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).

• Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

  PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

  aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr

• 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

• A novel POMT2 mutation causes mild congenital muscular dystrophy with normal brain MRI.

  PMID 18804929 · PMC2702532 · Brain & development · 2009 · 6 claims · 8 setups

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  A novel homozygous POMT2 mutation (c.604T>G, p.F202V) causes mild congenital muscular dystrophy with normal brain MRI

  skeletal genomic cos serum immunohistochemistry immunoblotting laminin

• Proteomics of human neurodegenerative diseases.

  PMID 18800015 · PMC2710115 · Journal of neuropathology and experimental neurology · 2008 · 8 claims · 8 setups

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  Proteomic techniques applied to autopsy brain and CSF from patients with neurodegenerative diseases provide insight into pathogenesis and enable biomarker discovery

  detergent-extractable thioflavin-s-stained tau-2-immunostained snca-immunoreactive 2-dimensional laser lc-ms-ms

• KCNQ4 mutations associated with nonsyndromic progressive sensorineural hearing loss.

  PMID 18797286 · PMC2743278 · Current opinion in otolaryngology & head and neck surgery · 2008 · 8 claims · 8 setups

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  KCNQ4 mutations at the DFNA2 locus on chromosome 1p34 cause autosomal dominant nonsyndromic progressive sensorineural hearing loss

  seven-generation dfna2 xenopus kcnq4 linkage mutation heterologous

• Prominent neuroleptic sensitivity in a case of early-onset Alzheimer disease due to presenilin-1 G206A mutation.

  PMID 18797263 · PMC4867177 · Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology · 2008 · 8 claims · 8 setups

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  A patient with the PS-1 G206A mutation developed prominent extrapyramidal signs (EPS) shortly after starting the atypical neuroleptic risperidone, which resolved completely after the drug was discontinued.

  cerebrospinal genomic brain blood elisa genetic apoe

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

  PMID 18795947 · PMC2585779 · The FEBS journal · 2008 · 8 claims · 8 setups

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  Two late acyltransferase genes, lpxX and lpxL, were identified in M. catarrhalis O35E by informatics analysis of the partial genome sequence

  lipid proteinase catarrhalis suspensions maldi-tof fatty sds-page

• The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

  PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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  P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

  sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net

• Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

  PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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  Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

  orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

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  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• 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

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  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

• The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

  PMID 18726985 · PMC2826114 · The Prostate · 2008 · 7 claims · 8 setups

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  Quercetin treatment of prostate cancer cells decreases cell proliferation and viability in a dose-dependent manner

  pc-3 excised prostate viability difference nano

• A novel mutation and phenotypes in phosphodiesterase 6 deficiency.

  PMID 18723146 · PMC2593460 · American journal of ophthalmology · 2008 · 8 claims · 8 setups

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  A high-throughput arRP genotyping microarray (APEX technology) combined with sequencing can efficiently identify disease-associated alleles across 17 arRP genes in RP patients

  blood-extracted family 8-member pde6-deficient arrp direct pedigree

• Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

  PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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  RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

  u937 saos-2 chip-chip chip-on-chip gene

• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

  PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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  A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

  jurkat computational immunoblotting structural protein-protein

• Endurance exercise as a countermeasure for aging.

  PMID 18716044 · PMC2570389 · Diabetes · 2008 · 8 claims · 8 setups

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  Reduced insulin sensitivity with age is likely related to adiposity and physical inactivity rather than being an inevitable consequence of aging.

  vastus mitochondria mitochondrial extracted euglycemic-hyperinsulinemic mitochondrial citrate

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

  PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups

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  Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors

  kidney proximal pbmcs macrophages gene qrt-pcr immunohistochemistry

• BRCA1 and BRCA2 mutation carriers in the Breast Cancer Family Registry: an open resource for collaborative research.

  PMID 18704680 · PMC2775077 · Breast cancer research and treatment · 2009 · 8 claims · 8 setups

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  The Breast Cancer Family Registry is an open resource for collaborative interdisciplinary and translational studies of the genetic epidemiology of breast cancer.

  breast california ashkenazi full two-dimensional denaturing