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).

• 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

• Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

  PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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  IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

  wtccc replication population cases genome-wide taqman snp

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• 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

• TAC3 and TACR3 mutations in familial hypogonadotropic hypogonadism reveal a key role for Neurokinin B in the central control of reproduction.

  PMID 19079066 · PMC4312696 · Nature genetics · 2009 · 8 claims · 5 setups

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  Homozygous loss-of-function mutations in TAC3 or TACR3 cause congenital hypogonadotropic hypogonadism in four consanguineous families

  consanguineous genomic hek293a hek293 genome sanger calcium

• Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

  PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

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  PITX1 polymorphisms and haplotypes are significantly associated with autism

  agre pitx1 parental family-based extended haplotype

• 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

• 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

• Recurring mutations found by sequencing an acute myeloid leukemia genome.

  PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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  Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

  aml-m1 tumor bone additional whole-genome snp gene-expression

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

  PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

  sporadic wilms fetal 293t loh multiplex genome-wide

• 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

• 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

• An integrated genomic analysis of human glioblastoma multiforme.

  PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

  gbm additional missense exome targeted snp

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• 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

• 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

• Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

  PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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  Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

  family additional unrelated mutant direct linkage targeted

• Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle.

  PMID 18836565 · PMC2556974 · Molecular vision · 2008 · 8 claims · 5 setups

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  Haplotype association analysis refines the BCSE-linked region on BTA18 to a 6.82 Mb interval spanning 56.05–62.87 Mb

  eye genomic tnnt1 cdna genomic snp