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).

• Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

  PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

  Has reproduction · 79

  196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

  rhizobium strains genotype genome whole-genome orthologous snp

• Designing candidate gene and genome-wide case-control association studies.

  PMID 17947991 · PMC4180089 · Nature protocols · 2007 · 8 claims · 4 setups

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  Common complex diseases are influenced by multiple genetic and environmental factors that individually are neither necessary nor sufficient to cause disease

  population monozygotic international genome-wide candidate twin

• Foster thy young: enhanced prediction of orphan genes in assembled genomes.

  PMID 34928390 · PMC9023268 · Nucleic acids research · 2022 · 7 claims · 8 setups

  Has reproduction · 84

  Each of the five gene-prediction pipelines under-predicts orphan genes, with detection as low as 11% under one prediction scenario.

  arabidopsis saccharomyces oryza direct braker maker

• Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

  PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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  Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

  cervical cdna microarray combinatorial

• 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

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco

• The genomics of probiotic intestinal microorganisms.

  PMID 15998456 · PMC1175979 · Genome biology · 2005 · 8 claims · 8 setups

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  Genomic characterization of probiotic and commensal intestinal bacteria will deepen understanding of their beneficial effects on host health

  lactobacillus bacteroides bifidobacterium host whole-genome inflammation microarray

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• Novel insights into adipogenesis from omics data.

  PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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  Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

  3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Relative impact of nucleotide and copy number variation on gene expression phenotypes.

  PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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  SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

  lymphoblastoid same computational subset gene snp array

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

  PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

  Has reproduction · 68

  The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.

  lactobacillus plantarum whole-genome novo gene

• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

  edna khumbu genome metabarcoding satellite

• The role of genomics in tracking the evolution of influenza A virus.

  PMID 19855818 · PMC2739293 · PLoS pathogens · 2009 · 8 claims · 5 setups

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  Antigenic drift, driven by selection for amino acid changes in exposed hemagglutinin epitope sites, is the main mechanism by which influenza A evades pre-existing immunity between pandemics.

  hemagglutinin influenza ferrets nonsynonymous antigenic whole-genome

• Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

  PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

  cd4+ jurkat hela computational chip-seq novo motif

• Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.

  PMID 32681306 · PMC7599172 · Current genetics · 2020 · 7 claims · 7 setups

  Has reproduction · 81

  A Random Forest machine-learning approach can predict gene essentiality from in vivo transposon insertion data across multiple yeast species and transposon systems

  cerevisiae pombe albicans hermes acds piggybac

• Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

  PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups

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  Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.

  osteichthyan aligned genome blast maximum comparative

• SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

  PMID 15774022 · PMC1274256 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  SNPHunter allows ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (physical position, function class, flanking sequences at user-defined lengths, heterozygosity) from NCBI dbSNP

  ncbi candidate tnf batch-mode snp gene