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).

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• Babesia divergens host cell egress is mediated by essential and druggable kinases and proteases.

  PMID 41593365 · PMC12872469 · Nature microbiology · 2026 · 8 claims · 8 setups

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  PKG, CDPK4, ASP2 and ASP3 mediate distinct sequential steps of B. divergens egress and/or invasion of red blood cells

  divergens flow time-lapse live

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• Developmental convergence and divergence in human stem cell models of autism.

  PMID 41611887 · PMC12999519 · Nature · 2026 · 8 claims · 8 setups

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  Different ASD-associated mutations show the largest mutation-specific transcriptional changes early in hCO differentiation but converge on shared transcriptional changes as development progresses

  cortical hips induced hco bulk whole-genome ip-ms

• Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

  PMID 41857393 · PMC13061643 · Nature neuroscience · 2026 · 8 claims · 6 setups

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  Adult spinal-cord-derived human oligodendroglia and astrocytes, but not microglia, show primed chromatin signatures at HOX loci and a putative SOX10 enhancer.

  postmortem induced lentiviral cns single-nucleus nanocut&tag high-resolution

• Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

  PMID 41935313 · PMC13188593 · Animal microbiome · 2026 · 8 claims · 8 setups

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  Genome-wide CNV scanning of dairy vs non-dairy goats identified 62,860 CNVs, with 115 under strong selection (top 1% Fst/Vst).

  goat gmecs lps-induced whole-genome immunofluorescence lentiviral

• Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

  PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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  CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

  lung candidate bulk normalized bulk ppi machine

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• TEAD4 and RXRA Regulate the Function of Nucleus Pulposus Cells in Intervertebral Disc Degeneration Via the TNF-α/NF-κB Pathway: An Integrated Analysis of Single-Cell RNA-Seq, Bulk RNA-Seq, and In Vitro Validation.

  PMID 41511606 · PMC12995935 · Applied biochemistry and biotechnology · 2026 · 8 claims · 8 setups

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  TEAD4 and RXRA play critical roles in IDD progression, likely regulating NP cell behavior and ECM metabolism via the TNF-α/NF-κB pathway

  differential il-1β-induced scrna-seq bulk gsea

• HIF3A-mediated aberrant activation of TXNIP promotes Alzheimer's disease progression.

  PMID 41807716 · PMC13096512 · Scientific reports · 2026 · 8 claims · 8 setups

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  OS activity is significantly elevated in AD and shows pronounced heterogeneity across brain cell types

  entorhinal brain middle c57bl scrna-seq bulk animal

• Forward genetic screening of mutants of the wild diploid ancestor Nicotiana sylvestris identifies aspartate oxidase 2 as a key gene for nicotine biosynthesis in cultivated allotetraploid tobacco (Nicotiana tabacum).

  PMID 41921204 · PMC13043189 · The Plant journal : for cell and molecular biology · 2026 · 7 claims · 8 setups

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  A large-scale, high-mutation-frequency EMS mutant library of N. sylvestris was constructed as a forward genetics resource

  sylvestris tabacum ems whole-genome rna-seq

• Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.

  PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)

  ipf degs differentially bleomycin-induced bulk methylation kegg

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Single-cell transcriptomics reveals heterogeneous neutrophil populations and diagnostic biomarkers in atherosclerosis.

  PMID 41847341 · PMC12989409 · Frontiers in physiology · 2026 · 8 claims · 8 setups

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  Integration of scRNA-seq data from six human carotid samples identified 16 distinct cell subtypes after batch effect correction with Harmony

  carotid neutrophil bulk c57bl scrna-seq hdwgcna lasso