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 704

System / cell line: analysis ✕ Assay: comparison ✕ Clear

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 96

gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

avian comparative correlation robustness
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

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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
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

genome genomic chromosome randomization
COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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COMP mutations were identified in 78% of families referred with PSACH

genomic sequence subset pcr bidirectional sequence
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

drosophila genome melanogaster real-time comparative gfp
Differential protein expression in human corneal endothelial cells cultured from young and older donors.

PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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Cultured HCEC protein profiles show age-related differences between young and older donors

corneal 2-d trypsin-digested confluent 2-d gel maldi-tof
Asthma investigators begin to reap the fruits of genomics.

PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

monkey models lung inbred cdna oligonucleotide northern
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

faecal rsr 16s sargasso shotgun blastn-based 16s
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
Analysis of recent segmental duplications in the bovine genome.

PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

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Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

bos bovine genes cattle genome fluorescent repeat
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

Has reproduction · 67

Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

frugiperda satellite million contigs comparative homology divergence
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

influenzae novel reference codon phylogenetic comparative
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.

PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups

Has reproduction · 90

Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.

zebrafish orthologs ortholog core bulk overrepresentation network
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 59

Short-term stress and long-term adaptations share common metabolic pathways

great embryonic gef mapk1 bulk gene transcription
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

otx sea elegans endo16 windowed reporter comparative
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

sputum phage metagenomes inferred metagenomic functional diversity
The global landscape of sequence diversity.

PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

fully eukaryotic complete gene blast-based est gene
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original

Experiments

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

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

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

Differential protein expression in human corneal endothelial cells cultured from young and older donors.

Asthma investigators begin to reap the fruits of genomics.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Analysis of recent segmental duplications in the bovine genome.

Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

Comparative genomics and understanding of microbial biology.

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.

Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

The global landscape of sequence diversity.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.