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).

• Evolutionary algorithms for the selection of single nucleotide polymorphisms.

  PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).

  simulated mhc evolutionary multiobjective

• 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

• Improvements to cardiovascular gene ontology.

  PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.

  coronary phospholamban mammalian lines gene expression large-scale

• Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene.

  PMID 11953843 · PMC2364178 · British journal of cancer · 2002 · 7 claims · 5 setups

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  Heterozygosity for the IVS14+1G>A DPYD splice-site mutation is associated with markedly reduced 5-FU clearance and severe 5-FU toxicity in the index patient.

  plasma peripheral pbm genomic reversed-phase pharmacokinetic dpd

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• Differential analysis for high density tiling microarray data.

  PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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  gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

  hl60 profiling chip-on-chip

• Characterization of genome-wide p53-binding sites upon stress response.

  PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

  u2os saos-2 chip-on-chip chip-qpcr western

• Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

  PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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  Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

  genomic pools training siddt individual pooled k-correction

• 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

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• Lamin C is required to establish genome organization after mitosis.

  PMID 34775987 · PMC8591896 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 76

  Lamin C, and not lamin A or lamin B1, is required for LAD:LAD cohesion, retention of LADs near the nuclear envelope, and overall chromosome territory organization.

  embryonic mefs clonal western growth damid-seq

• Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

  PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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  Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

  a549 nsclc expansion wst-1 flow

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

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  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative

• Personalized medicine: the future is not what it used to be.

  PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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  Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

  sw13 h295r drosophila acc drug synthetic gene

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

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  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular