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 22

System / cell line: significant ✕ Assay: test ✕ Clear

Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

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The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

same genes orangutan codeml gene sequence
"Reverse ecology" and the power of population genomics.

PMID 18752601 · PMC2626434 · Evolution; international journal of organic evolution · 2008 · 8 claims · 7 setups

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Population genomic data can be used to rapidly identify genes targeted by adaptive natural selection, an approach termed 'reverse ecology'.

cerevisiae melanogaster sapiens simulans likelihood mcdonald-kreitman mkprf
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.

PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups

Has reproduction · 64

Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.

unrelated chinese ljp individuals whole-genome d-statistic local
What can genome-wide association studies tell us about the genetics of common disease?

PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

case gwa simulated literature cochran-armitage computer
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

PMID 19073697 · PMC2632920 · Nucleic acids research · 2009 · 8 claims · 5 setups

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Combining high protein-interaction network scores with significant PID-related GO terms identifies novel PID candidate genes

immunome known protein-interaction gene comparative
Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

olfactory present same anova-significant microarray step-down peddada
Polyploidy and the petal transcriptome of Gossypium.

PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

Has reproduction · 51

Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

petal rna-seq commonly polyploid rna-seq read universal
The genetics of regulatory variation in the human genome.

PMID 16004727 · PMC3525257 · Human genomics · 2005 · 8 claims · 7 setups

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Naturally-occurring gene expression variation among individuals is common across species (yeast, Drosophila, mouse, fish, maize, primates, humans) and has a significant genetic component.

ceph immortalised lymphoblastoid individuals reporter allelic microarray
Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

Has reproduction · 100

Dutch traditional chicken breeds display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).

individuals dutch phased drenthe whole-genome principal phylogenetic
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

PMID 32542016 · PMC7295234 · PloS one · 2020 · 6 claims · 8 setups

Has reproduction · 51

Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC versus normal liver at mRNA and protein levels

cancer tcga-lihc gse89377 hcc pan-cancer rna-seq stage-wise
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

serum seldi seldi-tof serum univariate
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 7 claims · 6 setups

Has reproduction · 77

SurvConvMixer reformats KEGG Pathways-in-Cancer gene expression values into pathway-level 2D gene expression images and applies a ConvMixer-based model for overall survival prediction

luad lung bulk gene machine
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

dlbcl identified microarray oligonucleotide coupled
Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

zebrafish computational seven consolidated whole-adult-organism supervised quantitative
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

unrelated shanghai tsnps snp allele linkage

Experiments

Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

"Reverse ecology" and the power of population genomics.

Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.

What can genome-wide association studies tell us about the genetics of common disease?

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

Polyploidy and the petal transcriptome of Gossypium.

The genetics of regulatory variation in the human genome.

Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Patterns of evolutionary constraints on genes in humans.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.