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).

• Evaluation of models to predict BRCA germline mutations.

  PMID 17016486 · PMC2360540 · British journal of cancer · 2006 · 7 claims · 7 setups

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  Four commonly used BRCA risk prediction models (BRCAPRO, Manchester, Penn, Myriad-Frank) have only modest ability to rule in or rule out BRCA1/2 germline mutation carrier status at a 10% probability threshold.

  proband pedigrees randomly brca1 brcapro manchester

• Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

  PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

  coli plasmids plasmid white plasmid sequencing non-b

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.

  PMID 16998187 · PMC1636422 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The major BCL2 promoter G-quadruplex (bcl2Mid) is a well-defined, mixed parallel/antiparallel-stranded intramolecular structure with three G-tetrads, two lateral loops, one side loop, and four grooves of different widths

  synthetic bcl2mid bcl2pu39 nmr 31p site-specific

• Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

  PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

  sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

• Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

  PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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  Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

  genomic pcr-amplified tsc healthy dhplc direct pcr

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• A homozygous R262Q mutation in the gonadotropin-releasing hormone receptor presenting as constitutional delay of growth and puberty with subsequent borderline oligospermia.

  PMID 16968799 · PMC1865483 · The Journal of clinical endocrinology and metabolism · 2006 · 7 claims · 8 setups

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  A homozygous R262Q GNRHR mutation was identified in two brothers from an Asian Indian family, one of 11 families studied with delayed puberty or discordant IHH/delayed puberty siblings.

  blood serum younger brothers mutational hormone 24-hour

• AgBase: a functional genomics resource for agriculture.

  PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

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  AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

  pasteurella chicken maize gene proteogenomic mudpit differential

• First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

  PMID 16959032 · PMC1570496 · Retrovirology · 2006 · 8 claims · 6 setups

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  Nearly full-length sequencing of 10 HIV-1 seroincident MSM samples revealed 6 subtype B, 3 unique BF recombinants, and 1 novel B/C/F triple recombinant

  pbmcs assembled hiv-1 triple nearly phylogenetic bootscan

• Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

  PMID 16945957 · PMC1636363 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SILAC can be used for miRNA target identification

  hela 3'-utr silac microarray dual-luciferase

• Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

  PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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  Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

  genome sequences automatic manual sequence

• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

  PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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  AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

  genome human-mouse genes initio comparative extrinsic

• Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

  PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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  Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

  autosomal intronic chimpanzee genes comparative human-chimpanzee background

• V-MitoSNP: visualization of human mitochondrial SNPs.

  PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

  blood blood-derived mtdna standard agarose rflp

• Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

  PMID 16887033 · PMC1559599 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  A multiplexed suspension bead array (Luminex) assay was developed to genotype 8 Ashkenazi-prevalent disease alleles including GBA c.1448T>C

  genomic de-identified multiplex sanger clinical

• The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

  PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

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  Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

  143b ffpe blood cloned southern pcr rt-pcr

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• CEAS: cis-regulatory element annotation system.

  PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

  genome genomic chip-chip repeat-masked conservation