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 812

System / cell line: sequences ✕ Clear

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

cd4+ hela imr90 embryonic chip-seq computational gene
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

isolates genome snp snps multilocus genome bayesian
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

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Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

kegg 8192x8192 user-submitted species pathway zoomable sequence
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

PMID 19906711 · PMC2808952 · Nucleic acids research · 2010 · 6 claims · 4 setups

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PLANdbAffy is a database of Affymetrix probe alignments to the human genome for five widely used arrays (HG-U133A, HG-U133B, HG-U133 Plus 2.0, Human Exon 1.0, Human Gene 1.0)

hg-u133a ucsc dbsnp probe blat est snp
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

serum hbv full-length o-hbv nested phylogenetic quasispecies
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

tissues genome full-length genes full-length genome orf
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups

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HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin

hela computational living halochip halochip-chip chip-chip
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

hepg2 liver chip-seq quantitative co-immunoprecipitation
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

sporadic mitochondrial reported ataxia mitochondrial functional compensatory
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

PMID 19758467 · PMC2745585 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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MutationTagger achieves 87% F-measure for the mutation retrieval task on a benchmark dataset

pubmed uniprot five mutation gene sequence
High-throughput crystallography for structural genomics.

PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

recombinant recalcitrant hundred family hydrogen situ site-directed
Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

splenocytes pbmc-derived splenic genbank race pcr quantitative
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

asian fgf5 woolly savanna pcr structural blast
Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

PMID 19643205 · PMC2790030 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2009 · 8 claims · 6 setups

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The domain II loop of PvAMA-1 is almost completely conserved at the amino acid level, consistent with strong purifying selection.

plasmodium pvama-1 vivax pcr molecular merozoite
Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.

PMID 40191587 · PMC11970367 · NAR genomics and bioinformatics · 2025 · 8 claims · 5 setups

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44 individuals' fully haplotyped diploid genome assemblies (88 haplotypes) from the 1000 Genomes Project were used to comprehensively assess homozygous and heterozygous sequence variations around and within 5'ss

healthy reconstructed same 5'ss long-read computational statistical
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.

PMID 41924242 · PMC13037781 · Bio-protocol · 2026 · 7 claims · 5 setups

Has reproduction · 100

ECCFP significantly improves eccDNA detection sensitivity, accuracy, and runtime efficiency compared to other pipelines

nanopore trimmed aligned base sequencing adapter
B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence

Experiments

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

High-throughput crystallography for structural genomics.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand.

Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.

Prediction and assessment of splicing alterations: implications for clinical testing.

A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.