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).

• Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

  PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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  wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

  serum colon glioblastoma synthetic seldi-tof gene computational

• GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

  PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 96

  gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

  avian comparative correlation robustness

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

  PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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  Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

  deposit excised pooled worn sds-page in-gel lc-ms-ms

• Proteomic view of mitochondrial function.

  PMID 18331620 · PMC2374722 · Genome biology · 2008 · 8 claims · 8 setups

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  Most modulators of basal mitochondrial function identified in the Drosophila RNAi screen are located outside the mitochondrion, since only 17 of 152 hits had a clear mitochondrial function.

  drosophila saccharomyces caenorhabditis yeast genome-wide phenotypic morphology

• Proteomic approaches for studying alcoholism and alcohol-induced organ damage.

  PMID 23584750 · PMC3860448 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 7 setups

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  Chronic alcohol abuse produces persistent changes in brain function (tolerance, dependence, craving) likely resulting from alterations in gene and protein expression

  extracts trypsin-digested more yeast two-dimensional liquid mudpit

• Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

  PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

  probe-modified probe-gnp synthetic four uv-vis ssdna pcr

• Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.

  PMID 17537823 · PMC1919476 · Nucleic acids research · 2007 · 6 claims · 8 setups

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  Endogenous nuclear pre-mRNA processing complexes (supraspliceosomes) were purified at preparative scale from human HeLa cells and chicken DT40 pre-B cells for compositional analysis

  hela chicken supraspliceosome extracts glycerol tandem mass

• Tubulin proteomics: towards breaking the code.

  PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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  Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

  bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page

• Crunching the bio-numbers.

  PMID 14664241 · PMC1316909 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The eTag Assay System rapidly identifies genes and related proteins without complex sample preparation or follow-up bioinformatics, unlike microarrays

  blood model brain lung etag sirna addl

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

  PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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  PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

  porcine paec umbilical huvec methyltransferase sds-page fragmentation

• Applying proteomics to the diagnosis and treatment of ALS and related diseases.

  PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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  Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

  csf spinal biofluid muscle 2d-dige antibody luminex