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 · 7 claims · 5 setups

  Has reproduction · 75

  Short- and long-term HL responses in Arabidopsis leaves are driven by distinct transcriptional programs, with duration of HL treatment as the primary factor separating transcriptomic clusters.

  arabidopsis bulk hierarchical correlation

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 7 claims · 4 setups

  Has reproduction · 83

  A metabolite-centric reporter pathway analysis (RPAm) can infer cold-stress-associated metabolites and pathways in Arabidopsis directly from transcriptome data without metabolome data

  arabidopsis tripartite affymetrix metabolite-centric network

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• A2TEA: Identifying trait-specific evolutionary adaptations.

  PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups

  Has reproduction · 90

  A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment

  user-provided multi-species genes sequences rna-seq orthologous phylogenetic

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 7 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across 4 cotton species (G. arboreum 20, G. raimondii 20, G. hirsutum 38, G. barbadense 36), clustering into 5 groups (I, II, III, IVa, IVb).

  plant cotton hirsutum ghcngc genome-wide phylogenetic conserved

• 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

• Natural history of S-adenosylmethionine-binding proteins.

  PMID 16225687 · PMC1282579 · BMC structural biology · 2005 · 8 claims · 6 setups

  Full-text index only

  The last universal common ancestor (LUCA) of cellular life had between 10 and 20 SAM-binding proteins from at least 5 fold classes

  arabidopsis nicotianamine rossmann-fold cyclopropane psi-blast pdbblast comparative

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

  Full-text index only

  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn

• The most frequent short sequences in non-coding DNA.

  PMID 19966278 · PMC2831315 · Nucleic acids research · 2010 · 8 claims · 2 setups

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  Short frequent sequences (9-14 bases) in non-coding DNA may play a role in maintaining chromosome structure and function

  whole-genome genome-wide

• Genomic variability within an organism exposes its cell lineage tree.

  PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

  robinia arabidopsis randomly genotyping multiplex computer

• Spontaneous symmetry breaking in genome evolution.

  PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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  Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

  animal homo model genome-wide alternatively computational

• 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

• Computational verification of protein-protein interactions by orthologous co-expression.

  PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

  cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

  PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes

  orf coli rabbit cos-7 bioinformatic codon prokaryotic

• Large-scale trends in the evolution of gene structures within 11 animal genomes.

  PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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  Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

  annotated animal unannotated comparative all-against-all neighbor-joining

• Protein under-wrapping causes dosage sensitivity and decreases gene duplicability.

  PMID 18208334 · PMC2211539 · PLoS genetics · 2008 · 7 claims · 6 setups

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  Protein under-wrapping extent is negatively correlated with gene duplicability (family size) across six organisms (E. coli, yeast, worm, fly, human, thale cress)

  coli cerevisiae sapiens elegans structural comparative functional

• Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

  PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

  eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide