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).
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Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.
PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups
An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.
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F-SNP: computationally predicted functional SNPs for disease association studies.
PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups
F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation
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Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.
PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups
Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions
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Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.
PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups
None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.
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Genome-wide survey of allele-specific splicing in humans.
PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups
A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)
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SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.
PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups
SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools
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An optimized procedure for the design and evaluation of Ecotilling assays.
PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups
An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays
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PigGIS: Pig Genomic Informatics System.
PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups
PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons
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Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.
PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups
A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.
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Widespread ultraconservation divergence in primates.
PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups
The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.
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Has reproduction · 66
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.
PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups
HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.
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Functional analysis of novel SNPs and mutations in human and mouse genomes.
PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups
FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.
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A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups
A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types
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Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.
PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups
TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA
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Mutation analysis of the MSMB gene in familial prostate cancer.
PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups
No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases
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G2Cdb: the Genes to Cognition database.
PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups
G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.