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 41

System / cell line: predicted ✕ Assay: population ✕ Clear

BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

french-canadian families brca1-positive same targeted full-length multiplex
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

Has reproduction · 42

KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

small snps individual hg002 alignment-free kmer-based genotyping
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups

Has reproduction · 44

Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data

xylophilus snp smrt short-read bionano
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate
The evolution and genomic landscape of CGB1 and CGB2 genes.

PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

genomic great cgb1 chimpanzee pcr population hka
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

PMID 18557994 · PMC2481495 · Breast cancer research : BCR · 2008 · 8 claims · 8 setups

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Mutation frequencies in ATM, BRIP1, PALB2 and CHEK2 are many times higher in women with strong breast cancer family history (familial cases) than in population controls.

women familial finnish unselected germline international statistical
Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

Has reproduction · 68

200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

african lion crater simulated genome principal admixture
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
Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

Has reproduction · 64

Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

agaricia agaricites coral sites 2brad population hierarchical
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Whole genome association mapping by incompatibilities and local perfect phylogenies.

PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype
Prospective health care: the second transformation of medicine.

PMID 16522218 · PMC1431721 · Genome biology · 2006 · 8 claims · 7 setups

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Predictive biomarkers (genomic, proteomic, metabolomic) will enable quantification of disease risk and anticipation of onset before pathological damage occurs.

cancer circulating breast population gene-expression proteomic 21-gene
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

Has reproduction · 55

The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

corbicula six sediment filtered 16s radseq picrust2

Experiments

BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

The evolution and genomic landscape of CGB1 and CGB2 genes.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories?

Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

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.

Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Whole genome association mapping by incompatibilities and local perfect phylogenies.

Prospective health care: the second transformation of medicine.

Mutation analysis of the MDM4 gene in German breast cancer patients.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).