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 31

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

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

Full-text index only

Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

brasiliensis gp43 ratio codon-based mutational
Onto-Tools: new additions and improvements in 2006.

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

Full-text index only

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
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

Full-text index only

Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.

PMID 40416609 · PMC12103846 · PeerJ · 2025 · 8 claims · 6 setups

Has reproduction · 84

GBS colonization was detected in 51 of 1,924 (2.7%) pregnant women screened

vaginal-rectal agalactiae microbiological latex whole-genome
Optimized mixed Markov models for motif identification.

PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

Full-text index only

OMiMa can incorporate more than NNSplice's pairwise dependencies

simulated regulatory splice biological motif pairwise
Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

PMID 16855287 · PMC1524908 · Nucleic acids research · 2006 · 8 claims · 8 setups

Full-text index only

Splicing-affecting genomic variations can account for up to 50% of mutations leading to gene dysfunction in some genes

random trans-acting tpo fibronectin minigene selex cdna
Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

PMID 18433472 · PMC2386800 · BMC molecular biology · 2008 · 7 claims · 6 setups

Full-text index only

Co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves gives high-level transient expression of active, mismatch-specific ENDO1 via a simple purification protocol

benthamiana test genomic hiv-1 transient heteroduplex mutation
Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

Full-text index only

PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

genomic pools training siddt individual pooled k-correction
The evolution and genomic landscape of CGB1 and CGB2 genes.

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

Full-text index only

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
Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

Full-text index only

Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

pools individual same parental pooled individual test-retest
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

Full-text index only

Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

Full-text index only

Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

Has reproduction · 92

Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

post-mortem adra immunohistochemistry protein-protein pathway
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

Full-text index only

A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

upstream co-expression pre-b microarray-based motif gene
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

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

Full-text index only

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
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

Full-text index only

SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
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

Full-text index only

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

genomic pnmt promoter pcr population haplotype
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

Has reproduction · 30

MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

simplified genome-scale cerevisiae coli minspan spearman comparative
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

Full-text index only

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

Experiments

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Onto-Tools: new additions and improvements in 2006.

Species-specific protein sequence and fold optimizations.

Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.

Optimized mixed Markov models for motif identification.

Defective splicing, disease and therapy: searching for master checkpoints in exon definition.

Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

The evolution and genomic landscape of CGB1 and CGB2 genes.

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

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

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

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

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

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