify chronic SARS-Coronavirus-2 infections
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections Open
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants, many of which may have arisen during chronic infections of immunocompromised individuals. Here, we harness a gl…
View article: Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation Open
RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may l…
View article: Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation Open
RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may l…
View article: Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation
Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation Open
based on data: https://www.ncbi.nlm.nih.gov/sra/PRJNA902661 more details in github repository: https://github.com/Stern-Lab/ms2-mutation-rate
View article: Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation
Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation Open
based on data: https://www.ncbi.nlm.nih.gov/sra/PRJNA902661 more details in github repository: https://github.com/Stern-Lab/ms2-mutation-rate
View article: Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation
Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation Open
based on data: https://www.ncbi.nlm.nih.gov/sra/PRJNA902661 more details in github repository: https://github.com/Stern-Lab/ms2-mutation-rate
View article: Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation
Inferring the mutation rate of an RNA virus from time-series haplotype data via neural density estimation Open
based on data: https://www.ncbi.nlm.nih.gov/sra/PRJNA902661 more details in github repository: https://github.com/Stern-Lab/ms2-mutation-rate
View article: Deciphering microbial gene function using natural language processing
Deciphering microbial gene function using natural language processing Open
Revealing the function of uncharacterized genes is a fundamental challenge in an era of ever-increasing volumes of sequencing data. Here, we present a concept for tackling this challenge using deep learning methodologies adopted from natur…
View article: Deciphering microbial gene function using natural language processing
Deciphering microbial gene function using natural language processing Open
Dataset for the support of a journal publication. The data include both computed models presented in the paper and all data used for analysis.
View article: Deciphering microbial gene function using natural language processing
Deciphering microbial gene function using natural language processing Open
Dataset for the support of a journal publication. The data include both computed models presented in the paper and all data used for analysis.
View article: Deciphering microbial gene function using natural language processing
Deciphering microbial gene function using natural language processing Open
Dataset for the support of a journal publication. The data include both computed models presented in the paper and all data used for analysis.
View article: Drivers of adaptive evolution during chronic SARS-CoV-2 infections
Drivers of adaptive evolution during chronic SARS-CoV-2 infections Open
In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations i…
View article: Drivers of adaptive evolution during chronic SARS-CoV-2 infections
Drivers of adaptive evolution during chronic SARS-CoV-2 infections Open
In some immunocompromised patients with chronic SARS-CoV-2 infection, dramatic adaptive evolution occurs, with substitutions reminiscent of those in variants of concern (VOCs). Here, we searched for drivers of VOC-like emergence by consoli…
View article: Inferring protein function in an emerging virus: detection of the nucleoprotein in Tilapia Lake Virus
Inferring protein function in an emerging virus: detection of the nucleoprotein in Tilapia Lake Virus Open
Emerging viruses impose global threats to animal and human populations and may bear novel genes with limited homology to known sequences, necessitating the development of novel approaches to infer and test protein functions. This challenge…
View article: The association between SARS‐CoV‐2 infection and late pregnancy loss
The association between SARS‐CoV‐2 infection and late pregnancy loss Open
SARS‐CoV‐2 vertical transmission with confirmed placental infection, confirmed by whole genome sequencing of the virus, may be a contributing factor to fetal demise.
View article: The unique evolutionary dynamics of the SARS-CoV-2 Delta variant
The unique evolutionary dynamics of the SARS-CoV-2 Delta variant Open
The SARS-Coronavirus-2 (SARS-CoV-2) driven pandemic was first recognized in late 2019, and the first few months of its evolution were relatively clock-like, dominated mostly by neutral substitutions. In contrast, the second year of the pan…
View article: Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals
Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals Open
The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vacci…
View article: Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals
Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals Open
Summary The SARS-CoV-2 pandemic has been raging for over a year, creating global detrimental impact. The BNT162b2 mRNA vaccine has demonstrated high protection levels, yet apprehension exists that several variants of concerns (VOCs) can su…
View article: <i>In vivo</i>engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice
<i>In vivo</i>engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice Open
As a potential single-shot HIV therapy, transplanted engineered B cells allow robust secretion of broadly neutralizing antibodies (bNAbs). However, ex vivo engineering of autologous B cells is expensive and requires specialized facilities,…
View article: Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis
Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis Open
Background The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing…
View article: Globally defining the effects of mutations in a picornavirus capsid
Globally defining the effects of mutations in a picornavirus capsid Open
The capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral …
View article: Author response: Globally defining the effects of mutations in a picornavirus capsid
Author response: Globally defining the effects of mutations in a picornavirus capsid Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The capsids of non-enveloped …
View article: Inoculation route-dependent Lassa virus dissemination and shedding dynamics in the natural reservoir – <i>Mastomys natalensis</i>
Inoculation route-dependent Lassa virus dissemination and shedding dynamics in the natural reservoir – <i>Mastomys natalensis</i> Open
Lassa virus (LASV), a Risk Group-4 zoonotic haemorrhagic fever virus, affects sub-Saharan African countries. Lassa fever, caused by LASV, results in thousands of annual deaths. Although decades have elapsed since the identification of the …
View article: Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV
Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV Open
Site-specific evolutionary rate shifts are defined as protein sites, where the rate of substitution has changed dramatically across the phylogeny. With respect to a given clade, sites may either undergo a rate acceleration or a rate decele…