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).

• IL-6 trans-Signaling Regulates Neutrophilic Inflammation in Alcohol-Associated Hepatitis.

  PMID 40562277 · PMC13168973 · The American journal of pathology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Hepatic IL-6R expression progressively declines with increasing severity of alcohol-related liver disease, from normal to early ASH to nonsevere and severe AH

  liver hepatocytes hepg2 ptpn11 bulk immunohistochemistry single-cell

• Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

  PMID 41111196 · PMC12506984 · Hepatology communications · 2025 · 8 claims · 3 setups

  Has reproduction · 77

  2D culturing of primary hepatocytes for 24 hours causes extensive transcriptomic (>10,000 genes) and proteomic (>3000 proteins) rewiring compared with freshly isolated cells

  c57bl same bulk quantitative single-nucleus

• Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

  PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

  Has reproduction · 83

  scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

  liver hepatocyte detected adipose single-cell differential protein-protein

• Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

  PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

  hela liver gene peripheral retroviral transposon hydrodynamic

• Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

  PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

  Has reproduction · 85

  Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

  liver huh-7 bulk sirna lipid

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum

• Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

  PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

  Full-text index only

  Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

  cd4+ hela influenza-infected liver cdna microarray mass

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Emerging single-cell technologies have advanced or redefined understanding of the liver's immunological barrier function

  liver c57bl sorted pdgfrb-gfp scrna-seq single-molecule