Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 14

Assay: infectivity ✕ Clear

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

PMID 18312646 · PMC2270869 · Retrovirology · 2008 · 8 claims · 7 setups

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Infectivity of recombinant viruses carrying different Env proteins from the same patient varies over an approximately 10-fold range, even among viruses with similar tropism.

env u373 mt4-r5 u373-r5 phylogenetic infectivity flow
SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

PMID 40169992 · PMC11963337 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 2 setups

Has reproduction · 83

SIRE 2.0 is a novel Bayesian methodology and software tool for estimating polygenic contributions (variance components and additive genetic effects) to host susceptibility, infectivity and recoverability from temporal epidemic data using pedigree/genomic relationship matrices.

simulated bayesian systematic
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

falciparum berghei nano-lc-ms targeted gene
Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa
Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
Modulation of HERV Expression by Four Different Encephalitic Arboviruses during Infection of Human Primary Astrocytes.

PMID 36423114 · PMC9694637 · Viruses · 2022 · 6 claims · 7 setups

Has reproduction · 56

The four arboviruses commonly induce upregulation of HERVs in human primary astrocytes, with 15 HERVs co-modulated by all four viruses, including highly upregulated HERV4_4q22.1

astrocytes differentially bulk flow immunofluorescence
Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

PMID 18829386 · PMC2730674 · International journal of medical microbiology : IJMM · 2009 · 6 claims · 7 setups

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C. pneumoniae was cultured from two late-onset AD brain tissue samples (Tor-1 from hippocampus, Phi-1 from temporal cortex) from different North American regions.

tor-1 brain hep-2 pcr culture immunofluorescence
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome
Genomics and biology come together to fight HIV.

PMID 18366259 · PMC2270331 · PLoS biology · 2008 · 8 claims · 6 setups

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Genome-wide association studies have identified ~100 genetic polymorphisms robustly (genome-wide significant) linked to common human traits/diseases, but the biological mechanisms behind most remain unknown.

ceph hiv-positive elledge heritability linkage modified
An Asilomar moment.

PMID 12372138 · PMC244904 · Genome biology · 2002 · 7 claims · 3 setups

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The current push to restrict genomics/pathogen research funding and publication due to bioterrorism fears parallels the 1975 Asilomar Conference response to recombinant DNA risks.

mousepox chicken poliovirus gene targeted novo
Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.

PMID 32333836 · PMC7181998 · Cell · 2020 · 8 claims · 7 setups

Has reproduction · 87

Clinical-grade hrsACE2 significantly inhibits SARS-CoV-2 infection of Vero-E6 cells in a dose-dependent manner

nasopharyngeal vero-e6 ipsc-derived embryonic viral qrt-pcr organoid
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

Has reproduction · 93

An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

hff mrc5 chip-qpcr rt-qpcr chipseq
Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

Experiments

Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses.

SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

Modulation of HERV Expression by Four Different Encephalitic Arboviruses during Infection of Human Primary Astrocytes.

Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

Genomics and biology come together to fight HIV.

An Asilomar moment.

Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.

Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.