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).

• Integrative epigenetics and transcriptomics identify aging genes in human blood.

  PMID 41554691 · PMC12820199 · Nature communications · 2026 · 8 claims · 5 setups

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  Age-associated DNAm changes are considerably more replicable across cohorts than age-associated transcriptomic changes

  blood pbmc bulk methylation integrative

• Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella.

  PMID 41684216 · PMC12902445 · Microbial biotechnology · 2026 · 7 claims · 5 setups

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  Structured, recurrent promoter variation in epigenetically regulated operons is a novel layer of functional adaptation in Salmonella, complementing genetic and epigenetic mechanisms.

  complete annotated 220-nucleotide opvab comparative correlation blastn

• G-quadruplexes in promoters throughout the human genome.

  PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

  genome quiescent gene synthetic computational nuclease gene

• Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

  PMID 18475302 · PMC2391125 · British journal of cancer · 2008 · 7 claims · 5 setups

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  RUNX3 promoter hypermethylation is frequent in primary pancreatic cancer tissue

  pancreatic microsatellite methylation-specific bisulphite

• Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

  PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups

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  Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives

  genome encode computational tss manual

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Transcriptional bursting kinetics is regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 (PRC2) and transcription elongation factors

  cast knock-in mesc mescs single-cell single-molecule flow

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

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  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

  PMID 16969349 · PMC2360724 · British journal of cancer · 2006 · 8 claims · 8 setups

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  K-Ras codon 12 mutations are significantly associated with metastatic (M+) CRC

  crc 202-patient pcr-rflp sscp immunohistochemistry

• Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

  PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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  At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

  breast same selected hct116 expression methylation-specific rt-pcr

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

  PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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  PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

  sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression.

  PMID 41559111 · PMC12873405 · NPJ systems biology and applications · 2026 · 7 claims · 8 setups

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  NR2F1 is a central transcription factor in LUAD progression, identified independently through GRN architecture transitions and gene regulation dynamics analysis

  luad epithelial myeloid nr2f1 single-cell gene binding

• Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

  PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

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  PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

  gtex encode wi-38 thp-1 bulk eqtl variant-flowfish

• Comparative genomics of Drosophila and human core promoters.

  PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

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  Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

  drosophila core genome-wide mono gene

• Pharmacogenomics of gemcitabine: can genetic studies lead to tailor-made therapy?

  PMID 17595663 · PMC2360307 · British journal of cancer · 2007 · 8 claims · 14 setups

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  A SNP in the cytidine deaminase (CDA) gene (208G>A, haplotype *3) decreases gemcitabine clearance, increases Cmax/AUC, and increases neutropenia risk when gemcitabine is combined with platinum drugs or 5-FU

  japanese paraffin-embedded tumour recombinant prospective immunohistochemistry pcr