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 55

System / cell line: cohort ✕ Assay: identification ✕ Clear

Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

Has reproduction · 86

A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

known tnbc unique unknown gene machine term
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
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

PMID 16321154 · PMC1326206 · BMC neurology · 2005 · 7 claims · 6 setups

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CFS, PGI and fibromyalgia are highly overlapping symptom complexes likely reflecting a shared underlying pathophysiological mechanism rather than distinct diseases

pooled individual cerebrospinal subjects capillary trypsin elisa
Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

PMID 39256359 · PMC11387733 · Nature communications · 2024 · 8 claims · 7 setups

Has reproduction · 87

Heterozygous missense or loss-of-function variants in LRRC7 cause a dominant neurodevelopmental disorder in 33 identified individuals

genomes genematcher affected 293t genetic exome phenotype
The molecular landscape of ASPM mutations in primary microcephaly.

PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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ASPM mutations are the most common cause of MCPH

consanguineous genomic parents one polymorphic sanger family
Isolated populations and complex disease gene identification.

PMID 18771588 · PMC2575505 · Genome biology · 2008 · 8 claims · 5 setups

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Isolated/founder populations are useful for identifying genes underlying common complex diseases, not just rare monogenic diseases.

genetically icelandic finnish hutterites linkage genome-wide
The heterogeneous allelic repertoire of human toll-like receptor (TLR) genes.

PMID 19924287 · PMC2773936 · PloS one · 2009 · 8 claims · 8 setups

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Human TLR genes are unequally polymorphic: TLR2, 4, 7, 8 and 9 are comparatively least diverse, whereas TLR1, 5, 6 and 10 show substantial allelic diversity.

tlr10 tlr5 tlr1 tlr6 pcr-based
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

randomly heirs seattlesnps african resequencing genome-wide tag
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
Investigating the genetic association between ERAP1 and ankylosing spondylitis.

PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

patients cases genotype comparison snp meta-analysis resequencing
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

breast computational array-cgh gene bac
A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

PMID 19823678 · PMC2757911 · PloS one · 2009 · 6 claims · 4 setups

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SLC10A2 is a novel susceptibility gene for cholelithiasis in humans

genomic pooled sanger maldi-tof genotype-phenotype
Applying proteomics to the diagnosis and treatment of ALS and related diseases.

PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

csf spinal biofluid muscle 2d-dige antibody luminex
Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

unrelated same snps haplotype snp haplotype pairwise
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

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None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

genomic case-control nramp1 type sanger snp microsatellite
Association of GSK3B with Alzheimer disease and frontotemporal dementia.

PMID 18852354 · PMC2841136 · Archives of neurology · 2008 · 8 claims · 5 setups

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The GSK3B intronic polymorphism IVS2-68G>A is associated with increased risk of AD and FTD in a case-control cohort

genomic case-control family-based sib-pair pcr allele-specific fluorescence-polarization
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

Has reproduction · 78

A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

hcc-associated hcc malignant cd8+ single-cell bulk metabolomics
Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

asian random subjects unrelated arms-pcr msei sanger

Experiments

Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

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

Identification of common genetic variation that modulates alternative splicing.

A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

The molecular landscape of ASPM mutations in primary microcephaly.

Isolated populations and complex disease gene identification.

The heterogeneous allelic repertoire of human toll-like receptor (TLR) genes.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

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

Investigating the genetic association between ERAP1 and ankylosing spondylitis.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

Applying proteomics to the diagnosis and treatment of ALS and related diseases.

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

Association of GSK3B with Alzheimer disease and frontotemporal dementia.

Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.