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).

• 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

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.

  PMID 36725967 · PMC9892028 · Scientific reports · 2023 · 8 claims · 4 setups

  Has reproduction · 74

  JimenaE performs systematic, exhaustive calculation of all network system states rather than the heuristic approach used by SQUAD.

  mesenchymal arabidopsis dendritic comparison boolean dynamical network

• Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.

  PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 75

  Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes

  arabidopsis bulk hierarchical gene

• Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

  PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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  Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

  mcf7 arabidopsis specified different chip-seq microarray array-based

• Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

  PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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  Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

  yeast specified normal coli chip-on-chip chip-sequencing correlation-based

• Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

  PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

  Has reproduction · 58

  Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

  juncea promoter duplicated super genome-wide phylogenetic synteny

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

  Full-text index only

  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical