Core Technology

Our core technology at Knowledge Synthesis comprises a data model for integrating biomolecular measurements on a genome-wide scale, database, statistical computing engines, and CGI web applications. Built over a period of years with refinements motivated by the real-world demands of research and development projects, we have created a biomolecular measurement and pathway analysis system that brings together gene, protein, and chemical data. With those data in a computable format, we are able to implement computations to discover and statistically test findings in big data, including completely novel findings. We have confirmed positive controls for many data sets and carefully assessed a number of novel findings that the system generates. We designed our core technology with the benefit of decades of data analysis experience. The focus is to reduce big data to findings that move your organization forward.

Publications

Knowledge Synthesis technology and expertise have contributed to a range of scientfic publications:

  1. Levine DM, Dutta NK, Eckels J, Scanga C, Stein C, Mehra S, Kaushal D, Karakousis PC, Salamon H. A tuberculosis ontology for host systems biology. Tuberculosis (Edinb). 2015 Sep;95(5):570-4. doi: 10.1016/j.tube.2015.05.012. Epub 2015 Jun 30. PubMed: 26190839
  2. Shi L, Salamon H, Eugenin EA, Pine R, Cooper A, Gennaro ML. Infection with Mycobacterium tuberculosis induces the Warburg effect in mouse lungs. Sci Rep. 2015 Dec 10;5:18176. doi: 10.1038/srep18176. PubMed: 26658723
  3. Salamon H, Yamaguchi KD, Cirillo DM, Miotto P, Schito M, Posey J, Starks AM, Niemann S, Alland D, Hanna D, Aviles E, Perkins MD, and Dolinger DL. Integration of published information into a resistance-associated mutation database for Mycobacterium tuberculosis. J Infect Dis. 2015 Apr 1;211 Suppl 2:S50-7. doi: 10.1093/infdis/jiu816. PubMed: 25765106
  4. Salamon H, Bruiners N, Lakehal K, Shi L, Ravi J, Yamaguchi KD, Pine R, and Gennaro ML. Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection. J Immunol. 2014 Jul 1;193(1):30-4. doi: 10.4049/jimmunol.1400736. Epub 2014 Jun 4. PubMed: 24899504
  5. Campbell JD, Kell SA, Kozy HM, Lum JA, Sweetwood R, Chu M, Cunningham CR, Salamon H, Lloyd CM, Coffman RL, and Hessel EM. A limited CpG-containing oligodeoxynucleotide therapy regimen induces sustained suppression of allergic airway inflammation in mice. Thorax. 2014 Jun;69(6):565-73. doi: 10.1136/thoraxjnl-2013-204605. Epub 2014 Jan 24. PubMed: 24464743
  6. Toda M, Shao Z, Yamaguchi KD, Takagi T, D'Alessandro-Gabazza CN, Taguchi O, Salamon H, Leung LL, Gabazza EC, and Morser J. Differential gene expression in thrombomodulin (TM; CD141)(+) and TM(-) dendritic cell subsets. PLoS One. 2013 Aug 23;8(8):e72392. doi: 10.1371/journal.pone.0072392. eCollection 2013. PubMed: 24009678
  7. Salamon H, Qiao Y, Cheng JC, Yamaguchi KD, Soteropoulos P, Weiden M, Gennaro ML, and Pine R. Evidence for postinitiation regulation of mRNA biogenesis in tuberculosis. J Immunol. 2013 Mar 15;190(6):2747-55. doi: 10.4049/jimmunol.1202185. Epub 2013 Feb 1. PubMed: 23378427
  8. Kunnath-Velayudhan S, Davidow AL, Wang HY, Molina DM, Huynh VT, Salamon H, Pine R, Michel G, Perkins MD, Xiaowu L, Felgner PL, Flynn JL, Catanzaro A, and Gennaro ML. Proteome-scale antibody responses and outcome of Mycobacterium tuberculosis infection in nonhuman primates and in tuberculosis patients. J Infect Dis. 2012 Sep 1;206(5):697-705. doi: 10.1093/infdis/jis421. Epub 2012 Jun 25. PubMed: 22732925
  9. Croze E, Yamaguchi KD, Knappertz V, Reder AT, and Salamon H. Interferon-beta-1b-induced short- and long-term signatures of treatment activity in multiple sclerosis. Pharmacogenomics J. 2013 Oct;13(5):443-51. doi: 10.1038/tpj.2012.27. Epub 2012 Jun 19. PubMed: 22711062
  10. Kunnath-Velayudhan S, Salamon H, Wang HY, Davidow AL, Molina DM, Huynh VT, Cirillo DM, Michel G, Talbot EA, Perkins MD, Felgner PL, Liang X, and Gennaro ML. Dynamic antibody responses to the Mycobacterium tuberculosis proteome. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14703-8. doi: 10.1073/pnas.1009080107. Epub 2010 Jul 28. PubMed: 20668240