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).

• Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

  PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

  Full-text index only

  NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

  glioblastoma gbm matched sequenced copy gene methylation

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

  PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

  Full-text index only

  Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

  ftld grn genomic post-mortem clinical volumetric direct

• Survey of transcripts in the adult Drosophila brain.

  PMID 11276425 · PMC30707 · Genome biology · 2001 · 8 claims · 4 setups

  Full-text index only

  The adult Drosophila brain cDNA library contains approximately 6.75 million independent clones

  drosophila randomly brain cdna reverse sequence

• Allele quantification using molecular inversion probes (MIP).

  PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

  reference ffpe lines na18573 mip restriction quantitative

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

  Full-text index only

  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• Microproteomics: analysis of protein diversity in small samples.

  PMID 18271009 · PMC2743962 · Mass spectrometry reviews · 2008 · 8 claims · 8 setups

  Full-text index only

  Changes in gene/mRNA expression often do not correlate well with changes in protein expression, due to precursor cleavage, post-translational modification, localization, and variable protein lifetimes.

  lcm-dissected single few dense gel maldi capillary

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

  PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

  genomic postmortem nimhgi esr1 targeted case-control family-based

• Individual and additive effects of the CNR1 and FAAH genes on brain response to marijuana cues.

  PMID 20010552 · PMC2820137 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2010 · 6 claims · 4 setups

  Full-text index only

  Carriers of the CNR1 rs2023239 G allele show significantly greater neural activation to marijuana cues than A/A homozygotes in reward-related regions (OFC, IFG, insula, ACG).

  three-day-abstinent marijuana buccal fmri genotyping

• Ontological Discovery Environment: a system for integrating gene-phenotype associations.

  PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

  strains integrated bipartite phish gene differential pairwise

• Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin.

  PMID 16122393 · PMC1215486 · BMC neuroscience · 2005 · 8 claims · 8 setups

  Has reproduction

  Plexin B3 strongly and plexin B2 moderately stimulate neurite outgrowth of primary murine cerebellar neurons

  cos-7 cerebellar nih-3t3 yeast northern western situ

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

  PMID 18829386 · PMC2730674 · International journal of medical microbiology : IJMM · 2009 · 6 claims · 7 setups

  Full-text index only

  C. pneumoniae was cultured from two late-onset AD brain tissue samples (Tor-1 from hippocampus, Phi-1 from temporal cortex) from different North American regions.

  tor-1 brain hep-2 pcr culture immunofluorescence

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• An integrated genomic analysis of human glioblastoma multiforme.

  PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

  Full-text index only

  IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

  gbm additional missense exome targeted snp

• Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

  PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

  Full-text index only

  2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

  sporadic wilms fetal 293t loh multiplex genome-wide

• Neuroplasticity, psychosocial genomics, and the biopsychosocial paradigm in the 21st century.

  PMID 19728478 · PMC2933650 · Health & social work · 2009 · 8 claims · 8 setups

  Full-text index only

  Recent neuroplasticity and psychosocial genomics research validates and elaborates Engel's biopsychosocial paradigm by revealing mechanisms linking psychosocial experience to neurobiology.

  experienced long-term ocd women structural eeg attentional