- Flux Optimization in Human Specific Map-
Kinase Pathways: A Systems Biology Approach
to Study Cancer
Sahu, S. International Conference on Modeling, Optimization, and Computing. Used Protein Lounge Database to identify correlation between genome and metabolism. Also used Database to reconstruct the normal and mutated MAPK pathway.
- 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.
- Biological networks and analysis of
experimental data in drug discovery
Nikolsky Y,T Nikolskaya and A Bugrim. DDT 9: 653-662. Mentions Protein Lounge as a resource for pathway maps and process ontologies.
- Computational approaches to study transcriptional
Babu MM. Biochem Soc Trans 36: 758-765. Protein Lounge mentioned as a transcription factor database.
- Ganglioside GD1a suppresses TNFa expression via Pkn1 at the transcriptional level in mouse osteosarcoma-derived FBJ cells
Wang L, Y Wang, T Sato, S Yamagata and T Yamagata. Biochem and Biophys Res Comm 371: 230-235. Used Protein Lounge to identify target sequence of Pkn1 siRNA.
- Animal models of maple syrup urine disease
Skvorak KJ. J Inherit Metab Dis 32:229–246. Pathway Builder used to summarize BCAA Metabolism in a liver cell (Fig 1) and to make a figure of the GABA-glutamate/glutamine cycle (Fig 8).
- Gap junctional control of glial glutamate transporter expression
Figiel M, C Allritz, C Lehmann, and J Engele. Mol Cell Neurosci 35: 130–137. siRNA database used to design Rat Cx43 (accession number, NM 012567) siRNA (5!-AAAGTTGCTGCTGGACATGAA- 3!), and non-homologous (nh) siRNA (5!- AATTCTCCGAACGTGTCACGT-3!).
- SARS-CoV Virus-Host Interactions and Comparative
Etiologies of Acute Respiratory Distress Syndrome as
Determined by Transcriptional and Cytokine Profiling
of Formalin-Fixed Paraffin-Embedded Tissues
Baas T, JK Taubenberger, P Y Chong, P Chui, and MG Katze. J O Inteferon & Cytokine Research 26: 309-317. Mined Protein Lounge pathways to make biosets.
- 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.
- Production of Antipetide Antibodies
Lee BS, JS Huang, GD Lasanthi, P Jayathilaka, SS Lateef, and S Gupta. Recommends Protein Lounge database as a means of selecting antigenic peptide targets.
- Pathway Mapping Tools for Analysis of High Content Data
Ekins S, Y Nikolsky, A Bugrim, E Kirillov, and T Nikolskaya. Meth in Mol Bio 356: 319-349. Protein Lounge is mentioned as a pathway database.
- 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.