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).

• Human epigenome project--up and running.

  PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups

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  Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.

  expressed bat8 genetically methylation genome-wide phenotypic

• 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

• The role of medical structural genomics in discovering new drugs for infectious diseases.

  PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

  bacteria plasmodium candidate burkholderia high-throughput animal compound-target

• Toxicogenomics research consortium sails into uncharted waters.

  PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

  strains nervous mice liver microarray gene toxicogenomic

• New perspectives on an old disease: proteomics in cancer research.

  PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups

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  The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.

  plasma breast tumor genetically shotgun proteomics glycopeptide

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

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  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• A cell biological perspective on genome research.

  PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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  Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.

  saccharomyces caenorhabditis selected fruit genomic saturation physical

• 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