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).

• Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

  PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping

  pooled single same caucasian snp individual quantification

• Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study.

  PMID 19963597 · PMC2928997 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 6 claims · 4 setups

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  Developed an imaging genomic browsing system allowing whole genome and entire brain analyses via visual exploration

  mci same voxel-based snp genotype

• Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

  PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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  SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

  independent ceph same unrelated snp individual simulated

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

  PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

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  This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

  acropora millepora coral snp genetic segregation

• A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

  PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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  SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

  teds diagnosed ceph snp individual transmission

• Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

  PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

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  Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

  case hapmap snp individual allele

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• 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

• Twin peaks: the draft human genome sequence.

  PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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  The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

  genome genomic genes yeast whole-genome bac computational

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.

  PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups

  Has reproduction · 44

  Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data

  xylophilus snp smrt short-read bionano

• A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

  PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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  SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

  bac kidney genomic marathon genomic cdna pcr

• DNA sequence and analysis of human chromosome 9.

  PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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  The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

  bac chromosome fibres chimpanzee clone-based restriction computational

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

  PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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  CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

  treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf