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).
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An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.
PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups
shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.
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A statistical change point model approach for the detection of DNA copy number variations in array CGH data.
PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups
A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.
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Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.
PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups
Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer
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Protein interaction networks by proteome peptide scanning.
PMID 14737190 · PMC314469 · PLoS biology · 2004 · 8 claims · 7 setups
WISE (combining phage display-derived relaxed consensus patterns with SPOT peptide synthesis arrays) can identify proteome-wide binding partners of a peptide-recognition domain
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BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).
PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups
oaCGH, not BAC CGH arrays, is the platform that will prevail in the future
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Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.
PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups
A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk
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Has reproduction · 83
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.
PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups
CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile
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Functional copy-number alterations in cancer.
PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups
RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.
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Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.
PMID 18276640 · PMC2346606 · Nucleic acids research · 2008 · 8 claims · 5 setups
Illumina HumanHap300 arrays are substantially more efficient than Affymetrix Genechip HindIII arrays for DNA-pooling based GWAS
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Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.
PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups
SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers
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A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.
PMID 19941644 · PMC2789744 · BMC bioinformatics · 2009 · 7 claims · 4 setups
Feature variability strongly influences breast cancer signature composition even when array platform and patient stratification are identical.
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Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.
PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups
TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA
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Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.
PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups
37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN
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Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.
PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups
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.
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Has reproduction · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.
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Translating genome sequences into biological understanding.
PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups
Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.