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).

• Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion.

  PMID 14580259 · PMC314413 · Breast cancer research : BCR · 2003 · 7 claims · 4 setups

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  ER-negative cell clusters are far more likely than ER-positive clusters to overlie disrupted myoepithelial cell layers, both at the case level and the individual-disruption level

  paraffin selected microdissected double immunohistochemistry loss

• CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

  PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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  RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

  nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite

• Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

  PMID 15563733 · PMC544357 · BMC biotechnology · 2004 · 8 claims · 6 setups

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  A single-track sequencing (SSR) strategy on one PCR product can simultaneously address 24 genetic variants in the NAT1 gene using paired terminator tracks (A/G for coding region, A/T for 3' flanking region)

  genomic nat1 same pcr single-track single

• Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

  PMID 15528786 · PMC3839268 · Disease markers · 2004 · 8 claims · 5 setups

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  The Bethesda criteria, with a few modifications, are appropriate to identify families eligible for MMR mutation genetic testing

  colorectal endometrial microsatellite immunohistochemistry germline

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

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  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• Molecular analysis using DHPLC of cystic fibrosis: increase of the mutation detection rate among the affected population in Central Italy.

  PMID 15084222 · PMC419352 · BMC medical genetics · 2004 · 6 claims · 5 setups

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  DHPLC gene scanning of the CFTR gene increases the mutation detection rate compared to standard commercial mutation panel screening alone

  genomic pcr cftr inno-lipa pcr agarose

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.

  PMID 16351756 · PMC1866378 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  Meta-analysis of two independent BALB-neuT transcription profiling studies can identify new TAA candidates usable instead of or with Her2

  balb-neut normal breast probe microarray statistical enrichment

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

  PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

  normal aneuploid same genomiphi-amplified array-cgh

• Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.

  PMID 16212661 · PMC1282566 · BMC genetics · 2005 · 8 claims · 4 setups

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  The previously proposed P2-specific markers -551_-550insC and -160A>G do not correlate with P1/P2 phenotype, since they occur homozygously in many P1 individuals too

  genomic erythrocytes direct pcr pcr-asp

• Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

  PMID 15860768 · PMC1087789 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Selector oligonucleotides can circularize many distinct genomic restriction fragments in one reaction, enabling parallel amplification with a single universal primer pair instead of multiple target-specific primer pairs

  genomic 7776-clone selector-based cdna restriction

• A computational study of off-target effects of RNA interference.

  PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

  schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational

• Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

  PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 67

  Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

  cytoscape generated prior-knowledge iris software datarail logic

• Phylogenetic analysis of RhoGAP domain-containing proteins.

  PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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  RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

  rhogap aligned bayesian domain sequence maximum bayesian

• Novel integrative genomics strategies to identify genes for complex traits.

  PMID 16886998 · PMC2367618 · Animal genetics · 2006 · 8 claims · 7 setups

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  Forward genetics is restricted to genes harboring mutations, systematically missing network genes that causally influence disease without themselves being mutated.

  bxd mice bxh alox5 qtl knockout linkage

• Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

  PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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  NAT2 variants are homogeneously distributed across native populations of the American continent

  chromosomes same inferred american pcr statistical haplotype

• Disease-specific proteins from rheumatoid arthritis patients.

  PMID 16778393 · PMC2729955 · Journal of Korean medical science · 2006 · 8 claims · 6 setups

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  Fibronectin, semaphorin 7A precursor, growth factor receptor-bound protein 7 (GRB7), and immunoglobulin µ chain specifically associate with antibodies purified from RA synovial fluid

  synovium synovial synoviocytes western affinity antibody-affinity

• Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study.

  PMID 16672055 · PMC1468397 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  Molecular beacon-based real-time PCR assays for p.C282Y and p.H63D achieve complete genotype concordance with restriction enzyme digestion and direct sequencing

  genomic anonymized dried pcr-restriction direct molecular