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).

• Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.

  PMID 16034025 · PMC1179732 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Partial EC numbers are semantically ambiguous, and databases that assign a gene to all reactions sharing the same partial EC number make a faulty inference, causing systematic misannotation.

  e.coli biocyc vimss specific database comparative manual

• Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

  PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.

  genomic multiplex circularized circular multiplex probe-guided exonuclease

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Detection of p53 gene mutations in aspiration biopsy specimens from suspected breast cancers by polymerase chain reaction-single strand conformation polymorphism analysis.

  PMID 7730136 · PMC5920757 · Japanese journal of cancer research : Gann · 1995 · 4 claims · 4 setups

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  Detection of p53 gene mutation by PCR-SSCP in aspirated breast biopsy specimens is a helpful method for more accurate diagnosis of suspected breast cancer

  aspiration aspirated biopsy pcr-sscp flow p53

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in regions of increased calcite spicule formation in S. ciliatum, including known sclerocyte-specific biomineralization genes.

  sycon ciliatum cnidarian sponges differential go-term blastp

• Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

  PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

  pcr-amplified same sequence luciferase bioluminometric bati comparison

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• Proteomic solutions for analytical challenges associated with alcohol research.

  PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups

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  Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.

  general complex plasma selected shotgun label-free targeted

• Description of a PCR-based technique for DNA splicing and mutagenesis by producing 5' overhangs with run through stop DNA synthesis utilizing Ara-C.

  PMID 16137330 · PMC1208860 · BMC biotechnology · 2005 · 7 claims · 7 setups

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  Two adjacent Ara-C molecules incorporated into a PCR primer produce mild template-dependent polymerization termination, generating 5' overhangs usable for cohesive-end ligation.

  plasmid pcr gel-isolated ligated pcr gel ligation

• Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

  PMID 16554551 · PMC1409816 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A cleavage-free mismatch oxidation assay using potassium permanganate and a standard UV/Vis microplate reader can detect DNA mismatches spectrophotometrically at 420 nm.

  individual hybridized 38mer pbr322 colorimetric uv-vis mismatch

• PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

  PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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  PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

  hek293t pbmcs melanoma bone single-cell infercnv gene

• Back to basics.

  PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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  Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

  chromosome pendrin yeast carbonic genome gene mudpit

• Ankyrin-linked hereditary spherocytosis in an African-American kindred.

  PMID 18704959 · PMC11304496 · American journal of hematology · 2008 · 6 claims · 7 setups

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  A novel heterozygous initiator methionine mutation (ATG→ATA, Met1Ile), termed ankyrin New Haven, was identified in exon 1 of the ankyrin-1 gene as the cause of HS in this kindred.

  genomic erythrocyte rabbit dhplc sscp nucleotide

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• Pre-implantation embryo metabolism identified by PEMA reveals endogenous lactate insufficiency contributes to pre-implantation development arrest.

  PMID 42272466 · PMC13247451 · Fundamental research · 2026 · 6 claims · 7 setups

  Has reproduction

  PEMA, a computational tool that weights metabolic reactions using Ribo-seq data combined with RNA-seq-derived flux balance analysis, can characterize metabolic states of human and mouse pre-implantation embryos more precisely than existing methods like Compass.

  embryos pre-implantation ch3pn single-embryo immunofluorescence single-cell

• Profiling humoral immune responses to P. falciparum infection with protein microarrays.

  PMID 18937256 · PMC3021802 · Proteomics · 2008 · 7 claims · 5 setups

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  A protein microarray platform of 250 Pf proteins, individually expressed cell-free and printed unpurified, can profile serum antibody responses across donor groups of differing immune status

  sera coli genomic microarray immuno-dot elisa

• Genome-scale modeling identifies dynamic metabolic vulnerabilities during the epithelial to mesenchymal transition.

  PMID 39730911 · PMC11681178 · Communications biology · 2024 · 8 claims · 8 setups

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  EMT involves temporal, stage-specific metabolic reprogramming with distinct dependencies in glycolysis and glutamine metabolism.

  a549 recon1 cancer lung bulk single-cell genome-scale

• An ancient genome duplication event drives the development and evolution of spinnerets in spiders.

  PMID 41533794 · PMC12802834 · Science advances · 2026 · 8 claims · 8 setups

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  A single whole-genome duplication (WGD) event occurred in the Arachnopulmonata stem lineage during the Silurian (~438 Ma), supported by macrosynteny, Ks distributions, and WHALE gene-tree reconciliation.

  luthela chelicerate arachnid gene chromosome-scale phylogenomics macrosynteny

• 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