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SARS-CoV-2 variants, spike mutations and immune escape

Nature reviews. Microbiology, 2021-07, Vol.19 (7), p.409-424

2021

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The Evolution and Biology of SARS-CoV-2 Variants

Cold Spring Harbor perspectives in biology, 2022-05, Vol.12 (5), p.1

2022

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The origins of SARS-CoV-2: A critical review

Cell, 2021-09, Vol.184 (19), p.4848-4856

2021

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

PLoS biology, 2021-03, Vol.19 (3), p.e3001115

2021

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Predicting host taxonomic information from viral genomes: A comparison of feature representations

PLoS computational biology, 2020-05, Vol.16 (5), p.e1007894

2020

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Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Nature microbiology, 2020-11, Vol.5 (11), p.1408-1417

2020

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Redefining the ancestral origins of the interleukin-1 superfamily

Nature communications, 2018-03, Vol.9 (1), p.1156-12, Article 1156

2018

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In silico prediction of HIV-1-host molecular interactions and their directionality

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009720-e1009720

2022

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Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

Plant physiology (Bethesda), 2010-07, Vol.153 (3), p.1398-1412

2010

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Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma

Scientific reports, 2023-05, Vol.13 (1), p.8319-8319, Article 8319

2023

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Ancestry of the AUTS2 family-A novel group of polycomb-complex proteins involved in human neurological disease

PloS one, 2020-12, Vol.15 (12), p.e0232101-e0232101

2020

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A Survey of Bioinformatics Database and Software Usage through Mining the Literature

PloS one, 2016-06, Vol.11 (6), p.e0157989-e0157989

2016

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Defining the role of essential genes in human disease

PloS one, 2011-11, Vol.6 (11), p.e27368-e27368

2011

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Using set theory to reduce redundancy in pathway sets

BMC bioinformatics, 2018-10, Vol.19 (1), p.386-386, Article 386

2018

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HIHISIV: a database of gene expression in HIV and SIV host immune response

BMC bioinformatics, 2024-03, Vol.25 (1), p.125-125, Article 125

2024

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Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism

PloS one, 2017-10, Vol.12 (10), p.e0185790-e0185790

2017

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Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism

PloS one, 2012-11, Vol.7 (11), p.e49602-e49602

2012

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Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules

PLoS computational biology, 2024-01, Vol.20 (1), p.e1011795

2024

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SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations

PLoS pathogens, 2013-01, Vol.9 (1), p.e1003011-e1003011

2013

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A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns

Scientific reports, 2019-02, Vol.9 (1), p.2159-2159, Article 2159

2019

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The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness

PLoS pathogens, 2022-11, Vol.18 (11), p.e1010973-e1010973

2022

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Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism

Antimicrobial agents and chemotherapy, 2014-04, Vol.58 (4), p.2167-2185

2014

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The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting

PLoS biology, 2021-09, Vol.19 (9), p.e3001352-e3001352

2021

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The animal origin of SARS-CoV-2

Science (American Association for the Advancement of Science), 2021-08, Vol.373 (6558), p.968-970

2021

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SARS-CoV-2 variants, spike mutations and immune escape

The Evolution and Biology of SARS-CoV-2 Variants

The origins of SARS-CoV-2: A critical review

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Predicting host taxonomic information from viral genomes: A comparison of feature representations

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)

Redefining the ancestral origins of the interleukin-1 superfamily

In silico prediction of HIV-1-host molecular interactions and their directionality

Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma

Ancestry of the AUTS2 family-A novel group of polycomb-complex proteins involved in human neurological disease

A Survey of Bioinformatics Database and Software Usage through Mining the Literature

Defining the role of essential genes in human disease

Using set theory to reduce redundancy in pathway sets

HIHISIV: a database of gene expression in HIV and SIV host immune response

Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism

Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism

Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules

SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations

A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns

The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness

Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism

The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting

The animal origin of SARS-CoV-2

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