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).

• Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

  PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

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  Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

  k-562 targeted sanger

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

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  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

  PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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  MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

  acute mll lines bone ms-mlpa hhai methylation-specific

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• Human genome research in China.

  PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

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  China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

  genome chinese high-risk nb4 large-scale mutation positional

• Recurrent KRAS codon 146 mutations in human colorectal cancer.

  PMID 16969076 · PMC2714972 · Cancer biology & therapy · 2006 · 8 claims · 8 setups

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  KRAS A146 missense mutations are a recurrent, previously unrecognized class of somatic mutation in colorectal cancer

  colorectal sporadic familial cancer pcr direct chi-squared

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

  PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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  A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

  est acute 100-nt whole-genome est-based pcr-based secondary

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

  PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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  Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

  peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray

• Fingerprinting cancer development.

  PMID 14694892 · PMC1241638 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  Protein microarrays can detect phosphoprotein fingerprints that identify early-stage cancer or monitor drug toxicity.

  prostate blood model genes microarray proteomic gene