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).

• Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

  PMID 17672919 · PMC1973086 · BMC bioinformatics · 2007 · 6 claims · 8 setups

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  The Not-N algorithm, incorporated into the Minimum SNPs program, identifies small marker sets diagnostic for user-defined subgroups of genetic variants with 0% false negatives

  hcv campylobacter yersinia clostridium snp comparative cgh

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

  PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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  Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

  pbmc his-tagged cem mammalian pcr electrophoretic western

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

  PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

  lung analysis embryonic homologues shotgun microarray k-nearest

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Identification and characterization of insect-specific proteins by genome data analysis.

  PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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  Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

  drosophila insect-core locusta insect-specific comparative est functional

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

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  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern

• Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

  PMID 17296599 · PMC2315784 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 5 setups

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  SDS-PAGE combined with post-digest 18O/16O labeling and LC-MS/MS enables relative quantification of multiple P450 proteins from liver microsomes, including highly homologous isoforms

  liver recombinant tryptic sds-page western mascot

• Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

  PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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  Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

  liver chimpanzee h-invitational tar genome blastn secondary

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat

• Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

  PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

  coli sds-page glutathione pepck-gst sds-page maldi-tof native

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Information-based methods for predicting gene function from systematic gene knock-downs.

  PMID 18959798 · PMC2596148 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  Information-based metrics, which incorporate a phenotype's genomic frequency, outperform non-information-based metrics for detecting gene-gene functional similarity from phenotypic knock-down profiles.

  caenorhabditis elegans saccharomyces interference computational genome-wide

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

  PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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  A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

  cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

• Differential protein expression in human corneal endothelial cells cultured from young and older donors.

  PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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  Cultured HCEC protein profiles show age-related differences between young and older donors

  corneal 2-d trypsin-digested confluent 2-d gel maldi-tof