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).

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

  PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 8 claims · 7 setups

  Has reproduction · 88

  Flower buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are each defined by expression of genes in specific pathways, and the transcriptional state accurately captures the dormancy state.

  sweet garnet peach bulk forcing differential

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

  PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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  A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

  cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale

• 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

• Adaptively inferring human transcriptional subnetworks.

  PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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  A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

  liver proximal hela predicted microarray computational novo

• An Erg-driven transcriptional program controls B cell lymphopoiesis.

  PMID 32541654 · PMC7296042 · Nature communications · 2020 · 7 claims · 8 setups

  Has reproduction · 81

  Erg is essential for early B lymphoid differentiation

  erg b220+ prob wild-type lacz rna-seq flow

• 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

• Translation affects mRNA stability in a codon-dependent manner in human cells.

  PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 6 setups

  Has reproduction · 87

  Translation affects mRNA stability in a codon-dependent manner in human cells

  293t time-course orfome slam-seq