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 14

System / cell line: same ✕ Assay: beta ✕ Clear

Bayesian survival analysis in genetic association studies.

PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

Full-text index only

A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

simulated same sanad bayesian univariate partial
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

Full-text index only

85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Bayesian coestimation of phylogeny and sequence alignment.

PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

Full-text index only

Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

globin same four-sequence bayesian mcmc comparison
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

Has reproduction · 50

Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

sars-cov-2 publicly simulated simulated amplicon-based variant
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

Full-text index only

A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

astrocytoma same sage classical beta-binomial
Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

PMID 17716379 · PMC2063502 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 6 setups

Full-text index only

268 genes (177 over-expressed, 91 under-expressed) are differentially expressed in leiomyomas of African Americans compared to Caucasians (P<0.01, 2-fold cutoff)

paired same excised paraffin-embedded microarray realtime 2d-page
Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

Full-text index only

Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

case hapmap snp individual allele
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

Full-text index only

Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr
Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups

Has reproduction · 75

The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)

fecal same 16s otu alpha
Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

PMID 11676855 · PMC5926606 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 5 setups

Full-text index only

Gene amplification of p53 was detected in one nasal NK cell lymphoma

same shifted neoplasm cases southern pcr-sscp direct
Recent additions and improvements to the Onto-Tools.

PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

Full-text index only

The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

homo example mus functional pathway cross-database
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

Full-text index only

Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

Full-text index only

A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.

PMID 7669582 · PMC2033876 · British journal of cancer · 1995 · 8 claims · 5 setups

Full-text index only

A novel missense mutation (TGG→CGG, Trp133→Arg) in nm23-H2 was found in one stage III serous ovarian carcinoma

ovarian case matched same pcr-sscp subcloning loh

Experiments

Bayesian survival analysis in genetic association studies.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Bayesian coestimation of phylogeny and sequence alignment.

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

Recent additions and improvements to the Onto-Tools.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.