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).

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

  Full-text index only

  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

  PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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  -26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

  mcf-7 hela brca2 peripheral luciferase transcription genotyping

• Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

  PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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  The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

  asian fgf5 woolly savanna pcr structural blast

• Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

  PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups

  Has reproduction · 67

  Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines

  brain tumour gbm retrotransposon empty qrt-pcr

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.

  PMID 41407883 · PMC12712020 · Communications biology · 2025 · 8 claims · 6 setups

  Has reproduction · 32

  PTRs computed from integrated transcriptomic/proteomic data of 44 AML samples are highly conserved across AML subtypes and with 29 other human tissues, indicating broadly conserved post-transcriptional mechanisms.

  aml tissues eif4a1 rna-seq cross-tissue fast

• Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

  PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups

  Has reproduction · 88

  C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.

  elegans clash bioinformatic iclip

• Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

  PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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  Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

  chicken comparative amino phylogenetic

• Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

  PMID 17456229 · PMC1868706 · BMC medical genetics · 2007 · 7 claims · 4 setups

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  No mutations were identified in the VEGFR2 gene (exons 7, 18, 21, 27, promoter, or 5' UTR) in ALS patients

  genomic pcr als direct restriction allele

• An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

  PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

  example hepatitis minimum suboptimal multiple-point

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence