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).

• Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

  PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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  Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

  alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic

• Widespread ultraconservation divergence in primates.

  PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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  The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

  hg18 genome genes computed comparative snp gene

• Next-generation high-density self-assembling functional protein arrays.

  PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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  A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

  test high-density amine-coated array picogreen anti-gst fluorescently

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

  PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.

  promoter tred-retrieved computational literature relational

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

  PMID 15907206 · PMC1156890 · BMC genomics · 2005 · 8 claims · 5 setups

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  Regulation of mRNA stability accounts for as much as 50% of all measured changes in polyA mRNA levels, inferred from absence of corresponding nuclear transcription changes.

  jurkat nuclear polya single

• Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

  PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 96

  A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

  gastric gene scrna-seq tcga single-cell wgcna cell-cell

• Inferring combinatorial regulation of transcription in silico.

  PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

  upstream monocytes same tfbs microarray permutation

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

  PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

  est gene worm fly blat-based transcription comparative

• Cohesin regulates alternative splicing.

  PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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  Cohesin regulates alternative splicing independently of its effects on transcription.

  hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative

• From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.

  PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 88

  Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs

  flower sweet sequencing differential principal

• 7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

  PMID 39952919 · PMC11828898 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  Heat shock induces de novo transcription and nuclear accumulation of 7SL RNA together with SRP proteins, which then bind chromatin at promoters

  embryonic nih3t3 pro-seq fractionation fluorescence

• Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.

  heart degs gene genes bulk gene kegg

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

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  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• All systems GO for understanding mouse gene function.

  PMID 15610553 · PMC549721 · Journal of biology · 2004 · 7 claims · 4 setups

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  Quantitative, multivariate cross-tissue expression measurements are powerfully predictive of gene function

  diverse tissues computational dye-swap reverse-transcription-coupled support

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene