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).

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Prostate cancer genomics: towards a new understanding.

  PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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  Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

  germline families african-american combined genome-wide linkage admixture

• ChimerDB--a knowledgebase for fusion sequences.

  PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

  genome candidate pubmed omim blat splice-site ecgene

• Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

  PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

  genome insect yy1-related zinc blast sequence synonymous

• 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

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

  triticum taiqd wheat promoter genome-wide phylogenetic synteny

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

  Full-text index only

  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• Complex landscapes of somatic rearrangement in human breast cancer genomes.

  PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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  There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

  breast subset confirmed paired-end fish exon-exon

• A small-cell lung cancer genome with complex signatures of tobacco exposure.

  PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

  Full-text index only

  22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

  nci-h209 sclc lu-135 massively pcr multiplex

• Helminth genomics: The implications for human health.

  PMID 19855829 · PMC2757907 · PLoS neglected tropical diseases · 2009 · 8 claims · 7 setups

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  More than two billion people (one-third of humanity) are infected with helminth parasites, causing major morbidity, mortality, and poverty maintenance

  helminth nematode schistosoma strongyloides phylogenetic genome expressed

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• Alexander Meissner: learning the reprogramming code.

  PMID 19704017 · PMC2733751 · The Journal of cell biology · 2009 · 8 claims · 6 setups

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  A defined set of factors present in oocytes and embryonic stem (ES) cells can reprogram a somatic cell to pluripotency, as shown by nuclear transfer and ES cell/somatic cell fusion experiments

  blastocysts somatic fused genomic nuclear inducible fusion

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining