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).

• Designating eukaryotic orthology via processed transcription units.

  PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

  ortholog blat exon-intron blast-based

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• Computational verification of protein-protein interactions by orthologous co-expression.

  PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

  cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous

• Reference based annotation with GeneMapper.

  PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

  Full-text index only

  GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

  orthologous human-mouse chicken encode reference-based multi-species reciprocal

• Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.

  PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups

  Has reproduction · 38

  Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.

  diverse annotated same comparative enzyme trait

• Reconstruction of human protein interolog network using evolutionary conserved network.

  PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

  ppi sequences interaction predicted interolog orthology quasi-clique

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes

  melanogaster dgrp drosophila genes bulk locomotor gene

• DFAST and DAGA: web-based integrated genome annotation tools and resources.

  PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

  Has reproduction · 89

  DFAST is a web-based bacterial genome annotation and DDBJ submission pipeline with integrated CheckM quality assessment and ANI taxonomic assessment.

  lactobacillus genomes representative raw genome ortholog average

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

  PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

  Full-text index only

  QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

  chimpanzee prokaryotic promoters genome-wide cross-species

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

  PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

  human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

• Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

  PMID 18317809 · PMC2329726 · Molecular genetics and genomics : MGG · 2008 · 8 claims · 7 setups

  Full-text index only

  Strain 83972 is best described as a 'deconstructed pathogen' rather than a true commensal that acquired fitness properties

  coli microarrays microarray comparative processing

• Comparative genomic analysis of three Leishmania species that cause diverse human disease.

  PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

  infantum major braziliensis leishmania whole-genome comparative pcr

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups

  Has reproduction · 87

  A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).

  euglena gracilis five transcriptomes bulk novo transcriptome

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

  PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

  Full-text index only

  The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

  coli se11 rapd whole-genome gene

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read