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).

• Homeodomain protein Sxi1α independently controls cell-cell fusion and gene expression during sexual reproduction in Cryptococcus deneoformans.

  PMID 41818280 · PMC13001979 · PLoS genetics · 2026 · 8 claims · 8 setups

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  Sxi1α has a previously unrecognized inhibitory role in same-sex (α-α) cell-cell fusion during unisexual reproduction

  sxi1α cerevisiae deneoformans sxi1αδ alphafold3 yeast crispr

• Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

  PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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  Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

  csf brain normal 2d-dige label-free isotopic

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• Finding signals that regulate alternative splicing in the post-genomic era.

  PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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  Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

  intron-containing genome brain-specific cell-free computational comparative selex

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

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  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

  PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

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  D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

  liver pcr

• Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

  PMID 18384686 · PMC2359743 · BMC cell biology · 2008 · 8 claims · 8 setups

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  β1Int-HaloTag fusion protein localizes to the cell membrane in a pattern similar to endogenous β1 integrin, indicating the fusion does not disrupt normal integrin surface expression

  hela hek293 live immunocytochemistry live fluorescence