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).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: individual ✕ Assay: independent ✕ Clear

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

independent ceph same unrelated snp individual simulated
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

hela sirna secondary synthetic
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

real combined pre-mirna training random independent repeated
Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

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A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

fregene-simulated 80k-snp 480k 192k simulated null whole-genome
DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

PMID 31722211 · PMC6856714 · Cell reports · 2019 · 7 claims · 6 setups

Has reproduction · 50

The altered 3D genome of 2i-cultured ESCs (chromatin decompaction and loss of polycomb interactions at polycomb targets) is due to redistribution of polycomb away from its targets.

ring1b− e3.5 e14 3b3l fluorescence fish situ
Mutation analysis of the WT1 gene in myelodysplastic syndromes.

PMID 9765617 · PMC5921914 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 3 setups

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WT1 mutations are uncommon overall in MDS

bone pcr pcr-sscp subcloning direct
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

individually reference equimolar independently snp reference pooled
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
Backseat drivers take the wheel.

PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

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Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

pretreatment baf3 additional normal targeted baf3 immunoprecipitation
Challenges and standards in integrating surveys of structural variation.

PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

genomic hapmap reference independent comparative snp fosmid
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

Has reproduction · 98

Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

clinical dnaa isogenic h37rv genome-wide structural deep-sequencing
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

Has reproduction · 42

KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

small snps individual hg002 alignment-free kmer-based genotyping
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid

Experiments

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency.

Mutation analysis of the WT1 gene in myelodysplastic syndromes.

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

Backseat drivers take the wheel.

Challenges and standards in integrating surveys of structural variation.

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.