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).
-
Full-text index only
SIGMA: a system for integrative genomic microarray analysis of cancer genomes.
PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups
SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.
-
Full-text index only
Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.
PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups
Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting
-
Full-text index only
Comparing whole genomes using DNA microarrays.
PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups
DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.
-
Full-text index only
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
MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.
-
Full-text index only
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.
PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups
Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature
-
Has reproduction · 90
Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.
PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 6 setups
Commercially available bovine arrays are ineffective at capturing variants segregating among African indicine animals, with only 6% of high-LD (r2>0.8) variants captured by the best arrays versus 17% in African taurine and 25% in European taurine.
-
Full-text index only
High resolution array-CGH analysis of single cells.
PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups
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.
-
Full-text index only
Current and future directions in genomics of amyotrophic lateral sclerosis.
PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups
Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations
-
Full-text index only
Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.
PMID 18397339 · PMC2659379 · Brain pathology (Zurich, Switzerland) · 2008 · 8 claims · 2 setups
Whole-genome aCGH reveals chromosomal copy number abnormalities in 5 of 12 (42%) subependymoma cases
-
Full-text index only
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
WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays
-
Full-text index only
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups
Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts
-
Full-text index only
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.
PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups
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
-
Has reproduction · 98
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
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.
-
Full-text index only
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups
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.
-
Full-text index only
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.
PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups
WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.
-
Full-text index only
Kinetoplastid genomics: the thin end of the wedge.
PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups
Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.
-
Full-text index only
Personalized copy number and segmental duplication maps using next-generation sequencing.
PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups
mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.
-
Full-text index only
Recurring mutations found by sequencing an acute myeloid leukemia genome.
PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups
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.
-
Full-text index only
Accurate whole human genome sequencing using reversible terminator chemistry.
PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups
A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.
-
Has reproduction · 30
Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.
PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups
Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.