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).

• Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

  PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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  High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

  canine osteosarcoma independent third oligonucleotide cross-species quantitative

• MTHFR 677C>T and ACE D/I polymorphisms in migraine: a systematic review and meta-analysis.

  PMID 19925624 · PMC3071567 · Headache · 2010 · 6 claims · 3 setups

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  The MTHFR 677TT genotype is associated with increased risk of migraine with aura but not migraine without aura

  migraineurs pooled genotyping meta-analysis

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Methods for proteomic analysis of transcription factors.

  PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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  Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

  nuclear crude intact partially emsa southwestern systematic

• Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

  PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

  Has reproduction · 92

  Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

  post-mortem adra immunohistochemistry protein-protein pathway

• Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.

  PMID 16261191 · PMC1246807 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  A comprehensive stoichiometric model of the MAP was built comprising 197 metabolites, 219 reactions, and 28 proteins

  stoichiometric map tuberculosis flux systematic drug

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

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  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• Addressing the age-old question of old age.

  PMID 15287970 · PMC507873 · Genome biology · 2004 · 8 claims · 6 setups

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  Dietary restriction and reduced temperature extend Drosophila lifespan via intrinsically different demographic mechanisms: dietary restriction lowers intrinsic frailty, while lower temperature reduces the rate of senescence.

  drosophila populations australian centenarians demographic historical peptide

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• Population carrier frequency of hMSH2 and hMLH1 mutations.

  PMID 11104559 · PMC2363440 · British journal of cancer · 2000 · 6 claims · 6 setups

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  Population carrier frequency of hMSH2/hMLH1 mutations in people aged 15-74 years is estimated at 1:3139 (95% CI 1:1247-1:7626)

  peripheral scottish finnish baltimore cdna pedigree systematic

• Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

  PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

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  A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

  modeled analytic factorial power

• Relation of candidate genes that encode for endothelial function to migraine and stroke: the Stroke Prevention in Young Women study.

  PMID 19661472 · PMC2753702 · Stroke · 2009 · 8 claims · 6 setups

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  EDN SNP rs1800542 is associated with increased ischemic stroke risk in Caucasian women

  international spyw candidate haplotype population

• Public health genomics approach to type 2 diabetes.

  PMID 18971439 · PMC2570384 · Diabetes · 2008 · 7 claims · 3 setups

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  Combining GWAS-discovered genetic variants provides only weak predictive ability for type 2 diabetes and adds little beyond established clinical risk factors (age, sex, BMI).

  population-based white genetic genotyping systematic

• The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

  PMID 17145711 · PMC1751528 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  GermOnline is a cross-species systems browser providing comprehensive curated information on genes and gene products relevant for sexual reproduction across nine model organisms including human.

  saccharomyces mus rodent classical tiling comparative

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript