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 102

System / cell line: species ✕ Assay: mapping ✕ Clear

Reference based annotation with GeneMapper.

PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

orthologous human-mouse chicken encode reference-based multi-species reciprocal
miRBase: tools for microRNA genomics.

PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

species utrs genomic chromosome genome-wide target transcription
Assessing the gene space in draft genomes.

PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

caenorhabditis toxoplasma homo briggsae cegma blast tblastn
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
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

est unannotated trans-sa tus computational coding hybridization
AgBase: a functional genomics resource for agriculture.

PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

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AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

pasteurella chicken maize gene proteogenomic mudpit differential
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

est gene worm fly blat-based transcription comparative
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

family p2ry5 affected snp microsatellite sanger
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
SNP-VISTA: an interactive SNP visualization tool.

PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets

abo homologous acid snp multi-species blast-based
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

Has reproduction · 85

18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

aspergillus circularized core orthologous mitogenome read organellar
Genome-wide survey for biologically functional pseudogenes.

PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

human-mouse chimpanzee cross-species maximum-likelihood synteny
Animal models of gene-nutrient interactions.

PMID 19037208 · PMC2703433 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 5 setups

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Mice and rats are well-suited models for human food selection because they share food preferences with humans and are supported by extensive genetic tools (sequenced genome, inbred strains, gene targeting, Cre-lox).

interbred inbred pubmed genome qtl strain bibliometric
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Repeating patterns of mimicry.

PMID 17048984 · PMC1617347 · PLoS biology · 2006 · 7 claims · 4 setups

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The Yb locus controls presence of a yellow wing band in H. melpomene

heliconius lake genetic genomic comparative
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
The UCSC genome browser database: update 2007.

PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

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The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

hg17 genome lines xenopus comparative snp linkage
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

Has reproduction · 64

The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

caecilian caecilia archival lws pcr eye histology

Experiments

Reference based annotation with GeneMapper.

miRBase: tools for microRNA genomics.

Assessing the gene space in draft genomes.

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

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

AgBase: a functional genomics resource for agriculture.

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

Comparative genomics search for losses of long-established genes on the human lineage.

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

SNP-VISTA: an interactive SNP visualization tool.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

Genome-wide survey for biologically functional pseudogenes.

Animal models of gene-nutrient interactions.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Repeating patterns of mimicry.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

The UCSC genome browser database: update 2007.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.