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 190

System / cell line: amino ✕ Assay: analysis ✕ Clear

From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.

PMID 19840938 · PMC2787308 · The Journal of biological chemistry · 2009 · 8 claims · 8 setups

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γ-Glutamyl transpeptidase (GGT) activity in rat liver shows biphasic changes during azo dye-induced hepatocarcinogenesis, mirroring the oncofetal expression pattern of α-fetoprotein

liver tissues ascites hepatoma spectrophotometric enzyme glycan
A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

PMID 20003495 · PMC2802351 · Orphanet journal of rare diseases · 2009 · 8 claims · 7 setups

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A novel FAH gene mutation, c.103G>A (Ala35Thr), causes a mild, atypical form of tyrosinemia type I

fibroblasts liver genomic tnt northern western liver
Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates.

PMID 18036224 · PMC2231365 · BMC microbiology · 2007 · 8 claims · 4 setups

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Genotypes A, D, and F co-circulate in each of the five Brazilian geographic regions, with no other genotypes identified among 303 isolates

serum hbv pcr-rflp nucleotide phylogenetic
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
The role of genomics in tracking the evolution of influenza A virus.

PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

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Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

PMID 18028545 · PMC2211469 · Virology journal · 2007 · 8 claims · 4 setups

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Synthetic peptides corresponding to LLP-1, LLP-2, and LLP-3 domains partition into POPC:POPG lipid membranes and adopt amphipathic α-helical secondary structure

hiv-1 synthetic nbd 90%popc wimley-white circular tryptophan
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag
Global genetic diversity of human metapneumovirus fusion gene.

PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

hmpv llc-mk2 clinical rt-pcr sequence phylogenetic
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

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Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

hiv-1 same brazilian phylogenetic bootstrap pruning
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race

Experiments

From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.

A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

Evidence for a novel gene associated with human influenza A viruses.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

A surrogate-based approach for post-genomic partner identification.

Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

Species-specific protein sequence and fold optimizations.

Oligomeric protein structure networks: insights into protein-protein interactions.

The role of genomics in tracking the evolution of influenza A virus.

Molecular analysis of Plasmodium ovale variants.

Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

Genetic variation of St. Louis encephalitis virus.

Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

Global genetic diversity of human metapneumovirus fusion gene.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

Comparative genomics and understanding of microbial biology.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.