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 44

System / cell line: prediction ✕ Assay: genetic ✕ Clear

Public health genomics approach to type 2 diabetes.

PMID 18971439 · PMC2570384 · Diabetes · 2008 · 7 claims · 3 setups

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Combining GWAS-discovered genetic variants provides only weak predictive ability for type 2 diabetes and adds little beyond established clinical risk factors (age, sex, BMI).

population-based white genetic genotyping systematic
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

Has reproduction

Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

duroc 1000-individual real low-coverage genome-wide genomic
Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

PMID 19727905 · PMC2946578 · Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2010 · 7 claims · 6 setups

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Multiple SNPs and haplotypes in FLNB are significantly associated with BMD at lumbar spine, femoral neck, and total hip

southern same subjects genotype tag taqman dual-energy
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

peripheral wecare atm mutation case-control variant
Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

PMID 18616530 · PMC4732719 · Clinical genetics · 2008 · 8 claims · 8 setups

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TMC1 mutations were identified in seven of the families/patients segregating hearing loss linked to DFNA36/DFNB7-11

families affected tmc1 tjp2 genetic sequencing multiplex
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups

Has reproduction · 87

A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.

patients exome deep computer-assisted
Automatic discovery of cross-family sequence features associated with protein function.

PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

non-redundant same evolved eukaryotic self-supervised experiment self-organizing
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
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
Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

paired lung tissue-pair pooled hiv-1 maximum statistical
Advances in breast cancer: pathways to personalized medicine.

PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

population-based women breast high-risk germline genome-wide microarray
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
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
SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

PMID 40169992 · PMC11963337 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 2 setups

Has reproduction · 83

SIRE 2.0 is a novel Bayesian methodology and software tool for estimating polygenic contributions (variance components and additive genetic effects) to host susceptibility, infectivity and recoverability from temporal epidemic data using pedigree/genomic relationship matrices.

simulated bayesian systematic
Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

genomic pcr-amplified case-control pon1 single-strand direct genetic
Integrated omics in Drosophila uncover a circadian kinome.

PMID 32483184 · PMC7264355 · Nature communications · 2020 · 8 claims · 6 setups

Has reproduction · 98

iCMod, a computational pipeline integrating transcriptomic, proteomic, and phosphoproteomic circadian data, was developed to accurately identify normalized circadian p-sites (NCPs)

drosophila analysis tmt-based sequencing western
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

Has reproduction · 68

The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.

lactobacillus plantarum whole-genome novo gene

Experiments

Public health genomics approach to type 2 diabetes.

Ab initio identification of human microRNAs based on structure motifs.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women.

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

Automatic discovery of cross-family sequence features associated with protein function.

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

Identification of common genetic variation that modulates alternative splicing.

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Advances in breast cancer: pathways to personalized medicine.

Human synthetic lethal inference as potential anti-cancer target gene detection.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

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

SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

Integrated omics in Drosophila uncover a circadian kinome.

Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.