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).

• Recombination events restored the functional horned haplotypes in the offspring of polled parents.

  PMID 41174470 · PMC12579413 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 7 setups

  Has reproduction · 98

  In the Holstein-Friesian (HF) trio, the horned offspring arose from non-allelic homologous recombination in the gametes of the P_F/P_F sire.

  trio fleckvieh whole-genome snp pcr-based

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.

  gm12878 na12878 clinical whole-genome snv read-based

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

  PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups

  Has reproduction · 57

  About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.

  k562 hct116 subset chip-exo chip-seq western

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance.

  PMID 16168060 · PMC1249558 · BMC biotechnology · 2005 · 8 claims · 6 setups

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  Increased gDNA input into the MDA WGA reaction increases the proportion of double-stranded and human-specific PCR-amplifiable wgaDNA and improves genotyping performance.

  lymphoblastoid gdna ntc wgadna quantification displacement str

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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  Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

  viruses virus coli soluble large-scale bioinformatic recombinant

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

  Has reproduction · 59

  382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

  semibalanus individual rocky barnacles pool-seq sanger temperature

• The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

  PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

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  MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

  laser-capture-microdissected normal cancer fresh-frozen array gacgh laser

• Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

  PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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  WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

  wga non-amplified archived serum-derived snp purification whole-genome

• High resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Genetics of osteoarticular disorders, Florence, Italy, 22-23 February 2002.

  PMID 12223106 · PMC128940 · Arthritis research · 2002 · 8 claims · 8 setups

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  OP and OA are common, polygenic, multifactorial quantitative disorders influenced by both low-penetrance genetic variants and environmental factors

  patients twin families dutch association magnetic genome-wide

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

  PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

  hff mrc5 chip-qpcr rt-qpcr chipseq

• The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system.

  PMID 9579832 · PMC2150152 · British journal of cancer · 1998 · 5 claims · 6 setups

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  ARMS reliably detects K-ras codon 12/13 mutations in archival CRC DNA samples even when mutant sequence is under-represented relative to wild-type

  archival tumour tumour-derived haematoxylin arms direct pcr

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

  PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

  genomic anonymized dried pcr-restriction direct molecular

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species