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).

• Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

  PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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  PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

  colon gbm cancer dbtrg array pcr colony

• Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

  PMID 18939861 · PMC2669493 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  IEF provides superior reproducibility and resolution of peptide fractionation compared to SCX, for both large (100 µg) and small (10 µg) protein inputs

  rko rectal bovine shotgun comparative ief

• H-DBAS: human-transcriptome database for alternative splicing: update 2010.

  PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

  dld-1 rna-seq western real-time

• Characterisation and protein expression profiling of annexins in colorectal cancer.

  PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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  Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

  dukes colorectal immunised whole-cell gel immunohistochemistry elisa

• Managing incidental findings in human subjects research: analysis and recommendations.

  PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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  Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

  affected large research consent linkage genomic structural

• Divide and conquer: progress in the molecular stratification of cancer.

  PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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  Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

  breast nsclc colon early-stage immunohistochemistry gene comparative

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

  PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

  normal dld1 beas2b ramos tss comparative

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated