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 24

System / cell line: predicted ✕ Assay: density ✕ Clear

The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups

Has reproduction · 88

C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.

elegans clash bioinformatic iclip
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Genomic approaches to the genetics of alcoholism.

PMID 12875046 · PMC6683845 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 8 claims · 4 setups

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Alcoholism is a complex disease that develops from a combination of numerous genetic and environmental factors, unlike single-gene disorders such as cystic fibrosis or Huntington's disease.

specified genomic gene genomic exon
Pharokka: a fast scalable bacteriophage annotation tool.

PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups

Has reproduction · 84

Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command

enterobacteria staphylococcus crass-like predicted genome large-scale homology
DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

PMID 14519203 · PMC328457 · Genome biology · 2003 · 7 claims · 5 setups

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DiagHunter identifies large-scale synteny blocks within or between genomes efficiently despite background noise and genomic discontinuities, without performing sequence alignment

arabidopsis synthetic blastp-based blastn-based simulation
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Does distance matter? Variations in alternative 3' splicing regulation.

PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

intronic human-mouse same comparative polypyrimidine branch
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
The flexible pocketome engine for structural chemogenomics.

PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

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A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

pdb bacteriorhodopsin enr asn automated virtual energy-based
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
Sequence and structure signatures of cancer mutation hotspots in protein kinases.

PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

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Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

kinase common egfr autoinhibited database-driven structure-informed evolutionary
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups

Has reproduction · 67

RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical

intestine rodent duodenal neonatal bulk scrna-seq marker
Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

recombinant selenomethionine-substituted ge-gi models surface x-ray computational
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Truncation of retinoschisin protein associated with a novel splice site mutation in the RS1 gene.

PMID 18728755 · PMC2519029 · Molecular vision · 2008 · 8 claims · 5 setups

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Male patients exhibit typical bilateral foveal retinoschisis in two retinal layers detected by OCT

retina genomic rs1 optical full-field multifocal
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein

Experiments

The distribution of SNPs in human gene regulatory regions.

Distribution and effects of nonsense polymorphisms in human genes.

Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

Twin peaks: the draft human genome sequence.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Genomic approaches to the genetics of alcoholism.

Pharokka: a fast scalable bacteriophage annotation tool.

DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Does distance matter? Variations in alternative 3' splicing regulation.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

The flexible pocketome engine for structural chemogenomics.

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

Sequence and structure signatures of cancer mutation hotspots in protein kinases.

Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

Characterization of 954 bovine full-CDS cDNA sequences.

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

Identification of common genetic variation that modulates alternative splicing.

Truncation of retinoschisin protein associated with a novel splice site mutation in the RS1 gene.

Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.