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).

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• Engineered apoptotic nucleases for chromatin research.

  PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

  recombinant cerevisiae coli western plasmid serial

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Prediction of condition-specific regulatory genes using machine learning.

  PMID 32329779 · PMC7293043 · Nucleic acids research · 2020 · 8 claims · 6 setups

  Has reproduction · 85

  ConSReg integrates expression, DAP-seq TF-DNA binding, and ATAC-seq open chromatin data into machine learning models to predict condition-specific regulatory genes

  arabidopsis zea bulk dap-seq atac-seq

• Predicting enhancers in mammalian genomes using supervised hidden Markov models.

  PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

  Has reproduction · 70

  eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

  esc atac-seq chip-seq cage

• The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.

  PMID 41131451 · PMC12551222 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 8 setups

  Has reproduction

  Significant genetic introgression from Chinese pigs into commercial European pig lines is confirmed using SNP chip and resequencing data.

  chinese pigs duroc muscle snp genome low-coverage

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

  PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

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  The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

  populations genome genome-wide genome

• In silico meets in vivo.

  PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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  About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

  genome lines prokaryotic genomes genome genome-wide gene

• Complete human day 14 post-implantation embryo models from naive ES cells.

  PMID 37673118 · PMC10584686 · Nature · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  Genetically unmodified human naive ES cells, without transgene overexpression, can be aggregated to form complete SEMs recapitulating epiblast, hypoblast, extra-embryonic mesoderm and trophoblast compartments

  naive day igata3 sem facs immunofluorescence scrna-seq

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species