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 8

System / cell line: set ✕ Assay: partial ✕ Clear

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

domestic red same white partial comparative pcr
Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

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A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

simulated real analytical simulation application
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

Has reproduction · 67

Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

anas duck million random illumina read novo
Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups

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A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction

simulated diffuse simulation cdna
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

Has reproduction · 71

Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

cord maternal genes significant genome pm2.5 isolation
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
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
RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

PMID 19789336 · PMC2927135 · Cancer research · 2009 · 8 claims · 8 setups

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K-RAS and N-RAS mutation status differentially determine the level of TNFα-induced apoptosis in an isogenic colon carcinoma cell panel

isogenic same conditioned dld-1 flow luminex immunoblot

Experiments

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

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

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.

RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.