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 171

System / cell line: same ✕ Assay: sequencing ✕ Clear

A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
The minisequencing method: a simple strategy for genetic screening of MEN 2 families.

PMID 12042015 · PMC116428 · BMC genetics · 2002 · 6 claims · 4 setups

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Minisequencing reproduces the same mutation information obtained by direct sequencing of PCR products at RET codons 634 and 918 in all tested MEN 2 family members.

genomic pcr same white pcr minisequencing direct
Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

dart-possessing same land cantareus 28s shimodaira-hasegawa principal
A phase II trial of gefitinib as first-line therapy for advanced non-small cell lung cancer with epidermal growth factor receptor mutations.

PMID 17047648 · PMC2360715 · British journal of cancer · 2006 · 7 claims · 5 setups

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Gefitinib is highly active and well tolerated as first-line therapy for advanced NSCLC with EGFR mutations

paraffin-embedded patients same direct phase kaplan-meier
FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

PMID 17668422 · PMC2443273 · The Journal of pathology · 2007 · 8 claims · 4 setups

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FGFR3 mutations occur in 42% of primary urothelial carcinomas and are significantly associated with low tumour grade and stage

urothelial tumour direct manual immunohistochemistry
Widely variable endogenous retroviral methylation levels in human placenta.

PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

term placenta genome bisulfite rt-pcr genome-wide
Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

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A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

consanguineous same affected family sanger multiplex microsatellite
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk.

PMID 18612690 · PMC2768068 · Diseases of the colon and rectum · 2008 · 7 claims · 4 setups

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Germline missense APC alterations (S130G, E1317Q, D1822V, G2502S) identified in a CRC-multiple-polyp cohort do not confer significantly increased CRC risk when tested in a large population-based case-control series

germline same population-based ofccr manual dhplc nuclease
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

peripheral mhc2ta pcr sanger bisulfite cpg
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

PMID 19876656 · PMC2899680 · Pediatric nephrology (Berlin, Germany) · 2010 · 7 claims · 3 setups

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Self-identified Hispanic SRNS patients in the USA are genetically heterogeneous, being of either Caucasian or Mesoamerican (Native-American) descent

genomic same healthy direct genome-wide
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

Has reproduction · 68

Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

fecal horse dominant plasma shotgun taxonomic functional
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups

Has reproduction · 88

Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life

zymo bacterial reference shotgun comparative reference
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

Has reproduction · 50

Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

sars-cov-2 publicly simulated simulated amplicon-based variant
Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups

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The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.

crp simplex same serum direct family-based linkage
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

domestic red same white partial comparative pcr
Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

PMID 15563733 · PMC544357 · BMC biotechnology · 2004 · 8 claims · 6 setups

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A single-track sequencing (SSR) strategy on one PCR product can simultaneously address 24 genetic variants in the NAT1 gene using paired terminator tracks (A/G for coding region, A/T for 3' flanking region)

genomic nat1 same pcr single-track single
TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

genomic dog sage pcr northern sage
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell

Experiments

A comprehensive catalogue of somatic mutations from a human cancer genome.

The minisequencing method: a simple strategy for genetic screening of MEN 2 families.

Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

A phase II trial of gefitinib as first-line therapy for advanced non-small cell lung cancer with epidermal growth factor receptor mutations.

FGFR3 protein expression and its relationship to mutation status and prognostic variables in bladder cancer.

Widely variable endogenous retroviral methylation levels in human placenta.

Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk.

Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

Exome sequencing of a multigenerational human pedigree.

Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.