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).

• The HIV positive selection mutation database.

  PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

  hiv-1 stanford codon-specific selection conditional

• Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

  PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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  Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

  egfr tp53 laci lung literature comparative statistical

• Sequence and structure signatures of cancer mutation hotspots in protein kinases.

  PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

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  Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

  kinase common egfr autoinhibited database-driven structure-informed evolutionary

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

  PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

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  COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

  ab1 fasta mutation hemophilia base-calling sequence known-variant

• Increased frequency of the k-ras G12C mutation in MYH polyposis colorectal adenomas.

  PMID 15083190 · PMC2410274 · British journal of cancer · 2004 · 8 claims · 2 setups

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  Somatic k-ras mutations occur in 9 of 54 (16.7%) MYH polyposis colorectal tumours, with frequency increasing with degree of dysplasia.

  microdissected previously pcr literature-derived

• Web services and workflow management for biological resources.

  PMID 16351751 · PMC1866383 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  Workflow management systems combined with Web Services are a promising ICT approach for automating access to and integration of biomedical data.

  cabri iarc taverna web workflow database

• MutScreener: primer design tool for PCR-direct sequencing.

  PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

  sim4 cdna gene comparative sequence pcr

• 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

• SNAP predicts effect of mutations on protein function.

  PMID 18757876 · PMC2562009 · Bioinformatics (Oxford, England) · 2008 · 8 claims · 3 setups

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  SNAP is a publicly available web-server implementation predicting functional effects (neutral/non-neutral) of single amino acid substitutions.

  mutant insulin neural alanine mutation

• SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

  PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results

  omim pmd swissprot msipi database sequence tandem

• SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

  PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

  scientific pubmed cyp-drug cyp text mutation manual

• Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

  PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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  The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

  genomic electronic pcr pcr-restriction

• Biased exon/intron distribution of cryptic and de novo 3' splice sites.

  PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

  disease authentic hek293t nuclear literature shapiro-senapathy splicing

• Efficient algorithms for probing the RNA mutation landscape.

  PMID 18688270 · PMC2475669 · PLoS computational biology · 2008 · 8 claims · 4 setups

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  RNAmutants generalizes McCaskill's partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all k-point mutants, simultaneously computing MFE(k) and Z(k) for each k

  element hepatitis hiv utr partition deleterious mutation

• Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

  PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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  Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

  aku hgd recombinant hgd missense splice

• Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

  PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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  Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

  tumors cancer tumor lung direct database quantitative

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

  PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

  Has reproduction · 89

  MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

  eukdetect simulated zymobiomics read holdout mutation-rate

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron