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).

• Comprehensive phenotyping in multiple sclerosis: discovery based proteomics and the current understanding of putative biomarkers.

  PMID 17124343 · PMC3851054 · Disease markers · 2006 · 8 claims · 8 setups

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  No single diagnostic test exists for MS; diagnosis relies on clinical evaluation, MRI abnormalities, and CSF chemistry

  csf cns igg brain comprehensive immunohistochemical solid-phase

• Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

  PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

  simulated real apoe igf2 cubic pairwise haplotype

• Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

  PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

  cell-cycle-synchronized hela computational differentially tiling cdna statistical

• Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

  PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

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  Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

  serum prns-1-1 n-linked maldi solid tandem

• A mouse plasma peptide atlas as a resource for disease proteomics.

  PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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  A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

  plasma peptides fully tissues lc-ms anion database

• A genome search for primary vesicoureteral reflux shows further evidence for genetic heterogeneity.

  PMID 18197425 · PMC2259258 · Pediatric nephrology (Berlin, Germany) · 2008 · 8 claims · 7 setups

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  Genome-wide linkage analysis identifies several novel loci for primary VUR on chromosomes 1, 3, 4, and 22, supporting genetic heterogeneity.

  patients multiplex index pedigree genome-wide fine-mapping haplotype

• The oxazolidinone derivative locostatin induces cytokine appeasement.

  PMID 19917702 · PMC2799496 · Journal of immunology (Baltimore, Md. : 1950) · 2009 · 7 claims · 7 setups

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  RKIP is differentially localized (not differentially expressed) on the proteomic map after in vivo T cell recall compared to resting state

  ot-i splenocytes fractions serum intracellular proteomics sds-page

• Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

  PMID 33402206 · PMC7784341 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 74

  Disome-seq detects widespread, previously hidden ribosome collisions across endogenous coding sequences in fast-proliferating yeast cells.

  exponentially yeast sucrose disome-seq cryo-electron

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late

  mus mefs bulk independent allele-specific fluorescence-activated live

• Contribution of retrotransposition to developmental disorders.

  PMID 31604926 · PMC6789007 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 79

  De novo retrotransposition events, though rare, can be diagnostic causes of severe developmental disorders

  ddd overlapping ppg unaffected whole-exome bespoke whole-genome

• On the holobiont 'predictome' of immunocompetence in pigs.

  PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups

  Has reproduction · 40

  Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall

  duroc fecal plasma serum snp 16s immunoglobulin

• Single-cell RNA-sequencing highlights a curtailed NK cell function in convalescent COVID-19 pregnant women.

  PMID 40661959 · PMC12257036 · Frontiers in immunology · 2025 · 7 claims · 5 setups

  Has reproduction · 87

  NK cells show a sustained reduction during active SARS-CoV-2 infection and persisting after recovery in pregnant women

  pbmcs serum 14-color single-cell 13-plex

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence

• RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.

  PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML

  sorted mpn cd34+ aml bulk targeted mass

• 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

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

• Proteomic analysis of the mammalian nuclear pore complex.

  PMID 12196509 · PMC2173148 · The Journal of cell biology · 2002 · 8 claims · 7 setups

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  Mass spectrometry was used to identify all proteins present in a biochemically purified rat liver NPC fraction.

  liver empigen transiently mass sds-page electron

• Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

  PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups

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  The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.

  crp simplex same serum direct family-based linkage

• The application of basic science to translational cancer research.

  PMID 12620114 · PMC151297 · Genome biology · 2003 · 8 claims · 8 setups

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  Sister-chromatid separation at anaphase is triggered by degradation of securin, releasing the protease separase to cleave the cohesin ring holding chromatids together

  yeast lamin tumor breast protease-cleavage rad53 brdu