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 245

System / cell line: structure ✕ Assay: gene ✕ Clear

KEGG for linking genomes to life and the environment.

PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

protein-coding newly microarray kegg sequence computational glycan
Adapting to a changing world: RAG genomics and evolution.

PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

rag-1 patients zebrafish vertebrate comparative site-directed clinical
SVC: structured visualization of evolutionary sequence conservation.

PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

orthologous exonic tblastx blastn sliding-window
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
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
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

chromosome genomic training ghmm-based sequence parameter
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.

PMID 15980513 · PMC1160219 · Nucleic acids research · 2005 · 8 claims · 1 setups

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AUGUSTUS web server allows users to impose constraints (splice sites, translation start/stop, known exons, exonic/intronic intervals) on predicted gene structures

drosophila initio
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
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
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

fecal postnatal luminal pooled 16s shotgun body
Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

introns ribosomal rrna comparative orthologous pairwise
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
EGASP: Introduction.

PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

genome computational manual rt-pcr
Using ESTs to improve the accuracy of de novo gene prediction.

PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

elegans genome chromosome novo gene partial
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
Tissue compartment analysis for biomarker discovery by gene expression profiling.

PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

kidney pure serial rt-pcr sage histo-morphometry
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

Has reproduction · 55

The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

corbicula six sediment filtered 16s radseq picrust2
52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

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The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

molt-4 placental placenta fetal cdna genomic race

Experiments

KEGG for linking genomes to life and the environment.

Adapting to a changing world: RAG genomics and evolution.

SVC: structured visualization of evolutionary sequence conservation.

EGASP: the human ENCODE Genome Annotation Assessment Project.

The dystrobrevin-binding protein 1 gene: features and networks.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Reference based annotation with GeneMapper.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

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

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

EGASP: Introduction.

Using ESTs to improve the accuracy of de novo gene prediction.

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

Tissue compartment analysis for biomarker discovery by gene expression profiling.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.