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).

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• Polymorphix: a sequence polymorphism database.

  PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.

  eukaryotic clustered consensus aligned sequence blast phylogenetic

• Reconstructing the evolution of the mitochondrial ribosomal proteome.

  PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.

  proteomes eukaryotic aligned alignments iterative hmm-based neighbor-joining

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

  PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

  fish full-length tetraodon rt-pcr database molecular

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Genome-wide diversity and selective pressure in the human rhinovirus.

  PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

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  Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

  diverse hrv fully hrva genome phylogenetic pairwise

• Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

  PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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  Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

  genbank hiv-1 protease integrase blastp phylogenetic amino

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

  PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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  Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

  orthologous hox concatenated intronic sliding comparative molecular

• Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

  PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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  The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

  clinical concatenated cereus isolates multilocus phylogenetic pcr

• Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

  PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

  metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species

• Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

  PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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  Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

  yeast familial human-mouse comparative gene mutation

• Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

  PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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  The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

  hadv-37 predicted select genome cpg global

• Identifying cis-regulatory sequences by word profile similarity.

  PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

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  WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

  stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq