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).

• Type 1 diabetes in the Spanish population: additional factors to class II HLA-DR3 and -DR4.

  PMID 15842729 · PMC1097726 · BMC genomics · 2005 · 7 claims · 4 setups

  Full-text index only

  The ancestral haplotype AH 18.2 (DR3-TNFa1b5) confers significantly increased T1D risk compared to other DR3-positive haplotypes in the Spanish population.

  blood same genotype hla microsatellite haplotype

• Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

  PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

  tumor each rna-seq whole-genome targeted pcr-based

• Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

  PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

  Full-text index only

  Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

  swissprot nssnp-containing nssnps machine single-attribute sequence

• Inconsistencies in Neanderthal genomic DNA sequences.

  PMID 17937503 · PMC2014787 · PLoS genetics · 2007 · 8 claims · 6 setups

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  The Noonan et al. and Green et al. Neanderthal nuclear DNA datasets yield mutually inconsistent estimates of population split time and Neanderthal admixture proportion when analyzed with the same method

  neanderthal green neanderthal-specific population-genetic fragment-length-stratified hapmap

• Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

  PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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  EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

  microdissected formalin-fixed archival clinical pcr fluorescence laser

• Proteomic profiling of the amniotic fluid to detect inflammation, infection, and neonatal sepsis.

  PMID 17227133 · PMC1769412 · PLoS medicine · 2007 · 8 claims · 8 setups

  Full-text index only

  Higher MR scores (severe, 3-4) are associated with significantly shorter amniocentesis-to-delivery intervals than minimal (1-2) or no (0) inflammation

  amniotic placental blood seldi-tof elisa clinical

• Epidermal growth factor receptor abnormalities in the pathogenesis and progression of lung adenocarcinomas.

  PMID 19138956 · PMC3369271 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 4 setups

  Full-text index only

  EGFR mutations and protein overexpression are early phenomena in the pathogenesis of lung adenocarcinoma, occurring in histologically normal bronchial/bronchiolar epithelium (NBE)

  lung microdissection fluorescence immunohistochemistry

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

  Full-text index only

  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc

• Genetic divergence of hepatitis C virus: the role of HIV-related immunosuppression.

  PMID 18769357 · PMC3071283 · Journal of acquired immune deficiency syndromes (1999) · 2008 · 7 claims · 6 setups

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  HIV coinfection is associated with ~0.5 log10 higher HCV RNA levels, suggesting increased HCV replication

  chronically paired aligned hiv-infected direct genetic sliding-window

• Systems genetics of alcoholism.

  PMID 23584748 · PMC3860445 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 8 setups

  Full-text index only

  Alcoholism is a multifactorial disease driven by interacting genetic, social, and environmental factors, with genetics accounting for 50-60% of risk.

  families drosophila mice han linkage metabolic gene

• A biomarker panel for peripheral arterial disease.

  PMID 18687758 · PMC3133945 · Vascular medicine (London, England) · 2008 · 7 claims · 6 setups

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  β2-microglobulin (β2M) and cystatin C had the highest correlation with ABI among all plasma markers tested, higher than age, smoking, or diabetes status

  plasma fasting subjects biomarker nephelometric clinical ankle-brachial

• Neurofibrillary tau pathology modulated by genetic variation of alpha-synuclein.

  PMID 18661559 · PMC8957216 · Annals of neurology · 2008 · 7 claims · 5 setups

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  The SNCA intron 4 marker rs2572324 is associated with the extent of neurofibrillary tangle (Braak stage) pathology.

  postmortem whole-genome-amplified vantaa85+ neuropathological immunohistochemistry snp

• Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

  PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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  An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

  plasma discretized seldi-tof serum logical

• Improving melanoma classification by integrating genetic and morphologic features.

  PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

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  BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

  archival same subset patients histopathological mutation quantitative

• Pathways to injury in chronic pancreatitis: decoding the role of the high-risk SPINK1 N34S haplotype using meta-analysis.

  PMID 18414673 · PMC2289874 · PloS one · 2008 · 6 claims · 7 setups

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  SPINK1 N34S is strongly associated with chronic pancreatitis overall

  chronic alcoholic idiopathic tropical meta-analysis genotyping publication

• PIK3CA-activating mutations and chemotherapy sensitivity in stage II-III breast cancer.

  PMID 18371219 · PMC2397526 · Breast cancer research : BCR · 2008 · 7 claims · 4 setups

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  PIK3CA mutations are not associated with altered sensitivity to preoperative anthracycline-based or taxane-based chemotherapy in ER-positive and ER-negative breast tumors

  tumor breast stage direct immunohistochemistry fluorescence

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

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  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

• Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

  PMID 18212765 · PMC7116808 · Nature clinical practice. Endocrinology & metabolism · 2008 · 8 claims · 8 setups

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  Six high-density genome-wide association studies in over 19,000 individuals identified approximately ten T2D-susceptibility loci, including HHEX, IDE, SLC30A8, FTO, CDKAL1, CDKN2A/CDKN2B, and IGF2BP2.

  t2d icelandic population tcf7l2 genome-wide linkage candidate-gene

• Associations between polycyclic aromatic hydrocarbon-related exposures and p53 mutations in breast tumors.

  PMID 20064791 · PMC2854728 · Environmental health perspectives · 2010 · 8 claims · 5 setups

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  PAH-related exposures are associated with breast cancer differently according to tumor p53 mutation status, type, effect, and number

  archived breast peripheral study surveyor immunohistochemistry competitive