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).

• 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

• 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

• DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

  PMID 14519203 · PMC328457 · Genome biology · 2003 · 7 claims · 5 setups

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  DiagHunter identifies large-scale synteny blocks within or between genomes efficiently despite background noise and genomic discontinuities, without performing sequence alignment

  arabidopsis synthetic blastp-based blastn-based simulation

• Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

  PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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  3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

  arabidopsis phylogenetic tblastn subcellular

• Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

  PMID 18433472 · PMC2386800 · BMC molecular biology · 2008 · 7 claims · 6 setups

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  Co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves gives high-level transient expression of active, mismatch-specific ENDO1 via a simple purification protocol

  benthamiana test genomic hiv-1 transient heteroduplex mutation

• Phenotypic variation meets systems biology.

  PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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  Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

  thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing

• 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

• 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