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 20

System / cell line: for ✕ Assay: artificial ✕ Clear

Optimality driven nearest centroid classification from genomic data.

PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

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A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

artificial simulated previously-published simulated simulation clinical
What the Phage: a scalable workflow for the identification and analysis of phage sequences.

PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

Has reproduction · 76

WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

assembled illumina phage-predicted predicted multitool metagenome gene
Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

PMID 17118166 · PMC1775062 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 6 setups

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A critical ~36-hour window exists after progesterone withdrawal in macaques during which menstruation can still be blocked by progesterone add-back, after which it becomes inevitable

ovariectomized baboon endometrium macaque hormone laparoscopic immunohistochemistry
Development of animal models to test the fundamental basis of gene-environment interactions.

PMID 19037209 · PMC2703424 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

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Selective breeding for low and high intrinsic aerobic treadmill running capacity produced divergent rat lines (LCR and HCR) that contrast in propensity for complex disease

nih-derived lcr carotid treadmill body maximal
Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

breast sars serum tumour microarray custom mass
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

Has reproduction · 75

Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

pure enriched stec-negative extracted ont real-time artificial
MatchMiner: a tool for batch navigation among gene and gene product identifiers.

PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

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MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

nci-60 fish-mapped random batch fish-mapped cross-validation
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

independent ceph same unrelated snp individual simulated
POCUS: mining genomic sequence annotation to predict disease genes.

PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

omim genome disease comparative pocus expression-id
Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

PMID 15905472 · PMC1131937 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Introducing streptavidin-coated magnetic microparticles (MMPs) into a sandwich-type CP-based DNA sensor significantly improves selectivity against non-cognate DNA compared with previously reported CP-amplified sensors.

cell-free synthetic brca1-related artificial fluorescence magnetically salt-stringency
Minisequencing mitochondrial DNA pathogenic mutations.

PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

blood-derived same genomic pcr minisequencing automatic multiplex
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
The sequence and de novo assembly of the giant panda genome.

PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

giant panda whole-genome novo read
Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

genomic artificial simulated direct computational comparative
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

Has reproduction · 44

Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

plasmid coli wild-type artificial smrt read-mixing distributional
Correcting scale distortion in RNA sequencing data.

PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 76

Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)

tcga su2c gse47774 gtex bulk computational d'agostino
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population

Experiments

Optimality driven nearest centroid classification from genomic data.

What the Phage: a scalable workflow for the identification and analysis of phage sequences.

Detection of venous thromboembolism by proteomic serum biomarkers.

Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

Development of animal models to test the fundamental basis of gene-environment interactions.

Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

MatchMiner: a tool for batch navigation among gene and gene product identifiers.

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

POCUS: mining genomic sequence annotation to predict disease genes.

Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction.

Minisequencing mitochondrial DNA pathogenic mutations.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

The sequence and de novo assembly of the giant panda genome.

Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

Speeding disease gene discovery by sequence based candidate prioritization.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

Correcting scale distortion in RNA sequencing data.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.