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 33

System / cell line: sequence ✕ Assay: developmental ✕ Clear

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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169 gene products in the Ciona genome were identified as putative GPCRs

ciona sequence molecular est
Genomic organization of zebrafish microRNAs.

PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups

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Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.

zebrafish candidate hairpin blast secondary comparative
Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

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Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

chicken blast microarray est
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups

Has reproduction · 89

Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.

actias genomes translated luna genome hmm manual
Widespread ultraconservation divergence in primates.

PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

hg18 genome genes computed comparative snp gene
The changing face of genomics.

PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

yeast drosophila zebrafish elegans chip-chip comparative insertional
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Similarities and differences in genome-wide expression data of six organisms.

PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental
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
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
Application of ecotoxicogenomics for studying endocrine disruption in vertebrates and invertebrates.

PMID 16818254 · PMC1874166 · Environmental health perspectives · 2006 · 8 claims · 8 setups

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Estrogen-responsive genes in mouse uterus are induced in a dose-dependent, ER-α-dependent manner, as shown by loss of induction in ER-α knockout mice.

reproductive american xenopus fundulus cdna receptor developmental
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups

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GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.

ligand gpcr glida principal sequence gene
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

Has reproduction · 70

Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

ihh additional chd7 sanger targeted rt-pcr
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups

Has reproduction · 46

De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases

sparassis latifolia bulk transcriptome sequence
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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P. falciparum encodes substantially more membrane transport proteins than originally annotated

falciparum genome-wide bioinformatic quantification
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

triticum taiqd wheat promoter genome-wide phylogenetic synteny

Experiments

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

Genomic organization of zebrafish microRNAs.

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

Widespread ultraconservation divergence in primates.

The changing face of genomics.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Similarities and differences in genome-wide expression data of six organisms.

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

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Application of ecotoxicogenomics for studying endocrine disruption in vertebrates and invertebrates.

GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.