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: unique ✕ Assay: test ✕ Clear

Next-generation high-density self-assembling functional protein arrays.

PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

test high-density amine-coated array picogreen anti-gst fluorescently
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

anopheles gambiae reanocds05 initio full-length rt-pcr
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 6 claims · 4 setups

Has reproduction · 86

A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes.

known tnbc unique unknown gene machine term
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

Has reproduction · 42

KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

small snps individual hg002 alignment-free kmer-based genotyping
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

brain hbrr topo-cloned tag microarray quantitative
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
G2Cdb: the Genes to Cognition database.

PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

brain nervous genome synaptic proteomic large-scale sequence
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

Has reproduction · 79

AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

aureus complete extracted agr kmer-based sheep mash
Using random walks to identify cancer-associated modules in expression data.

PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

Has reproduction

Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

hepatocellular breast sporadic geo gene differential interaction
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
Lineage specific recombination rates and microevolution in Listeria monocytogenes.

PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Recombination is more prevalent in lineage II than in lineage I

listeria allelic unique monocytogenes multilocus sawyer's genealogical
Genetic differences between avian and human isolates of Candida dubliniensis.

PMID 19788816 · PMC2819872 · Emerging infectious diseases · 2009 · 7 claims · 6 setups

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13 of 14 avian-associated C. dubliniensis isolates form a genetically distinct subgroup within MLST clade C1, separate from human isolates

candida fecal avian-associated multilocus pcr multiplex
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo

Experiments

Next-generation high-density self-assembling functional protein arrays.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

G2Cdb: the Genes to Cognition database.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

Using random walks to identify cancer-associated modules in expression data.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

Genetic differences between avian and human isolates of Candida dubliniensis.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.