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 biofilm-associated cluster (bac) in Pseudomonas aeruginosa involved in biofilm formation and virulence.

  PMID 19065261 · PMC2587700 · PloS one · 2008 · 8 claims · 8 setups

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  A ΔpA3731 mutant is highly biofilm-defective on abiotic (polystyrene) and biotic (A549 pneumocyte) surfaces compared with wild-type PAO1

  aeruginosa a549 lung crystal biofilm adhesion

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

  PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

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  Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

  mnt-1 melanocyte melanocytes genome-wide secondary quantitative

• Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample.

  PMID 19052543 · PMC2879626 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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  The interaction between SNP3^G+ genotypes and SNP8^T/T genotype significantly increases risk for cocaine dependence in EA family and EA case-control samples.

  family case-control pooled unrelated snp family-based case-control

• The genomic analysis of lactic acidosis and acidosis response in human cancers.

  PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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  Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

  mammary hmec gene breast gene real-time bayesian

• In-frame deletion in the seventh immunoglobulin-like repeat of filamin C in a family with myofibrillar myopathy.

  PMID 19050726 · PMC2672961 · European journal of human genetics : EJHG · 2009 · 8 claims · 8 setups

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  A 12-nucleotide deletion (c.2997_3008del) in FLNC exon 18, predicting an in-frame four-residue deletion (p.Val930_Thr933del) in the seventh Ig-like repeat of filamin C, was identified in a German family with MFM (mother and daughter).

  genomic muscle skeletal direct topo genescan

• Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

  PMID 19028587 · PMC2686088 · Journal of structural biology · 2009 · 8 claims · 8 setups

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  Nucleotide-bound (ADP and ANP/AMP-PNP) Mer kinase domain adopts an autoinhibited DFG-Asp-in/αC-Glu-out conformation with an activation-loop residue inserted into the active site

  recombinant phosphorylated mer x-ray positional differential

• Gene-environment interaction and obesity.

  PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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  Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

  framingham european individuals healthy genome-wide candidate gene-diet

• Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.

  PMID 19015641 · PMC2633425 · Oncogene · 2009 · 8 claims · 8 setups

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  E884K works in concert with L858R in-cis, in a dominant fashion, to differentially alter EGFR downstream signaling and inhibitor sensitivity in an inhibitor-specific manner

  cos-7 kinase japanese western cellular mts

• Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

  PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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  IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

  saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• Proteomic analysis of RCL2 paraffin-embedded tissues.

  PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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  RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols

  normal rcl2p ffpe frozen yield 1-dimensional 2-dimensional

• Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

  PMID 19011694 · PMC2582945 · PloS one · 2008 · 8 claims · 8 setups

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  A 16-microRNA signature (9 up, 7 down) distinguishes osteoarthritic from normal cartilage.

  patient-derived normal integrated taqman qrt-pcr northern

• Profiling human androgen receptor mutations reveals treatment effects in a mouse model of prostate cancer.

  PMID 19010817 · PMC2748651 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Somatic AR mutations in h/mAR-TRAMP tumors are non-random and their genomic location correlates with treatment type (castration/antiandrogen vs intact).

  mar-tramp testis cv-1 ar-negative immunohistochemistry serum survival

• Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

  PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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  Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

  serous same lmp braf-mutant gene hotspot erbb2

• Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

  PMID 18997096 · PMC4836613 · Investigative ophthalmology & visual science · 2009 · 7 claims · 8 setups

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  High T8993C mutant load (>77%) is associated with severe neurologic and/or retinal abnormalities, while low mutant load (42-54%) causes no detectable abnormalities.

  retina blood visual adaptive real-time genetic

• Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

  PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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  A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

  saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• The diploid genome sequence of an Asian individual.

  PMID 18987735 · PMC2716080 · Nature · 2008 · 8 claims · 8 setups

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  First diploid genome sequence of an Asian (Han Chinese) individual generated using massively parallel Illumina sequencing

  han donor genome genomic whole-genome g-banded snp