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).

• 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

• A comprehensive catalogue of somatic mutations from a human cancer genome.

  PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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  Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

  colo-829 additional whole-genome conventional pcr

• Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

  PMID 18648550 · PMC2481298 · PloS one · 2008 · 7 claims · 4 setups

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  Influenza A(H3N2) seasonality is largely explained by global viral migration, with similar viruses appearing in different countries at different times

  influenza same hong gene maximum-likelihood protein-coding

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

  PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

  cell-cycle-synchronized hela computational differentially tiling cdna statistical

• A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

  PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

  genomic same synthetic invader pyrosequencing hplc

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

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  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• Randomised trial of a decision aid and its timing for women being tested for a BRCA1/2 mutation.

  PMID 14735173 · PMC2410151 · British journal of cancer · 2004 · 6 claims · 3 setups

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  The DA had no impact on well-being (anxiety, depression, cancer-related distress, general health)

  women brca1 same randomised comparative validated

• Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.

  PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B

  sonnei same shigella assembled illumina oxford novo

• Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

  PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 92

  cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

  jejuni same subset isolate cgmlst hqsnp genome

• ATM variants and cancer risk in breast cancer patients from Southern Finland.

  PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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  Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

  familial brca1 same genotype genotyping denaturing direct

• A clinical genetic method to identify mechanisms by which pain causes depression and anxiety.

  PMID 16623937 · PMC1488826 · Molecular pain · 2006 · 8 claims · 4 setups

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  Pain-triggered depression/anxiety are mediated by distinct spino-parabrachial-hypothalamic-amygdalar neurochemical pathways compared to mood disorders independent of pain

  sciatica genomic snp sf-36 candidate-gene exploratory

• A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

  PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

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  A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

  peripheral pedigree nuclear family snp two-point multipoint

• CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

  PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

  Has reproduction · 97

  CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

  simulated wgs reference same novo blast-based k-mer

• Calibration-free NGS quantitation of mutations below 0.01% VAF.

  PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 96

  QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

  h37rv repository healthy same single-plex 10-plex 22-plex

• 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

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal

• High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

  PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

  single bac amplified pi-scei array quantitative dot