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).

• fREDUCE: detection of degenerate regulatory elements using correlation with expression.

  PMID 17941998 · PMC2174516 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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  fREDUCE is a computational method that detects weak or degenerate binding motifs from gene expression or ChIP-chip data by exhaustive search of degenerate IUPAC oligonucleotides

  saccharomyces cerevisiae hepatocytes chip-chip motif-finding gene

• 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

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• 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

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

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

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  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

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

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

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

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

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• 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

• 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

• Mathematical models in mammalian cell biology.

  PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups

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  A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.

  culture skin hela mammalian live-cell confocal phosphoprotein

• Centromere-associated protein-E is essential for the mammalian mitotic checkpoint to prevent aneuploidy due to single chromosome loss.

  PMID 12925705 · PMC2173788 · The Journal of cell biology · 2003 · 7 claims · 8 setups

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  CENP-E-null cells cannot sustain a mitotic checkpoint arrest in response to one or a few unattached kinetochores, causing cells to enter anaphase with missegregating chromosomes and become aneuploid

  embryonic mefs hepatocytes bubr1 real-time quantitative immunofluorescence

• Defining disease with laser precision: laser capture microdissection in gastroenterology.

  PMID 18619446 · PMC3736118 · Gastroenterology · 2008 · 8 claims · 8 setups

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  LCM allows isolation of pure cell populations from heterogeneous tissue without damaging DNA, RNA, or protein integrity.

  esophagus gastric colorectal colonic maldi cdna profiling

• 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

• 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

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  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

• Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

  PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 71

  CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.

  monocyte-macrophage cd4+ kidney metabolic bulk single-cell codon

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna