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).

• Proteomic identification of non-Gal antibody targets after pig-to-primate cardiac xenotransplantation.

  PMID 18957049 · PMC2586876 · Xenotransplantation · 2008 · 8 claims · 6 setups

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  Non-Gal antibody response after cardiac xenotransplantation is directed to a diverse set of stress response, inflammation-related, cytoskeletal and metabolic pig EC antigens, with several immunodominant targets remaining undefined

  gt-ko spots explanted flow western nanolc

• Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

  PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

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  Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

  ceacam1 meningitidis influenzae ha3 homology site-directed receptor

• Solving structures of protein complexes by molecular replacement with Phaser.

  PMID 17164524 · PMC2483468 · Acta crystallographica. Section D, Biological crystallography · 2007 · 7 claims · 4 setups

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  Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components using a 'tree search with pruning' approach implemented in Phaser's automated MR mode.

  β-lactamase rop antibody ap2 molecular

• Functional analysis of human mutations in homeodomain transcription factor PITX3.

  PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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  Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

  lens western immunocytochemistry electrophoretic

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• The Proteomic Code: a molecular recognition code for proteins.

  PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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  The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

  anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide

• beta- Catenin mutations and aberrant nuclear expression during endometrial tumorigenesis.

  PMID 11161379 · PMC2363713 · British journal of cancer · 2001 · 7 claims · 4 setups

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  Cell membrane β-catenin immunoreactivity shows a stepwise decrease from normal endometrium, through atypical hyperplasia, to grade 3 carcinoma.

  endometrial immunohistochemistry rt-pcr pcr

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• 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

• Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.

  PMID 18787705 · PMC2527523 · PloS one · 2008 · 8 claims · 5 setups

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  Reduction in V3's net positive charge makes V3 less variable due to limited positive selection

  hiv-1 recombinant plasma gp120 sequence single-round v3-peptide-based

• 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

• Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

  PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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  PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

  falciparum escherichia coli-expressed recombinant pcr recombinant sds-page

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Proteomic profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry.

  PMID 19012186 · PMC3163445 · The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians · 2008 · 8 claims · 6 setups

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  Amniotic fluid protein composition can be analyzed by combining 2D liquid chromatography and mass spectrometry to identify differentially expressed proteins in preterm labor

  pooled amniotic two-dimensional sds-page maldi-tof

• Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

  PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

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  34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

  hepg2 excised identified recombinant two-dimensional western in-gel

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

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  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

  PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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  M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

  pooled m-lac excised individual high-performance sds-page lectin

• A new era for proteomics research?

  PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups

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  Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable

  proteins lines kinases breast mass silac kinase-specific

• The use of proteomics in biomarker discovery in neurodegenerative diseases.

  PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups

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  A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis

  csf serum two-dimensional seldi liquid-phase

• Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

  PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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  TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence

  hep-2 archival pneumoniae immunohistochemistry western gel