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 302

System / cell line: amino ✕ Clear

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

Full-text index only

Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

pbmc his-tagged cem mammalian pcr electrophoretic western
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

Full-text index only

Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
Genome-wide diversity and selective pressure in the human rhinovirus.

PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

Full-text index only

Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

diverse hrv fully hrva genome phylogenetic pairwise
Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

Full-text index only

Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

minimally-passaged pylori coli arginase urease heterologous
Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

Full-text index only

The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

bovine panel agresearch intact random gene northern
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

Full-text index only

Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

private disease uniprot snps database controlled sequence
Functional analysis of novel SNPs and mutations in human and mouse genomes.

PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

Full-text index only

FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

apoe 11-nucleotide sequence genomic manual automated exonic
Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

Full-text index only

A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

genomic stra6 direct variant
ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

Full-text index only

Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI

clinical gonorrhoeae coli mic spontaneous pcr
INTERFEROME: the database of interferon regulated genes.

PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

Full-text index only

INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

chimp ifn-treated tissues irg microarray in-house basal
In silico analysis of missense substitutions using sequence-alignment based methods.

PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

Full-text index only

Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

clinically sequence curated deep blosum62 sift align-gvgd
Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

Full-text index only

Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

Full-text index only

No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
The genome of the simian and human malaria parasite Plasmodium knowlesi.

PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

Full-text index only

The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

knowlesi predicted type whole-genome comparative pfam
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

Full-text index only

Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
WebScipio: an online tool for the determination of gene structures using protein sequences.

PMID 18801164 · PMC2644328 · BMC genomics · 2008 · 7 claims · 4 setups

Full-text index only

WebScipio, a web interface to Scipio, determines gene structure from a query protein sequence against an assembled eukaryotic genome with quality approaching manual annotation.

homo pongo callithrix mus spliced
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

Full-text index only

Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
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

Full-text index only

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
The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

Full-text index only

Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

pbmcs clonal env deduced nested maximum-likelihood positive
Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.

PMID 18667071 · PMC2515332 · Malaria journal · 2008 · 8 claims · 4 setups

Full-text index only

Only two OR fragment types were identified in P. falciparum isolates from the Brazilian Amazon: OR-I (175 bp) and OR-II (199 bp)

falciparum pcr-amplified p126 sera nested agarose sequencing

Experiments

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

Genome-wide diversity and selective pressure in the human rhinovirus.

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

INTERFEROME: the database of interferon regulated genes.

In silico analysis of missense substitutions using sequence-alignment based methods.

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Tubulin proteomics: towards breaking the code.

WebScipio: an online tool for the determination of gene structures using protein sequences.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

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

The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.