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).

• mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

  PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

  mitochondrial aligned compilation sequence multi-locus

• Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

  PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

  mandenka worldwide hapmap nat2 full snp analysis

• A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

  PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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  A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

  cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

  PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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  Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

  falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr

• 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

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  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

• Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

  PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

  Has reproduction · 45

  Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

  original sire-son whole-genome multi-sample graph-based

• 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

• Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

  PMID 16202172 · PMC1260020 · BMC medical genetics · 2005 · 8 claims · 3 setups

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  HA-1 allele and genotype frequencies were determined in 131 unrelated Italian subjects (HA-1H=0.43, HA-1R=0.57), consistent with Hardy-Weinberg equilibrium and prior North American Caucasian data.

  genomic sequence-specific direct melting

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

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

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

  vivax genome comparative microsatellite

• A novel nonsense mutation in CRYBB1 associated with autosomal dominant congenital cataract.

  PMID 18432316 · PMC2324115 · Molecular vision · 2008 · 7 claims · 5 setups

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  A novel heterozygous nonsense mutation (c.C737T, p.Q223X) in CRYBB1 is responsible for autosomal dominant congenital nuclear cataract in this family.

  three-generation genomic crybb1 family genotyping direct restriction

• 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

• Modeling the amplification dynamics of human Alu retrotransposons.

  PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

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  Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

  simulated genome population computer comparative population

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Comparative analysis of cancer genes in the human and chimpanzee genomes.

  PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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  All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

  chimpanzee non-human cancer comparative pcr targeted

• Novel CYP1B1 mutations in consanguineous Pakistani families with primary congenital glaucoma.

  PMID 18989382 · PMC2579935 · Molecular vision · 2008 · 7 claims · 6 setups

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  Missense mutations in CYP1B1 are most likely responsible for PCG in these three Pakistani families

  genomic family ethnically affected genotyping two-point sanger

• 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

• Continued colonization of the human genome by mitochondrial DNA.

  PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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  NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

  homo genomic chimpanzee genome genome-wide pcr sanger

• Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

  PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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  Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

  build chimpanzee unrelated ceph comparative three-color pcr

• Lineage specific recombination rates and microevolution in Listeria monocytogenes.

  PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Recombination is more prevalent in lineage II than in lineage I

  listeria allelic unique monocytogenes multilocus sawyer's genealogical