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 43

System / cell line: tree ✕ Assay: annotation ✕ 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
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
Large-scale trends in the evolution of gene structures within 11 animal genomes.

PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

annotated animal unannotated comparative all-against-all neighbor-joining
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
Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

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Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

hcv-1a phylogenetic sequence nucleotide
Ensembl 2008.

PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

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The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

embryonic amniota multi-species individuals automated chip-chip comparative
Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

hadv-37 predicted select genome cpg global
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
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
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

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The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

dentium core whole-genome 3d-structure comparative
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

user-submitted query genomes proteins domain profile-profile comparative
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

anoplophora glabripennis insect whole-genome genome orthology
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
The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

strongylocentrotus sprej purpuratus full-length cdna secondary real-time
Comparative genomic analysis of prion genes.

PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

vertebrate multi-tissue aligned sprn comparative gene cdna
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
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
Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.

PMID 36226801 · PMC9713440 · G3 (Bethesda, Md.) · 2022 · 8 claims · 7 setups

Has reproduction · 84

The assembled draft genome of H. charlesbogerti totals 2.31 Gb, similar in size to related species

blood charlesbogerti reptile annotated whole-genome novo repeat

Experiments

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

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

Large-scale trends in the evolution of gene structures within 11 animal genomes.

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

Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

Ensembl 2008.

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

Ensembl 2013.

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

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

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

The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

Comparative genomic analysis of prion genes.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

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

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes.