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 30

System / cell line: type ✕ Assay: structural ✕ Clear

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

PMID 19958498 · PMC2788387 · BMC genomics · 2009 · 8 claims · 4 setups

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Comparative homology modeling of wild-type and mutant α-mannosidase across human, cow, cat and guinea pig reveals a significant correlation between genotype severity and phenotype severity in α-mannosidosis

lysosomal full-length pro-peptide bovine homology sequence weblogo
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

coli flp il10 flp-holliday recombination site-specific computational
MutDB: update on development of tools for the biochemical analysis of genetic variation.

PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

proteins mutdb nonsynonymous genes sequence web functional
Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

p53 1bpi mutations disease-associated graph correlation structural
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups

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None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.

ensembl swissprot same structural foldx side
Cancer biomarker AKR1B10 and carbonyl metabolism.

PMID 19028477 · PMC6193474 · Chemico-biological interactions · 2009 · 8 claims · 6 setups

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AKR1B10 reduces the anticancer drug daunorubicin to daunorubicinol, decreasing its chemotherapeutic effectiveness

recombinant fenofibrate enzyme sds-page x-ray
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

Has reproduction · 85

Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

ligand gpcr glida principal sequence gene
Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

library database oligovalent b-cells glycan bioinformatics one-pot
Human genetics branches out in Barcelona.

PMID 18710599 · PMC2575509 · Genome biology · 2008 · 8 claims · 8 setups

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A meta-analysis of three GWAS scans (DIAGRAM) identifies new type 2 diabetes susceptibility loci (JAZF1, CDC123/CAMK1D, ADAMTS9, THADA) with modest individual effect

patients families lymphoblastoid genome genome-wide gwas genetic
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual
A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

PMID 18618005 · PMC2447816 · Molecular vision · 2008 · 6 claims · 4 setups

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A heterozygous c.327C>A transversion in exon 3 of CRYGC causes a nonsense mutation (C109X) that cosegregates with autosomal dominant congenital nuclear cataract in a Chinese family.

genomic type family γc-crystallin pcr comparative clinical
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

example hepatitis minimum suboptimal multiple-point
Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

PMID 16429166 · PMC1342637 · PLoS genetics · 2005 · 8 claims · 5 setups

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PANTHER subPSEC scores correctly predicted the functional impact of >94% (16/17) of tested naturally occurring ABCA1 variants

abca1 stably subpsec cholesterol rt-pcr
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

PMID 19015641 · PMC2633425 · Oncogene · 2009 · 8 claims · 8 setups

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E884K works in concert with L858R in-cis, in a dominant fashion, to differentially alter EGFR downstream signaling and inhibitor sensitivity in an inhibitor-specific manner

cos-7 kinase japanese western cellular mts
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 55

Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

haploid mistral assembled masked whole-genome k-mer genome-wide
Novel selection and genetic characterisation of an etoposide-resistant human leukaemic CCRF-CEM cell line.

PMID 8382508 · PMC1968246 · British journal of cancer · 1993 · 8 claims · 5 setups

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CEM/VP-1 is 15-fold more resistant to etoposide than parental CCRF-CEM cells

ccrf-cem cem nuclear cytogenetic pcr allele-specific
Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

PMID 16764716 · PMC1586026 · BMC cancer · 2006 · 8 claims · 6 setups

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The 9106C>T (Q2960X) and IVS16-2A>G BRCA2 mutations are recurrent in MBC families from North-East Italy and may reflect a founder effect.

blood germline tumor family mutation mlpa microsatellite

Experiments

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

Cancer biomarker AKR1B10 and carbonyl metabolism.

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

Human genetics branches out in Barcelona.

Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Novel selection and genetic characterisation of an etoposide-resistant human leukaemic CCRF-CEM cell line.

Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.