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).

Publications 1.3k Datasets 392.5k Experiments 30

System / cell line: across ✕ Assay: nonsynonymous ✕ Clear

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

patients unaffected sanger restriction
Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.

PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups

Has reproduction · 80

α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination

rhizobium core same site intragenic nucleotide
Genomics--from Neanderthals to high-throughput sequencing.

PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

bacterial ion-channel drosophila arrays next-generation pooled multiplex
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
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
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
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

tuberculosis putative orthologous genomewide blastp clustal nei-gojobori
A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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Expression context is largely conserved between orthologs across four eukaryote species.

elegans pairwise orthologs cerevisiae microarray ortholog functional
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
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
Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

unique hmpv sequence neighbor-joining codon
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Exome sequencing identifies the cause of a mendelian disorder.

PMID 19915526 · PMC2847889 · Nature genetics · 2010 · 8 claims · 7 setups

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Exome sequencing of a small number of unrelated affected individuals, combined with filtering against public SNP databases and HapMap exomes, is sufficient to identify the causal gene for a monogenic disorder of unknown etiology.

patients chromosomes dhodh utero exome directed sanger
Evolutionary history of the UCP gene family: gene duplication and selection.

PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

vertebrate ucp human-mouse ucp1 sequence phylogenetic gene
Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression.

PMID 18769357 · PMC3071283 · Journal of acquired immune deficiency syndromes (1999) · 2008 · 7 claims · 6 setups

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HIV coinfection is associated with ~0.5 log10 higher HCV RNA levels, suggesting increased HCV replication

chronically paired aligned hiv-infected direct genetic sliding-window
Targeted capture and massively parallel sequencing of 12 human exomes.

PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

hapmap unrelated na18507 randomly targeted array-based molecular
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

Experiments

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.

Genomics--from Neanderthals to high-throughput sequencing.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Patterns of evolutionary constraints on genes in humans.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

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

Distribution and effects of nonsense polymorphisms in human genes.

Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

Identification and characterization of insect-specific proteins by genome data analysis.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

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.

Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Exome sequencing identifies the cause of a mendelian disorder.

Evolutionary history of the UCP gene family: gene duplication and selection.

Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression.

Targeted capture and massively parallel sequencing of 12 human exomes.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.