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  1. Zymosan suppresses leukotriene C4 synthase activity in differentiating monocytes: antagonism by aspirin and protein kinase inhibitors.
    Used Pathway Builder to design a graphic representing proposed mechanisms for control of LTC4S activity during differentiation of monocytic cells(Figure not labeled).
  1. Fangjiomics: In Search of Effective and Safe Combination Therapies.
    ProteinLounge mentioned as a systems biology database(Table II).
  1. Pathogenesis of Y. enterocolitica and Y. pseudotuberculosis in Human Yersiniosis.
    Pathway Builder used (Fig 3).
  1. RECOMBINANT VECTORS.
    Patent. Plans to use Protein Lounge siRNA Database to obtain suitable sequences and targets.
  1. Synthetic Lethal Screen of an EGFR-Centered Network to Improve Targeted Therapies.
    Astsaturov I et al. Sci Signal 3: 140. EGF pathway used to get EGFR protein names.
  1. Changing Mechanisms of Opiate Tolerance and Withdrawal during Early Development: Animal Models of the Human Experience.
    Pathway adapted for use in the paper from Protein Lounge (Fig 5).
  1. Impact of different isolation procedures on the functionality of zein and kafirin
    Used protein hydroplotter to predict hydrophobic regions in an amino acid sequence.
  1. Distribution of ecto-nucleotidases in mouse sensory circuits suggests roles for nucleoside triphosphate diphosphohydrolase-3 in nociception and mechanoreception
    Used pathway builder tool to construct figure
  1. Tuberous Sclerosis: Update in Diagnosis and Treatment
    Orrin Devinsky. ProteinLounge mTor pathway used.
  1. Systematic discovery of condition specific Wnt signaling subnetworks
    Saha S and RE Ewing. BIBM Workshops 2011. Used Protein Lounge Database to identify core sets of proteins for Wnt Pathway.
  1. GM3 Upregulation of Matrix Metalloproteinase-9 Possibly Through PI3K, AKT, RICTOR, RHOGDI-2, and TNF-A Pathways in Mouse Melanoma B16 Cells
    Wang P, X Wang, P Wu, J Zhang, T Sato, S Yamagata, and T Yamagata. The Molecular Immunology of Complex Carbohydrates-3. Used Easy siRNA to select target sequence of ST3GAL5.
  1. Copy number variants and infantile spasms: evidence for abnormalities in ventral forebrain development and pathways of synaptic function
    Paciorkowski AR et al. Euro J of Hum Gen 19: 1238–1245. Pathway Builder used for illustration of the GABA-receptor subunit genes expressed in the post-synapse with abnormal copy number in subjects with ISS identified in this study (Fig 2B).
  1. Exploring and challenging the network of angiogenesis.
    Used Protein Lounge Database for information on angiogenesis.
  1. Severe Traumatic Brain Injury in the United States and the Role of Public Health
    LC McGuire. Intracellular calcium signaling ProteinLounge custom pathway for SA Biosciences used.
  1. Pilot and feasibility study: prospective proteomic profiling of mammary epithelial cells from high-risk women provides evidence of activation of pro-survival pathways
    Used Pathway map from SA Biosciences(pathway designed by Protein Lounge)(Fig 4).
  1. NF-kappaB in Aging and Disease
    Protein Lounge pathways adapted for IKK pathway (Fig 2).
  1. The Neuroproteomics of Schizophrenia
    English JA, K Pennington, MJ Dunn, and DR Cotter. Biol Psych 69:163–172. Protein lounge is listed as a core facility for proteomic analysis.
  1. Ectopic expression of CD74 in Ikkˇ-deleted mouse hepatocytes
    Koch KS and HL Leffert. Acta Histochemica 113: 428–435. Used Protein Lounge database to normalize and group RNA data.
  1. A Fission Yeast-Based Platform for Phosphodiesterase Inhibitor HTSs and Analyses of Phosphodiesterase Activity
    Demirbas D, O Ceyhan, AR Wyman, and CS Hoffman. Phosphodiesterases as Drug Targets, Handbook of Experimental Pharmacology 204. Pathway Builder used to make S. Pombe glucose/cAMP signaling pathway (Fig 1).
  1. A systems biology representation of developmental anatomy
    SABiosciences/ProteinLounge Rho GTPase network diagram used (Fig 3).
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