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: genomics ✕ Assay: homology ✕ Clear

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

homo peroxisomal bona eukaryotic annotation comparative sequence
Human synthetic lethal inference as potential anti-cancer target gene detection.

PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

saccharomyces sapiens ihsln genes database phylogenetic gene
Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues.

PMID 17029625 · PMC1613252 · BMC genomics · 2006 · 8 claims · 3 setups

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A database of 82 allergen sequences was compiled and used to search 22 fungal genomes for orthologues.

fungal fumigatus enolase comparative epitope
The post-genomic era for a select few.

PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

takifugu physcomitrella coli vibrio comparative genetic dna-microarray
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

Has reproduction · 66

S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative
Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

PMID 19930606 · PMC2785843 · BMC genomics · 2009 · 8 claims · 7 setups

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Reannotation excluded 608 CDSs from the original RefSeq annotation, mostly unfunctional 'hypothetical'/'putative' genes

coli c0139r blastp rps-blast initio
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

genes autosomes dog genome comparative blat sliding-window
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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202 novel box H/ACA RNA-related sequences were identified in the human genome

genome chimpanzee aca flanking megablast comparative sequence
DBD--taxonomically broad transcription factor predictions: new content and functionality.

PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups

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DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.

proteomes eukaryotic genomes hmm-based comparative heatmap
The RCSB PDB information portal for structural genomics.

PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

structural nih genome sequence target production
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
The many uses of a genome sequence.

PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

recombinant mammalian chromosome chimpanzee x-ray quantitative tiling
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Kinetoplastid genomics: the thin end of the wedge.

PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

brucei major cruzi kinetoplastid whole-genome gene shotgun
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

genome functional registered omim comparative kendall's homology
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
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

Has reproduction · 92

A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

panax ginseng whole-genome genome rna-seq
Charting the map of life.

PMID 11171541 · PMC1242061 · Environmental health perspectives · 2001 · 8 claims · 8 setups

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Only 3-5% of the human genome, corresponding to 30,000-100,000 genes, is thought to be biologically functional

drosophila genome haemophilus domestic genetic map-based whole-genome
Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.

PMID 40416609 · PMC12103846 · PeerJ · 2025 · 8 claims · 6 setups

Has reproduction · 84

GBS colonization was detected in 51 of 1,924 (2.7%) pregnant women screened

vaginal-rectal agalactiae microbiological latex whole-genome

Experiments

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

Human synthetic lethal inference as potential anti-cancer target gene detection.

Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues.

The post-genomic era for a select few.

RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

DBD--taxonomically broad transcription factor predictions: new content and functionality.

The RCSB PDB information portal for structural genomics.

Patterns of evolutionary constraints on genes in humans.

The many uses of a genome sequence.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Kinetoplastid genomics: the thin end of the wedge.

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

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

Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

Charting the map of life.

Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance.