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 79

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

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

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PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

input gene genome-wide genes sequence gene numerical
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
Neuronal Small RNAs Control Behavior Transgenerationally.

PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups

Has reproduction · 49

Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations

elegans prab-3 dissected worms small sequencing facs
Onto-Tools: new additions and improvements in 2006.

PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups

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OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files

specified pathway functional example
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

PMID 34909283 · PMC8641482 · PeerJ · 2021 · 7 claims · 5 setups

Has reproduction · 75

The FEM algorithm converts each cell's gene expression matrix (GEM) into a functional expression matrix by applying Fisher's exact test enrichment per cell and per gene set, then encoding adjusted p-values as information content.

peripheral pancreas liver pbmc scrna-seq differential dimensionality
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
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

Has reproduction · 83

scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

liver hepatocyte detected adipose single-cell differential protein-protein
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
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
Towards precise classification of cancers based on robust gene functional expression profiles.

PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

nci60 lymphoma fep go-annotated cdna recursive hypergeometric
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.

PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups

Has reproduction · 65

SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians

provided amygdala rna-seq differentially pipeline bulk rna-based
miRGator: an integrated system for functional annotation of microRNAs.

PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

genome predicted tissues organs computational functional mirna
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription
Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

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A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

blood edta reliably genome-wide twin sub-type
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
Protein length in eukaryotic and prokaryotic proteomes.

PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families

eukaryotic proteins genomic cog comparative orthology domain
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
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups

Has reproduction · 77

Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.

appswe app gut 16s open picrust2

Experiments

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

Gene losses during human origins.

Neuronal Small RNAs Control Behavior Transgenerationally.

Onto-Tools: new additions and improvements in 2006.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

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

Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

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

Towards precise classification of cancers based on robust gene functional expression profiles.

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.

miRGator: an integrated system for functional annotation of microRNAs.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

CLEAN: CLustering Enrichment ANalysis.

Protein length in eukaryotic and prokaryotic proteomes.

Patterns of evolutionary constraints on genes in humans.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.