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 37

System / cell line: under ✕ Assay: comparative ✕ Clear

The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

Full-text index only

Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
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
Protein under-wrapping causes dosage sensitivity and decreases gene duplicability.

PMID 18208334 · PMC2211539 · PLoS genetics · 2008 · 7 claims · 6 setups

Full-text index only

Protein under-wrapping extent is negatively correlated with gene duplicability (family size) across six organisms (E. coli, yeast, worm, fly, human, thale cress)

coli cerevisiae sapiens elegans structural comparative functional
Comparing whole genomes using DNA microarrays.

PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

Full-text index only

DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

genome saccharomyces mitochondrial sars array comparative resequencing
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

Full-text index only

38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

hg18 zebrafish bystander human-mouse comparative synteny orthologous
Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups

Has reproduction · 65

Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

tepidariorum drosophila rna-seq whole-mount parental
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups

Has reproduction · 89

Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa

aureus reduced genome cgmlst comparative
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

Full-text index only

GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

chromosome genomic comparative phylohmmcons conserved
Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

coli cerevisiae comparative machine single-gene
Comparative genomics of Drosophila and human core promoters.

PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

drosophila core genome-wide mono gene
Genome-wide identification of human functional DNA using a neutral indel model.

PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

Full-text index only

A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

chromosome human-mouse genome individual whole-genome probabilistic comparative
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

Full-text index only

C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

chimpanzee intergenic genome-wide chi-square nucleotide-content
Design considerations for workflow management systems use in production genomics research and the clinic.

PMID 34737383 · PMC8569008 · Scientific reports · 2021 · 8 claims · 2 setups

Has reproduction · 57

The choice of WfMS depends both on intrinsic language/engine features and on adoption, collaboration, and technical support within bioinformatics consortia.

local variant-calling scalability-testing
Ensembl 2009.

PMID 19033362 · PMC2686571 · Nucleic acids research · 2009 · 8 claims · 6 setups

Full-text index only

Ensembl provides comprehensive, consistently annotated genome information for chordate genomes with automatically generated genesets and comparative genomics data

horse mammalian chromosome ensembl post-gene-build genome gerp
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

synthetic eukaryotic simulated 16-species analytical comparative simulation
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

Has reproduction · 94

The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

casei orthogroups unclassified selected whole-genome comparative pairwise
An "omics" approach to uropathogenic Escherichia coli vaccinology.

PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

Full-text index only

An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

upec vaccination comparative two-dimensional
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

Full-text index only

Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.

PMID 36895650 · PMC9988679 · iScience · 2023 · 8 claims · 8 setups

Has reproduction · 49

C. agrestis and K. uniflora are sister species with contrasting reproductive modes, providing a natural system to test effects of sexual vs asexual reproduction on genome evolution

circaeaster agrestis genome gene kmer-based
Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.

PMID 36560952 · PMC9763275 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 54

Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress

lupinus saiceupsm^t greenhouse enzymatic mercury

Experiments

The role of positive selection in determining the molecular cause of species differences in disease.

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

Protein under-wrapping causes dosage sensitivity and decreases gene duplicability.

Comparing whole genomes using DNA microarrays.

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Comparative genomics of Drosophila and human core promoters.

Genome-wide identification of human functional DNA using a neutral indel model.

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

Design considerations for workflow management systems use in production genomics research and the clinic.

Ensembl 2009.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

An "omics" approach to uropathogenic Escherichia coli vaccinology.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.

Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.