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 17

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

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

bifidobacterium longum xbai-digested whole-genome base codon
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
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
A novel mutation in the WFS1 gene identified in a Taiwanese family with low-frequency hearing impairment.

PMID 17517145 · PMC1890544 · BMC medical genetics · 2007 · 7 claims · 6 setups

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A novel heterozygous missense mutation Y669H (2005T>C) in exon 8 of WFS1 was identified in affected family members but not in 100 controls (200 chromosomes)

family genomic 10-member wfs1 pure direct pcr-rflp
A novel WFS1 mutation in a family with dominant low frequency sensorineural hearing loss with normal VEMP and EcochG findings.

PMID 18518985 · PMC2435521 · BMC medical genetics · 2008 · 7 claims · 6 setups

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A novel heterozygous WFS1 mutation c.2054G>C (p.R685P) segregates faithfully with dominant LFSNHL in an American family

family wolframin pure-tone vestibular electrocochleography
Autoimmune disease in a DFNA6/14/38 family carrying a novel missense mutation in WFS1.

PMID 18688868 · PMC2586182 · American journal of medical genetics. Part A · 2008 · 8 claims · 5 setups

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A novel missense mutation c.2576G→A (p.R859Q) in WFS1 exon 8 causes autosomal dominant LFSNHL in this American family

genomic wfs1 ceph affected pcr sanger population
Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

PMID 15138484 · PMC2409464 · British journal of cancer · 2004 · 8 claims · 4 setups

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High-grade breast tumours show a high frequency of LOH and/or abnormal expression of ATM, BRCA1 and TP53

early-onset same peripheral breast allelotyping immunohistochemistry direct
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

simulated same snp type two-locus 2lomb benchmark
Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

genomic retina cdna protocadherin str pcr rt-pcr
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

faecal mcra pure pcr rflp 16s
Digital sorting of complex tissues for cell type-specific gene expression profiles.

PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 85

The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

liver im-9 immune deconvolved microarray simulation roc
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

PMID 18820594 · PMC2905378 · Pharmacogenetics and genomics · 2008 · 7 claims · 8 setups

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The tRNA-Thr G15927A mutation has a potential modifier role that increases penetrance and expressivity of A1555G-associated deafness.

blood genomic lymphoblastoid same pcr-rflp mitochondrial northern
Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

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Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

mcf7 promoter cdna quantitative computational
Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population.

PMID 19671850 · PMC2865649 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 6 setups

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20 of 358 (5.6%) lung adenocarcinomas from Western institutions harbored ALK rearrangements

formalin-fixed lung sections poorly fluorescent immunohistochemistry mutational
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
Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

PMID 17262083 · PMC2360051 · British journal of cancer · 2007 · 8 claims · 6 setups

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C-Ca is associated with a significantly higher incidence of differentiated-type tumours and lymphatic vessel invasion (LVI) compared with D-Ca

resected c-ca microdissected formalin-fixed histopathological immunohistochemistry pcr-single-strand

Experiments

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

Tissue compartment analysis for biomarker discovery by gene expression profiling.

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

A novel mutation in the WFS1 gene identified in a Taiwanese family with low-frequency hearing impairment.

A novel WFS1 mutation in a family with dominant low frequency sensorineural hearing loss with normal VEMP and EcochG findings.

Autoimmune disease in a DFNA6/14/38 family carrying a novel missense mutation in WFS1.

Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population.

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

Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.