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).

• 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

• Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

  PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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  14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

  h3n2 meme sequence entropy

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna

• Evolutionary trace annotation of protein function in the structural proteome.

  PMID 20036248 · PMC2831211 · Journal of molecular biology · 2010 · 8 claims · 7 setups

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  ET-ranked residue clusters can be used to build 3D templates that predict GO function in enzymes and non-enzymes alike, without prior knowledge of functional mechanism.

  structural pdb pairs annotated evolutionary template support

• Inferring a spatial code of cell-cell interactions across a whole animal body.

  PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 90

  cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

  elegans computational single-cell random genetic

• Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

  PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

  Has reproduction · 80

  DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

  transcripts platforms bacillus multi-subcellular simulated negative benchmark

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

  PMID 33247935 · PMC7698665 · Database : the journal of biological databases and curation · 2020 · 8 claims · 6 setups

  Has reproduction · 75

  GETc enables discovery and visualization of time-course gene expression data and analytical results from GEO

  geo time-course researcher filtered regular metamap ode-based

• 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

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple