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 161

System / cell line: novel ✕ Clear

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

PMID 18507832 · PMC2427034 · BMC microbiology · 2008 · 7 claims · 6 setups

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A2143G point mutation of the H. pylori 23S rRNA gene causes clarithromycin resistance

fasting subjects serum pylori pcr 13c-urea elisa
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
ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

PMID 18465152 · PMC2441586 · Neurogenetics · 2008 · 8 claims · 8 setups

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37% (16/43) of Dutch index patients with early-onset recessive cerebellar ataxia carry SACS mutations, indicating ARSACS is far more frequent than previously estimated

genomic identified sacs-mutation-positive alleles pcr clinical brain
Metagenomic analysis of human diarrhea: viral detection and discovery.

PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

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Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

stool divergent extract preparations sequence-independent maximum enzyme
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.

PMID 19963937 · PMC5859565 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 5 setups

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Crosstalk between multiplexed QD-antibody reporters occurs and can be on the same order of magnitude as the intended signal, varying by tissue and reagent.

ffpe prostate renal pure multiplexed single-primary-antibody wavelength-resolved
Searching for SNPs with cloud computing.

PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

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Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

han local short simulated whole-genome cloud
Targeted capture and massively parallel sequencing of 12 human exomes.

PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

hapmap unrelated na18507 randomly targeted array-based molecular
Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

PMID 19649175 · PMC2718852 · Molecular vision · 2009 · 8 claims · 6 setups

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A heterozygous missense mutation c.607G>A in exon 6 of CRYBB2, causing p.Val187Met, is the probable causative mutation for congenital nuclear cataract in this family

genomic basotho pcr restriction secondary
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.

PMID 41854267 · PMC13098197 · mSystems · 2026 · 8 claims · 6 setups

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SPF scalably and robustly estimates the fraction of bacterial and archaeal reads in a metagenome using detection of prokaryotic single-copy marker genes, without requiring eukaryotic or viral reference genomes

zymo cami simulated fecal simulated shotgun spf
With the finished human genome in hand, what next?

PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

domestic saccharomyces systemic schistosoma comparative functional genetic
Rats go genomic.

PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

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A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

recombinant genes serotonin adenomatous genome-wide targeted knockout
NEIBank: genomics and bioinformatics resources for vision research.

PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

dissected eye retina cdna est serial sequence
Bioinformatics in Malaysia: hope, initiative, effort, reality, and challenges.

PMID 19714208 · PMC2723929 · PLoS computational biology · 2009 · 8 claims · 4 setups

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Bioinformatics in Malaysia began informally in the early 1990s but its systematic development was curtailed by an early focus on the biotechnology industry, leaving gaps in human capital, research, and commercialization.

virus alkalophilic extremophilic parasite high-throughput
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
Comparative genomics.

PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

Experiments

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

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

ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

Metagenomic analysis of human diarrhea: viral detection and discovery.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.

Searching for SNPs with cloud computing.

Targeted capture and massively parallel sequencing of 12 human exomes.

Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.

With the finished human genome in hand, what next?

Rats go genomic.

NEIBank: genomics and bioinformatics resources for vision research.

Bioinformatics in Malaysia: hope, initiative, effort, reality, and challenges.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

The nuclear pore complex.

Comparative genomics.