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).

• Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families.

  PMID 9099970 · PMC2222784 · British journal of cancer · 1997 · 6 claims · 6 setups

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  No germline TP53 mutations (exons 5-8) were found in 128 breast cancer patients from 109 families with familial cancer.

  genomic tumour paired constant restriction sequencing

• TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

  PMID 8761369 · PMC2074687 · British journal of cancer · 1996 · 8 claims · 8 setups

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  CDGE can be used to successfully detect TP53 mutations (exons 5-8) in DNA extracted from archival paraffin-embedded breast carcinoma tissue

  archival pcr breast tumour pcr-cdge direct restriction

• Negotiating the boundary between medicine and consumer culture: online marketing of nutrigenetic tests.

  PMID 20022680 · PMC2824846 · Social science & medicine (1982) · 2010 · 8 claims · 3 setups

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  Nutrigenetic testing companies create a new social/marketing space for their products positioned between medicine and consumer culture, rather than being simply delegitimized by boundary work.

  webpages same fda qualitative framing document

• Searching for genes underlying behavior: lessons from circadian rhythms.

  PMID 18988844 · PMC3744585 · Science (New York, N.Y.) · 2008 · 8 claims · 5 setups

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  Forward genetic mutagenesis screens successfully identified the molecular components of the circadian clock across Drosophila, Neurospora, cyanobacteria, Arabidopsis, and mouse.

  c57bl genomic automated contextual psychostimulant-induced

• A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm.

  PMID 16002787 · PMC1174901 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  An evolution-mimicking algorithm (EMA) that shuffles and mutates loop sequences while keeping the G-quartet intact can screen DNA aptamers based on inhibitory activity rather than binding affinity.

  plasma bovine clot-inhibition binding

• In silico segmentations of lentivirus envelope sequences.

  PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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  C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

  eiav hiv hmm-based hmm artificial

• Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

  PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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  Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

  sporadic msi-positive tumour unstable microsatellite denaturing sequencing

• Modeling the amplification dynamics of human Alu retrotransposons.

  PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

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  Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

  simulated genome population computer comparative population

• Integrated omics in Drosophila uncover a circadian kinome.

  PMID 32483184 · PMC7264355 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 98

  iCMod, a computational pipeline integrating transcriptomic, proteomic, and phosphoproteomic circadian data, was developed to accurately identify normalized circadian p-sites (NCPs)

  drosophila analysis tmt-based sequencing western

• Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.

  PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 84

  SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA

  model dipicolinic hek293t 28s crosslinking nmr crosslink

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry.

  PMID 19788317 · PMC2764328 · Analytical chemistry · 2009 · 7 claims · 4 setups

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  ProtMapMS automates data format conversion, mass spectrum interpretation, peptide detection/verification, modification site confirmation, and quantification of peptide oxidation extent from covalent labeling MS data

  insulin oxidative enzymatic computational

• Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models.

  PMID 36536288 · PMC9762025 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 4 setups

  Has reproduction · 93

  Structural equation models can decompose the total genetic effect on a production trait into a direct host genetic effect and an indirect effect exerted through the microbiota.

  rabbits cecal host bayesian 16s snp

• A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.

  PMID 41031900 · PMC13131251 · Journal of sleep research · 2026 · 7 claims · 6 setups

  Has reproduction · 96

  Meta-analysis of 18 SD-vs-control contrasts identified 182 genes differentially expressed in the murine cortex in response to sleep deprivation (FDR < 0.05).

  c57bl full genes meta-analysis affymetrix rna-seq random-effects

• L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

  PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

  Has reproduction · 74

  L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

  coli growth crystal colony

• Digital evolution.

  PMID 14551915 · PMC212697 · PLoS biology · 2003 · 7 claims · 5 setups

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  Digital organisms (Avidians) evolved from simple self-replicators, through an unexpected transitional form, to complex performers of many logic functions, with the full genealogy traceable and no missing links.

  digital bacteria long-term digital test gene-expression

• Protein interaction networks by proteome peptide scanning.

  PMID 14737190 · PMC314469 · PLoS biology · 2004 · 8 claims · 7 setups

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  WISE (combining phage display-derived relaxed consensus patterns with SPOT peptide synthesis arrays) can identify proteome-wide binding partners of a peptide-recognition domain

  cerevisiae synthetic yeast tap-tagged phage spot surface

• A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

  PMID 17440616 · PMC1847701 · PloS one · 2007 · 8 claims · 6 setups

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  PAMP enriches deletion-breakpoint-spanning DNA because shorter mutant amplicons are preferentially amplified over much longer wild-type sequences when using approximated flanking primer pairs.

  detroit serial hs578t pamp individual nested

• Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

  PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

  hela protein-free dual-luciferase reporter thermodynamic