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).

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• DupyliCate: mining, classifying, and characterizing gene duplications.

  PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups

  Full-text index only

  DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.

  arabidopsis thaliana brassicales phytozome sequence duplication runtime

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

  Full-text index only

  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional

• Evolution of motif variants and positional bias of the cyclic-AMP response element.

  PMID 17288573 · PMC1796609 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  Canonical CRE positional bias toward the -1 to -150 bp TSS region is present in vertebrates (human, mouse, rat, chicken, frog, zebrafish) but absent in sea squirt, fruit fly and worm.

  tss-spanning cres genome known genome-wide comparative cpg

• Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

  PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

  Full-text index only

  NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

  complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• Inverse symmetry in complete genomes and whole-genome inverse duplication.

  PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups

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  Reverse and complement symmetries are essentially absent in genomic sequences at all scales.

  complete coli individual coding k-mer comparison segmental

• GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

  PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 96

  gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

  avian comparative correlation robustness

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

  PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.

  top100h decoys i-tasser non-homologous statistical rdcc comparative

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 7 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign performs pairwise local, global, and semiglobal (query search) alignment and progressive multiple alignment (global and local) using incremental ensemble mountain height, running in O(n^3) time and O(n^2) space for two sequences of length n

  sequences sets target single secondary pairwise sequence

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp