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).

• 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

• Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

  PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

  disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

  PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

  Full-text index only

  P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

  vivax genome comparative microsatellite

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

  Full-text index only

  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

  Full-text index only

  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

  PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

  Full-text index only

  MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

  trachomatis pneumoniae chlamydiales mlst eburst upgma

• The gentle art of gene arrangement: the meaning of gene clusters.

  PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

  Full-text index only

  Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

  populations mhc interphase cartilaginous sequence codon comparative

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

  PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

  Full-text index only

  The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

  healthy mrp1 population novo population functional

• Increased constraints on MC4R during primate and human evolution.

  PMID 19011902 · PMC9947067 · Human genetics · 2009 · 6 claims · 7 setups

  Full-text index only

  There is a significant paucity of genetic diversity at MC4R in humans but not in chimpanzees.

  hgdp-ceph germans central additional dhplc direct coding

• Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.

  PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups

  Has reproduction · 84

  Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).

  pseudomonas filamentous axenically semi-continuous morphometric whole-genome

• Getting positive about selection.

  PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

  Full-text index only

  Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

  genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood

• SARS-CoV genome polymorphism: a bioinformatics study.

  PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

  Full-text index only

  SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

  sars-cov annotated spike whole-genome positional codon

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

  Full-text index only

  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

  PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

  cynomolgus 3-year-old macaque est full-insert oligonucleotide