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).

• Identification of serum biomarkers for colon cancer by proteomic analysis.

  PMID 16755300 · PMC2361335 · British journal of cancer · 2006 · 8 claims · 8 setups

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  Complement C3a des-arg, α1-antitrypsin and transferrin were identified as serum proteins with diagnostic potential for CRC.

  serum pooled seldi seldi-tof seldi artificial

• Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

  PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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  The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

  recombinant selenomethionine-substituted ge-gi models surface x-ray computational

• A clinical genetic method to identify mechanisms by which pain causes depression and anxiety.

  PMID 16623937 · PMC1488826 · Molecular pain · 2006 · 8 claims · 4 setups

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  Pain-triggered depression/anxiety are mediated by distinct spino-parabrachial-hypothalamic-amygdalar neurochemical pathways compared to mood disorders independent of pain

  sciatica genomic snp sf-36 candidate-gene exploratory

• Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

  PMID 16554551 · PMC1409816 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A cleavage-free mismatch oxidation assay using potassium permanganate and a standard UV/Vis microplate reader can detect DNA mismatches spectrophotometrically at 420 nm.

  individual hybridized 38mer pbr322 colorimetric uv-vis mismatch

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing

• Genetic requirement for pneumococcal ear infection.

  PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

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  STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

  pneumoniae bioluminescent balb signature-tagged bioluminescent transmission

• Emergence of recombinant forms of HIV: dynamics and scaling.

  PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

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  A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

  cd4+ scid-hu splenocytes computational single-round replication-competent proviral

• Improved weight management using genetic information to personalize a calorie controlled diet.

  PMID 17945020 · PMC2151062 · Nutrition journal · 2007 · 7 claims · 4 setups

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  Personalizing a weight-management diet using nutrigenetic test results improves long-term BMI reduction and weight loss maintenance compared to a standard diet.

  buccal patients serum genotyping case-control fasting

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

  PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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  MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

  genitalium clinical urine pairwise pcr serial

• Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

  PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

  genome synthetic c-kit87 c-kit genome-wide circular molecular

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

  PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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  Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

  pbmc his-tagged cem mammalian pcr electrophoretic western

• Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

  PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

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  Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

  hela post-mitotic pulsed fluorescence selective

• Contribution of oncoproteomics to cancer biomarker discovery.

  PMID 17407558 · PMC1852117 · Molecular cancer · 2007 · 6 claims · 8 setups

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  Oncoproteomic biomarker panels (2-DE/MS-based) show higher sensitivity and specificity than currently used single tumor markers across multiple cancer types (Table 1)

  serum bladder nipple colorectal 2-de isotope-coded immunoblotting

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Human neuronal cell protein responses to Nipah virus infection.

  PMID 17553172 · PMC1896155 · Virology journal · 2007 · 8 claims · 4 setups

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  NiV infection induces differential protein expression in SK-N-MC human neuronal cells detectable by 2D-PAGE

  sk-n-mc spots 2d-page maldi-tof tandem

• Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

  PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

  coli sds-page glutathione pepck-gst sds-page maldi-tof native

• Synergistic effects of the MTHFR C677T polymorphism and hypertension on spatial navigation.

  PMID 19013496 · PMC2685204 · Biological psychology · 2009 · 7 claims · 4 setups

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  Hypertensive carriers of the MTHFR 677T allele show significantly worse spatial navigation (longer distance to platform) than hypertensive C677C homozygotes

  healthy same buccal virtual blood mthfr