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).

• Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

  PMID 18546365 · PMC2891192 · Human mutation · 2008 · 8 claims · 4 setups

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  POLG mutations cause at least 6 major heterogeneous phenotypes of neurodegenerative mitochondrial disease (MCHS, Alpers syndrome, ANS, MEMSA, arPEO, adPEO)

  blood parental model sanger parental microsatellite

• Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

  PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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  Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

  pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• Transcription dynamics.

  PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

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  Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

  living linker lac glucocorticoid frap single-molecule nucleosome

• Long non-coding RNA LINC00607 epigenetically regulates endothelial TSPAN18 to promote hypoxia-induced thromboinflammation.

  PMID 41581880 · PMC12992942 · The Journal of biological chemistry · 2026 · 8 claims · 8 setups

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  LINC00607 is a hypoxia-inducible, endothelial-enriched lncRNA that positively regulates TSPAN18 expression

  huvecs rna-seq gro-seq atac-seq

• PAF15-PCNA exhaustion governs the strand-specific control of DNA replication.

  PMID 41606318 · PMC12979207 · Nature · 2026 · 8 claims · 8 setups

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  Excessive origin firing saturates chromatin-bound PCNA, restricting further PCNA loading and lagging-strand synthesis when checkpoint control is lost.

  u2os embryonic qibc confocal western

• The TRIP12's intrinsically disordered region induces chromatin condensates and interferes with nuclear processes.

  PMID 41660270 · PMC12876695 · iScience · 2026 · 8 claims · 8 setups

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  TRIP12 overexpression induces dose-dependent formation of chromatin condensates enriched in heterochromatin marks

  hela u2os trip12 immunofluorescence cellular isoelectric

• Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila.

  PMID 41735587 · PMC12987734 · Nature genetics · 2026 · 8 claims · 8 setups

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  Pico-C, a low-input Micro-C method, enables high-resolution, temporally resolved 3D genome mapping in early Drosophila embryos using as few as ~60,000 nuclei

  hand-staged early drosophila pico-c chip-seq atac-seq

• BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

  PMID 15757512 · PMC555852 · Retrovirology · 2005 · 8 claims · 3 setups

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  BioAfrica's HIV-1 Proteomics Resource integrates protein structure, gene expression, post-translational modification, functional activity and protein-macromolecule interaction data with bioinformatics tools in a single website.

  hiv-1 motif sequence literature-derived

• Integrative functional genomics.

  PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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  Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

  yeast tissue-cultured mammalian genomic comparative targeted chip-chip

• Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

  PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

  Has reproduction · 67

  Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

  frugiperda satellite million contigs comparative homology divergence

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

  PMID 41547832 · PMC12914055 · Nature communications · 2026 · 8 claims · 8 setups

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  Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

  recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation

• FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster.

  PMID 41551930 · PMC12805895 · NAR genomics and bioinformatics · 2026 · 7 claims · 8 setups

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  FLYNC, an explainable boosting machine (EBM) model, accurately predicts the probability that a newly identified RNA transcript in D. melanogaster is a lncRNA

  melanogaster drosophila automated ebm hyperparameter