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).

• 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

• Spontaneous symmetry breaking in genome evolution.

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

  Full-text index only

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

  animal homo model genome-wide alternatively computational

• Duplication count distributions in DNA sequences.

  PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups

  Full-text index only

  Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.

  genome elegans thaliana melanogaster genome-wide transposable homogeneous

• 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

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Active (R) and silent (S) epialleles are associated with distinct sRNA size classes: mainly 21 nt sRNAs at R and mostly 24 nt sRNAs at S, regardless of ploidy.

  day-old seedlings tetraploid arabidopsis small hygromycin crispr-cas9

• Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

  PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups

  Has reproduction · 100

  Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.

  synechocystis gradient proteins grad-seq grad-seq denaturing sds-polyacrylamide

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• An extensive evaluation of read trimming effects on Illumina NGS data analysis.

  PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.

  homo arabidopsis prunus saccharomyces rna-seq snp novo

• 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

  Full-text index only

  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

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing