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  1. The antimicrobial peptide LL-37 induces synthesis and release of cysteinyl leukotrienes from human eosinophils – implications for asthma
    ProteinLounge Pathway Builder used to draw a model for LL-37-mediated eosinophil recruitment and cellular signaling leading to cys-LT and ECP release(Fig 6).
  1. Cellular adaptive response of distal renal tubular cells to high-oxalate environment highlights surface alpha-enolase as the enhancer of calcium oxalate monohydrate crystal adhesion
    Pathway Builder used to create background image for Gene expression data (Fig 3).
  1. Journal of the Medical Library Association : Protein Lounge
    Protein Lounge provides a more graphical approach in visualizing pathways. Protein Lounge is an exceptional product that would be a useful tool for users in the areas of molecular biology and biochemistry.
  1. The Role of the Tumour Suppressor p53 in the Elimination of Hepatitis B Virus-infected Hepatocytes - Implications for Viral Clearance
    PathwayBuilder used to draw p53 pathway (Fig 1.2), DNA Damage Response Signaling Pathway (Fig 1.3), apoptosis signaling pathway (Fig 1.5), elimination of hepatitis B infected hepacytes (Fig 4.1), illustrate the concept The AP-1 element in the 5’ UTR of the CD95L gene is responsible for CD95L expression in HBV-infected hepatocytes" (Fig 4.2), HBV infection triggering the phosphorylation of p53 through the DNA damage response (Fig 4.3), HDV infection (Fig 4.4), and Caspase independent apoptosis induction (Fig 4.5).
  1. METHODS FOR IDENTIFICATION OF NOVEL PROTEIN DRUG TARGETS AND BIOMARKERS UTILIZING FUNCTIONAL NETWORKS
    Patent. Mentions Protein Lounge as a potential tool to determine Protein-Protein Interaction to supplement high-throughput experimentation(Table 5).
  1. Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays
    Searched curated T2D-associated genes using Oracle SQL Developer with comprehensive integrated pathway data in HPD version 2.1 (which includes pathway data from Protein Lounge)
  1. Molecular And Cellular Networks in Critical Illness Associated Muscle Weakness: Skeletal Muscle Proteostasis in the Intensive Care Unit
    Banduseela, V. C. 2012. Molecular And Cellular Networks in Critical Illness Associated Muscle Weakness: Skeletal Muscle Proteostasis in the Intensive Care Unit. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 841. 63 pp. Uppsala. ISBN 978-91-554-8542-9. IGF-1/AKT/mTor pathway, autophagy lysosome pathway, the branches of the UPR pathway and proteostasis network and protein fates pathway drawn using pathway builder(Figs 2, 3, 5 & 6).
  1. Methods of predicting response of a neoplasm to an EGFR inhibitor and detecting interactions between EGFR and an EGFR regulatory protein
    Plans to use the Protein Lounge Protein Intraction Database to identify potential EGFR interactive proteins.
  1. Pathophysiology of GPCR Homo- and Heterodimerization: Special Emphasis on Somatostatin Receptors
    Somvanshi RK and U Kumar. Pharmaceuticals 5: 417-446. Used PathwayBuilder from ProteinLounge to depict regulation of receptor signaling through G-proteins(Fig 1A-D).
  1. Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer
    ProteinLounge database used to determine 73 apoptosis related genes. ProteinLounge tools used to visualize gene-gene and protein-protein interactions.
  1. Characterization of the role of Hydroxyprostaglandin dehydrogenase 15-(NAD)in human regulatory T cells
    Modified ProteinLounge IL-2 pathway (Fig 2).
  1. Srp20 regulates TrkB pre‐mRNA splicing to generate TrkB‐Shc transcripts with implications for Alzheimer''s disease
    Pathway Build Tool with minor modifications used: TrkB alternative transcripts and protein isoforms(Fig 1) and Various TrKB compounds (Fig 9).
  1. Pro- and anti-angiogenic agents
    ProteinLounge graphics used to explain the formation of a capillary network around a tumour body(Fig 2).
  1. INTEGRATIVE SYSTEM BIOLOGY STUDIES ON HIGH THROUGHPUT GENOMICS AND PROTEOMICS DATASET
    Madhankumar Sonachalam. Thesis. Protein Lounge Pathway Database mentioned as a source for Human Pathway Database
  1. PRODUCER CELLS FOR REPLICATION COMPETENT RETROVIRAL VECTORS
    Patent. Plans to use the ProteinLounge siRNA database to find suitable siRNA sequences and targets.
  1. MMMDB: Mouse Multiple Tissue Metabolome Database
    Mentioned as Pathway Database.
  1. Functional genomics studies of Rhipicephalus (Boophilus) annulatus ticks in response to infection with the cattle protozoan parasite, Babesia bigemina
    Protein Lounge database was used to analyze protein ontology.
  1. Role of estrogen and estrogen receptors in cancer pathology
    Pathway Builder Tool used to create ligand-dependent pathways of estrogen (Fig 1).
  1. Database Resources for Proteomics-Based Analysis of Cancer
    Zhang GL, DS DeLuca, and V Brusic. Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, 723: 349-364. Human Pathway Database is mentioned as containing data from Protein Lounge.
  1. Effects of Novel Angiogenesis Inhibitors for the Treatment of Cancer on the Cardiovascular System.
    VEGF Pathway Figure. Protein Lounge Pathway Templates.
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