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).

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

  PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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  Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

  genomic commercial plco unrelated targeted long-range genotyping

• 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

• 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

• Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

  PMID 19644707 · PMC2778717 · Human genetics · 2009 · 7 claims · 5 setups

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  Resequencing of the 97-kb 10q11.2 region identified 241 novel polymorphisms not previously reported in dbSNP

  genomic plco hapmap computational targeted long-range genotype

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

  PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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  Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

  genomic postmortem nimhgi esr1 targeted case-control family-based

• Microdroplet-based PCR enrichment for large-scale targeted sequencing.

  PMID 19881494 · PMC2779736 · Nature biotechnology · 2009 · 7 claims · 5 setups

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  Microdroplet PCR enables massively parallel singleplex amplification (up to ~1.5 million reactions, up to 4,000 targets) for targeted sequencing enrichment

  genomic single targeted scale-up variant

• Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

  PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

  brain exon targeted principal

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Applying proteomics to the diagnosis and treatment of ALS and related diseases.

  PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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  Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

  csf spinal biofluid muscle 2d-dige antibody luminex

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• Metabolomics applied to diabetes research: moving from information to knowledge.

  PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups

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  Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status

  ins-1-derived pancreatic liver stedman 13c targeted ms-based

• 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

• AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

  PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

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  AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

  training kinase capillary targeted

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 99

  Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.

  coli lymphoblastoid na12878 mixture nanopore cas9-targeted whole-genome

• Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.

  PMID 33021470 · PMC7538157 · eLife · 2020 · 8 claims · 8 setups

  Has reproduction · 62

  Plasma AHR ligands derived from heme metabolism (biliverdin, bilirubin) and tryptophan/kynurenine pathway metabolites increase during acute Pc malaria in mice and acute cerebral malaria in humans

  c57bl pediatric littermate untargeted targeted bilirubin

• Proteomic solutions for analytical challenges associated with alcohol research.

  PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups

  Full-text index only

  Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.

  general complex plasma selected shotgun label-free targeted

• In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

  PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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  Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

  strains genomic celera blast-based targeted phred

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide