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).

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

  PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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  NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

  complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

  PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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  Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

  build chimpanzee unrelated ceph comparative three-color pcr

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

  PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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  Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

  peripheral array custom snp

• Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

  PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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  There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

  genomic pcr large outbred comparative denaturing pcr

• Identification of functional SNPs in the 5-prime flanking sequences of human genes.

  PMID 15717931 · PMC550646 · BMC genomics · 2005 · 6 claims · 5 setups

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  7 of 10 candidate SNPs tested by EMSA showed reproducible allele-specific differences in TF-DNA complex binding/stability

  flanking synthetic genomic cloned comparative electrophoretic rflp

• Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

  PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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  Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

  genomic maternal 22qtdr chromosome semi-quantitative pcr fish

• Comparative analysis of cancer genes in the human and chimpanzee genomes.

  PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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  All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

  chimpanzee non-human cancer comparative pcr targeted

• Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

  PMID 16420694 · PMC1382255 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  SNPscan is a web-accessible tool that displays SNP copy number, genotype call, and LOH p-value data together in a single plot per sample

  lymphoblastoid skin ceph genomic snp array pcr

• Efficacy assessment of SNP sets for genome-wide disease association studies.

  PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

  hapmap affymetrix illumina genome-wide swept comparative

• Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

  PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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  B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

  dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based

• Fast-evolving noncoding sequences in the human genome.

  PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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  1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

  chimpanzee genome hapmap comparative genomic segmental

• Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

  PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups

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  A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC

  pig lemur cv-1 b-prop1 bac comparative transient

• The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

  PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

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  The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

  genotypes neural inbred viable phenotype phylogenetic comparative

• Iterative pruning PCA improves resolution of highly structured populations.

  PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

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  ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

  simulated hapmap cattle shriver's simulated snp comparative

• The role of genomics in the identification, prediction, and prevention of biological threats.

  PMID 19855827 · PMC2757898 · PLoS biology · 2009 · 8 claims · 5 setups

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  Genomics should be used proactively, not just reactively, to build biopreparedness against biological threats

  bacillus escherichia sars pandemic whole-genome pangenomic low-resolution

• Application of OMICS technologies in occupational and environmental health research; current status and projections.

  PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups

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  Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics

  population genomic blood genome array-based comparative gene

• Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora.

  PMID 19900279 · PMC3091320 · Genome biology · 2009 · 8 claims · 6 setups

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  This is the first genetic linkage map constructed for any coral species or any non-Bilaterian animal

  acropora millepora coral snp genetic segregation