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).

• 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

• A note on generalized Genome Scan Meta-Analysis statistics.

  PMID 15717930 · PMC551600 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  An Edgeworth series approximation to the null distribution of the weighted GSMA statistic provides a more accurate representation than the normal approximation, especially in the tails

  simulated schizophrenia monte genome numerical

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Characterization of genome-wide p53-binding sites upon stress response.

  PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

  u2os saos-2 chip-on-chip chip-qpcr western

• A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

  PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

  unigene shuffled real genomes genome-wide alignment gene

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

• Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

  PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

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  A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

  fregene-simulated 80k-snp 480k 192k simulated null whole-genome

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

  PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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  Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

  bxd simulated subset populations genome-wide simulation genotype-phenotype

• Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

  PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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  The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

  elegans whole-genome rnase pharmacological

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• The genome of Brugia malayi - all worms are not created equal.

  PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups

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  Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.

  malayi elegans wbm-infected filarial whole-genome genome-wide comparative

• DNA methylation of cancer genome.

  PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

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  Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

  embryonic germ heterozygous cancer gene hypomorphic methyltransferase

• Evolutionary origins of human apoptosis and genome-stability gene networks.

  PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

  apoptosis fully same orthologous protein-protein comparative orthology

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes.

  PMID 17672902 · PMC1950089 · BMC medical genetics · 2007 · 8 claims · 6 setups

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  The major APOE haplotype (Hap1) is significantly associated with SAH

  caucasian same genomic snp rflp genome

• Modeling ChIP sequencing in silico with applications.

  PMID 18725927 · PMC2507756 · PLoS computational biology · 2008 · 8 claims · 4 setups

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  Observed ChIP-seq tag counts follow an initial power-law distribution followed by a long right tail.

  stat1 ncbi chip-seq motif

• Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

  PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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  A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

  hcv 5'ncr serum maximum sequence recombination