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).

• COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

  PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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  COMP mutations were identified in 78% of families referred with PSACH

  genomic sequence subset pcr bidirectional sequence

• Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

  PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

  genome chimpanzee sult1a3 est blast-like comparative pairwise

• Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

  PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

  ensembl genomic simulation pcr maldi-tof

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• Familial hypercholesterolemia in St-Petersburg: the known and novel mutations found in the low density lipoprotein receptor gene in Russia.

  PMID 15701167 · PMC551615 · BMC medical genetics · 2005 · 8 claims · 6 setups

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  21 rare sequence variations of the LDL receptor gene were identified in St.-Petersburg FH patients, 19 of which are probably pathogenic and 2 (P518P, T705I) neutral.

  genomic pcr proband restriction sscp automated

• Insights into vertebrate evolution from the chicken genome sequence.

  PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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  Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

  red chicken whole-genome comparative synteny

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• High resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

  PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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  C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

  chimpanzee intergenic genome-wide chi-square nucleotide-content

• Expression profiling of drug response--from genes to pathways.

  PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups

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  Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.

  blastocyst skin specified cortex pathway two-color microarray

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• miRGen: a database for the study of animal microRNA genomic organization and function.

  PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

  animal genome mouse-human mirna genomic mirna cross-species

• OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci.

  PMID 17098932 · PMC1669730 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  OncoDB.HCC integrates human HCC LOH, CGH, microarray/proteomic expression, PubMed-reported gene data, and rodent HCC QTLs into a single physical-map-based database

  paired hcc rodent semi-quantitative microarray comparative

• Mining expressed sequence tags identifies cancer markers of clinical interest.

  PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

  dbest cancer gene est human-mouse leave-one-out

• Eighth major clade for hepatitis delta virus.

  PMID 17073101 · PMC3294742 · Emerging infectious diseases · 2006 · 7 claims · 7 setups

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  Three HDV isolates (dFr644, dFr2072, dFr2736) form a monophyletic group distinct from HDV-1 through HDV-7, constituting a new eighth major clade (HDV-8) of the Deltavirus genus.

  serum-derived complete same shd rt-pcr sequence phylogenetic

• Genomic signatures of human versus avian influenza A viruses.

  PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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  52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

  throat clinical 401-genome avian rt-pcr immunofluorescent sequence

• Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

  PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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  EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

  blood genomic genes housekeeping microarray repeat est-based

• Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

  PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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  The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

  dog hamster pcr primer pcr blast sequence

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval