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).

• SPRINT: a new parallel framework for R.

  PMID 19114001 · PMC2628907 · BMC bioinformatics · 2008 · 8 claims · 1 setups

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  SPRINT is a prototype R framework that wraps parallelised functions, requiring minimal modification to existing sequential R scripts and no parallel programming expertise from the user

  simulated pairwise

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

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

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  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

• KEGG for linking genomes to life and the environment.

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

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  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

• SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.

  PMID 18208605 · PMC2265264 · BMC bioinformatics · 2008 · 8 claims · 1 setups

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  SignS is a web-based tool and R package implementing four gene-selection/signature-building methods for survival data (Dave et al., Gui and Li, random forests with conditional inference trees, and boosting with component-wise Cox models).

  microarray gene-by-gene

• BTW: a web server for Boltzmann time warping of gene expression time series.

  PMID 16845055 · PMC1538860 · Nucleic acids research · 2006 · 5 claims · 4 setups

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  Symmetric time warping distance is more flexible than Euclidean distance or correlation coefficient for identifying genes with similar temporal expression profiles, especially across sequences of different length.

  cerevisiae homologous yeast boltzmann histogram time

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• 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

• 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

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

  elegans pairwise orthologs cerevisiae microarray ortholog functional

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

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  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-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

• 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

• 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

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise

• From genomics to chemical genomics: new developments in KEGG.

  PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.

  enzymatic substrate kegg complete chemical number ortholog

• Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

  PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

  seraseq simulated small processed targeted simulated computation

• Genome-wide prediction of DNase I hypersensitivity using gene expression.

  PMID 29051481 · PMC5715040 · Nature communications · 2017 · 8 claims · 5 setups

  Has reproduction · 79

  Gene expression can, to a large extent, predict genome-wide DNase I hypersensitivity (chromatin accessibility)

  distinct same training encode dnase-seq exon bird

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

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

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  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

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene