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).

• Chipping away at 'stemness'.

  PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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  Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

  microarray sage custom

• Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

  PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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  Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

  pools individual same parental pooled individual test-retest

• A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.

  PMID 41031900 · PMC13131251 · Journal of sleep research · 2026 · 7 claims · 6 setups

  Has reproduction · 96

  Meta-analysis of 18 SD-vs-control contrasts identified 182 genes differentially expressed in the murine cortex in response to sleep deprivation (FDR < 0.05).

  c57bl full genes meta-analysis affymetrix rna-seq random-effects

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.

  PMID 18208605 · PMC2265264 · BMC bioinformatics · 2008 · 8 claims · 1 setups

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  SignS is a web-based tool and R package implementing four gene-selection/signature-building methods for survival data (Dave et al., Gui and Li, random forests with conditional inference trees, and boosting with component-wise Cox models).

  microarray gene-by-gene

• 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

• Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

  PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups

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  Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA

  pooled pool snps snp snapshot individual

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Sources of variability and effect of experimental approach on expression profiling data interpretation.

  PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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  Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

  skeletal muscle spleen myogenic affymetrix duplicate unsupervised

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• MatchMiner: a tool for batch navigation among gene and gene product identifiers.

  PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

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  MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

  nci-60 fish-mapped random batch fish-mapped cross-validation

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• EGASP: Introduction.

  PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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  Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

  genome computational manual rt-pcr

• The UCSC Genome Browser Database: 2008 update.

  PMID 18086701 · PMC2238835 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes.

  zebrafish yale vertebrate non-human sage expression snp

• Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

  PMID 17542650 · PMC1885280 · PLoS genetics · 2007 · 8 claims · 7 setups

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  H3me3K9 and H3me3K27 mark largely mutually exclusive, distinct classes of transcription factor genes: H3me3K9 at ZNF genes, H3me3K27 at homeobox genes

  ntera2 fibroblasts chip-chip chip-pcr expression

• Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

  PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

  genome transcripts tissues proteins comparative taf250 cpg