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).

• Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

  PMID 34599324 · PMC8557840 · Genome biology and evolution · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  The divergence of the MT+ and MT- alleles predates speciation events within the Ostreococcus genus

  mamiellales ostreococcus tauri shared comparative orthology synteny

• A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• 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

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• Long-range regulation is a major driving force in maintaining genome integrity.

  PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

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  Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

  opossum genome comparative identification statistical

• 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

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• 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

• Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.

  PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups

  Has reproduction · 84

  Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.

  solanum bulk term novo

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

  PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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  MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

  mip diagnostic is900-specific pgg

• The Origin at 150: is a new evolutionary synthesis in sight?

  PMID 19836100 · PMC2784144 · Trends in genetics : TIG · 2009 · 8 claims · 4 setups

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  The Modern Synthesis (neo-Darwinism) has crumbled and its central tenets are overturned or radically revised in the post-genomic era

  cellular hundreds organisms genes rrna comparative

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

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

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  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

• Widespread ultraconservation divergence in primates.

  PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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  The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

  hg18 genome genes computed comparative snp gene

• In silico meets in vivo.

  PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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  About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

  genome lines prokaryotic genomes genome genome-wide gene

• Web-based resources for comparative genomics.

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

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  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