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).

• Application of OMICS technologies in occupational and environmental health research; current status and projections.

  PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups

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  Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics

  population genomic blood genome array-based comparative gene

• HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

  PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

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  Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

  plasma transmitter subject genomic full-length population ifn-γ

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.

  PMID 19864251 · PMC2811011 · Nucleic acids research · 2010 · 7 claims · 8 setups

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  SPEX-type approaches preferentially access genetic information from damaged, degraded endogenous ancient DNA templates over modern human contaminant DNA

  iceman hb50 pe168 lq4 relative pcr spex

• RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

  PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 41

  Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

  pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

• Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

  PMID 19819359 · PMC2818390 · Journal of proteomics · 2010 · 8 claims · 8 setups

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  Proteomic techniques (LC-MS/MS, iTRAQ, immunochemical/biochemical methods) can monitor and validate each production step of pd F IX isolation

  plasma in-process chromatographic one-stage competitive elisa

• Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

  PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

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  Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

  breast hek293 erβ1 allelic luciferase stability

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

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  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

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  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.

  PMID 39423268 · PMC11488575 · Science advances · 2024 · 8 claims · 5 setups

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  An unsupervised ML pipeline using the extended isolation forest (EIF) algorithm can reliably detect ribosome pausing sites from noisy, coverage-biased RiboSeq data across expression levels

  saccharomyces simulated yeast riboseq simulated comparative

• Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.

  PMID 34282405 · PMC8285288 · Frontiers in cellular and infection microbiology · 2021 · 8 claims · 7 setups

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  iPSC-derived pancreatic endocrine and exocrine (acinar/ductal) cultures express ACE2 and TMPRSS2, enabling SARS-CoV-2 entry

  ipsc-derived post-mortem vero-e6 immunofluorescence sars-cov-2 rt-qpcr

• Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells.

  PMID 41485059 · PMC12930946 · Journal of ovarian research · 2026 · 8 claims · 6 setups

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  Acute 10 Gy X-ray irradiation does not significantly affect viability (ATP levels, mitochondrial dehydrogenase activity) of cPOCs and mPOCs over 7 days.

  kgn cpocs celltiter-glo mtt immunofluorescence

• Optimized library preparation, sequencing, and data analysis protocols for the generation of orbivirus consensus sequences.

  PMID 41527034 · PMC12809950 · BMC genomics · 2026 · 8 claims · 8 setups

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  Optimized sample and library preparation protocols achieved comparable results to established methods while requiring simpler sample preparation.

  btv17 purification carrier dnase

• Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development.

  PMID 41577697 · PMC12932823 · Nature communications · 2026 · 8 claims · 6 setups

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  DOE-based multifactorial screening combined with bulk RNA-seq comparison to scRNA-seq pharyngeal atlases identifies signaling factors that optimize iPSc differentiation toward thymic epithelial progenitors (TEPs)

  ipsc embryonic ipsc-derived bulk scrna-seq qpcr

• A cost-effective and scalable barcoded library construction method for deep mutational scanning studies.

  PMID 41671286 · PMC12923136 · PLoS biology · 2026 · 8 claims · 4 setups

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  A two-step cloning strategy (Gibson assembly followed by Golden Gate assembly) using degenerate oligo pools (oPools) with co-synthesized DNA barcodes enables construction of scalable DMS libraries for large genes.

  yeast short-read transformation barcode

• Omics-aided design genome editing strategy for challenging human immortalized cell models.

  PMID 41678468 · PMC12900285 · PloS one · 2026 · 6 claims · 4 setups

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  Omics profiling identifies bottlenecks associated with poor precise KI efficiency in hard-to-engineer cells

  mcf7 deep-targeted bulk dia-based

• pmid-41701697

  PMID 41701697 · PMC12912608 · 8 claims · 7 setups

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  Nanodroplets facilitate parallel fragmentation of up to 96 genomic DNA samples in a modified/adapted Qsonica sonication device using inexpensive PCR plates.

  gdna yeast fragmented acoustic gel ngs

• Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

  PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

  Has reproduction · 74

  Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

  peripheral rna-seq flow edu antibody

• Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data.

  PMID 19704920 · PMC2688763 · Journal of biomedicine & biotechnology · 2009 · 8 claims · 3 setups

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  Kernel-based methods (e.g., SVM) can capture nonlinear dose-volume interactions relevant to predicting radiation pneumonitis

  nsclc inoperable blood retrospective prospective 3-way