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).

• Global analysis of community-associated methicillin-resistant Staphylococcus aureus exoproteins reveals molecules produced in vitro and during infection.

  PMID 17217429 · PMC2064037 · Cellular microbiology · 2007 · 6 claims · 3 setups

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  Proteomic analysis (2-DGE coupled with ADI-MS/MS) identified 250 unique exoproteins produced by MW2 and LAC culture supernatants during growth in vitro.

  mw2 mice neutrophils 2-dimensional infection confocal

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

  PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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  The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

  aureus 2-d 1-d gelc-ms

• X-linked isolated growth hormone deficiency: expanding the phenotypic spectrum of SOX3 polyalanine tract expansions.

  PMID 19654509 · PMC2763399 · Clinical dysmorphology · 2009 · 7 claims · 5 setups

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  A 21bp in-frame insertion causing a 7-alanine expansion in the SOX3 polyalanine tract causes X-linked isolated growth hormone deficiency (IGHD) without learning disability.

  affected family patients pedigree sanger pcr-based endocrine

• Proteomics in alcohol research.

  PMID 12875051 · PMC6683837 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 7 claims · 8 setups

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  The proteome is larger and more complex than the genome due to differential splicing, post-translational modifications (PTMs), and protein-protein interactions.

  mixtures tryptic liver plasma two-dimensional liquid maldi-tof

• Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

  PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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  S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

  enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

  PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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  The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

  monocytogenes additional food j774 whole-genome comparative pcr

• Metabolism as a complex genetic trait, a systems biology approach: implications for inborn errors of metabolism and clinical diseases.

  PMID 18836848 · PMC4319114 · Journal of inherited metabolic disease · 2008 · 7 claims · 8 setups

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  Synergistic heterozygosity — cumulative heterozygous mutations at multiple loci in functionally related metabolic pathways — can cause physiologically relevant reduction of pathway flux and disease.

  models liver sucrose vlcad-deficient physiological blue sucrose

• Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

  PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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  E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

  e2348 hep-2 blast colony transformation

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional

• Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

  PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors

  ht1080 coli ht1080-derived synthetic novo gel transposition

• Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

  PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

  magi pbmc 293t supt1 sensitive rt-pcr western

• The use of multiple displacement amplification to amplify complex DNA libraries.

  PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

  hes3 hes3-derived coli plasmids isolation flcdna gis-pet

• Chemical genomics: what will it take and who gets to play?

  PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups

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  Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.

  iccb fluorescently yeast engineered cell-based small-molecule expression

• P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

  PMID 20046837 · PMC2798614 · PloS one · 2009 · 8 claims · 8 setups

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  p19 regulates telomerase activity through its interaction with p73α/β proteins

  yeast hela yeast facs pkc

• An "omics" approach to uropathogenic Escherichia coli vaccinology.

  PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

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  An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

  upec vaccination comparative two-dimensional

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular